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Light-Driven Hybrid Nanoreactor Harnessing the Synergy of Carboxysomes and Organic Frameworks for Efficient Hydrogen Production
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  • Jing Yang
    Jing Yang
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
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  • Qiuyao Jiang
    Qiuyao Jiang
    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
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  • Yu Chen
    Yu Chen
    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
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  • Quan Wen
    Quan Wen
    Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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  • Xingwu Ge
    Xingwu Ge
    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
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  • Qiang Zhu
    Qiang Zhu
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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  • Wei Zhao
    Wei Zhao
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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    Orcidhttps://orcid.org/0000-0003-0265-2590
  • Oluwatobi Adegbite
    Oluwatobi Adegbite
    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
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  • Haofan Yang
    Haofan Yang
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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  • Liang Luo
    Liang Luo
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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  • Hang Qu
    Hang Qu
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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  • Veronica Del-Angel-Hernandez
    Veronica Del-Angel-Hernandez
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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  • Rob Clowes
    Rob Clowes
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
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  • Jun Gao
    Jun Gao
    Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
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    Orcidhttps://orcid.org/0000-0002-6692-1828
  • Marc A. Little*
    Marc A. Little
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    Institute of Chemical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, U.K.
    *Email: [email protected]
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    Orcidhttps://orcid.org/0000-0002-1994-0591
  • Andrew I. Cooper*
    Andrew I. Cooper
    Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    *Email: [email protected]
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    Orcidhttps://orcid.org/0000-0003-0201-1021
  • Lu-Ning Liu*
    Lu-Ning Liu
    Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
    College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao 266003, China
    *Email: [email protected]
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    Orcidhttps://orcid.org/0000-0002-8884-4819
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ACS Catalysis

Cite this: ACS Catal. 2024, 14, 24, 18603–18614
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https://doi.org/10.1021/acscatal.4c03672
Published December 6, 2024

Copyright © 2024 The Authors. Published by American Chemical Society. This publication is licensed under

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Abstract

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Synthetic photobiocatalysts are promising catalysts for valuable chemical transformations by harnessing solar energy inspired by natural photosynthesis. However, the synergistic integration of all of the components for efficient light harvesting, cascade electron transfer, and efficient biocatalytic reactions presents a formidable challenge. In particular, replicating intricate multiscale hierarchical assembly and functional segregation involved in natural photosystems, such as photosystems I and II, remains particularly demanding within artificial structures. Here, we report the bottom-up construction of a visible-light-driven chemical–biological hybrid nanoreactor with augmented photocatalytic efficiency by anchoring an α-carboxysome shell encasing [FeFe]-hydrogenases (H–S) on the surface of a hydrogen-bonded organic molecular crystal, a microporous α-polymorph of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP-α). The self-association of this chemical–biological hybrid system is facilitated by hydrogen bonds, as revealed by molecular dynamics simulations. Within this hybrid photobiocatalyst, TBAP-α functions as an antenna for visible-light absorption and exciton generation, supplying electrons for sacrificial hydrogen production by H–S in aqueous solutions. This coordination allows the hybrid nanoreactor, H–S|TBAP-α, to execute hydrogen evolution exclusively driven by light irradiation with a rate comparable to that of photocatalyst-loaded precious cocatalyst. The established approach to constructing new light-driven biocatalysts combines the synergistic power of biological nanotechnology with the multilength-scale structure and functional control offered by supramolecular organic semiconductors. It opens up innovative opportunities for the fabrication of biomimetic nanoreactors for sustainable fuel production and enzymatic reactions.

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Introduction

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Solar energy harvesting and conversion have the potential to contribute to a sustainable, carbon-neutral environment. (1−3) In nature, multicomponent photosynthetic systems capture solar energy and use enzymatic cascades to orchestrate charge separation and catalytic proton-coupled electron transfer reactions to produce diverse natural products, albeit with certain intrinsic limitations, such as a relatively narrow light-harvesting window and susceptibility to chemical and structural damage by higher energy photons. (4−7) Artificial photocatalysts employ synthetic materials, often inorganic semiconductors, to mimic natural photosynthetic systems, typically by combining various components to achieve the essential functions. (8) For example, semiconductor particles have the capability of absorbing light, and when platinum nanoparticles are placed on the surface of the semiconductor, they could facilitate the reduction of protons to generate hydrogen gas. (9−11) While these synthetic hybrids can achieve high solar-to-hydrogen efficiencies, particularly in the ultraviolet range of the solar spectrum, (12) they lack the complex, hierarchically structured functionality and selectivity that are present in natural photosynthetic systems. Moreover, it is still challenging to develop artificial systems that can use the whole solar spectrum, and the most effective direct photocatalysts for overall water splitting operate in the ultraviolet spectral range, which constitutes only about 7% of total solar energy. (13)
One promising strategy to leverage the advantages of both biological and abiotic systems is to synergistically integrate natural biological machinery (such as enzymes, organelles, or whole cells) with artificial materials to construct new chemical–biological hybrid systems. (14−17) Such hybrid systems can, in principle, combine broadband light absorption and high exciton generation efficiency from synthetic semiconductors and the selectivity and catalytic power of living biocatalysts. Chemical–biological hybrids can be generated through surface engineering (e.g., surface ionization (18,19)), redox mediator addition (e.g., methyl viologen (20)), and enzyme encapsulation in porous materials. (21) However, establishing an efficient physical-chemical connection between biological and nonliving materials, which is crucial for facilitating electron cascades and energy transfer to catalytic centers and exceeding the catalytic potential of each component, poses a significant challenge. (22) A major obstacle lies in the incompatibility between biocatalysts and synthetic materials in their working environment. Thus, there is a pressing need for more designable and effective approaches to constructing chemical–biological hybrid nanoreactors, allowing for precise structural control across various length scales.
Carboxysomes are anabolic bacterial microcompartments (BMCs) responsible for biological carbon fixation in cyanobacteria and some chemoautotrophic bacteria. (23−25) The carboxysome sequesters the central CO2-fixing enzyme, Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisco), and carbonic anhydrase (CA) within a self-assembling proteinaceous shell. The carboxysome shell is composed of numerous protein paralogs that are in the form of hexamers and pentamers and allows the entry of HCO3– to create a CO2-rich microenvironment for facilitating carboxylation. (26−28) These natural features of carboxysomes have inspired the design and reprogramming of carboxysome structures by using synthetic biology for various biotechnological applications. In addition, hydrogenases are native catalysts for H2 production in bacteria, archaea, and some eukaryotes with exceptional catalytic activity and efficiency and act as valid candidates for biological H2 production. (29,30) In particular, [FeFe]-hydrogenases are highly active for H2 generation but are limited by their high oxygen sensitivity and irreversible inactivation by oxygen. (31) Therefore, the carboxysome shell has demonstrated great potential to serve as novel nanoreactors to boost H2 evolution. (32,33) However, the reported carboxysome-based H2-evolving nanoreactors require a constant supply of electrons from methyl viologen, which is not sustainable.
Here, we report a bottom-up approach to constructing a visible-light-driven chemical–biological hybrid nanoreactor by interfacing a porous crystalline organic semiconductor, microporous α-polymorph of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP-α), with recombinant α-carboxysome shells (with an average diameter of 90 nm) that encase [FeFe]-hydrogenases (H–S). (33) The resulting hybrid photobiocatalyst was characterized by electron microscopy, confocal microscopy, isothermal titration calorimetry, photoluminescence and photoelectrochemical assays, and computational simulations. Our results demonstrate that the intimate bio- and abiotic interface, established through extensive hydrogen bonds, mediates charge transport between the organic semiconductor and the biocatalyst. This allows the light-driven hybrid nanoreactor (H–S|TBAP-α) to exhibit a high sacrificial H2-evolution efficiency compared to the photocatalyst alone, and the efficiency of this photobiocatalyst is comparable with analogous synthetic photocatalysts that use expensive precious metals, such as platinum.

Results and Discussion

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Preparation of Porous Crystalline Photocatalyst TBAP-α

Light-driven chemical–biological hybrid nanoreactors should comprise light-harvesting antenna with strong visible-light absorption, high exciton production efficiency in moderate aqueous solution, and favorable hydrolytic stability to integrate with biological machinery with robust stability and high catalytic conversion. Hydrogen-bonding organic framework (HOF) photocatalysts that contain discrete hydrogen-bonding molecular building blocks, in principle, possess great potential for this application due to their inherent structure-tunability, functionality, and solution processability. (34)
1,3,6,8-tetra(4′-carboxyphenyl)pyrene molecule (TBAP) has been investigated as a building block in HOFs, (35) metal–organic frameworks (MOFs), (36) and protein-HOFs assemblies. (37) TBAP has a pyrene core that can π–π stack and carboxylic acid groups that can hydrogen-bond (Figures S1–S3), making it an ideal candidate for assembling HOFs. The α-polymorph of TBAP, referred to hereafter as TBAP-α, was successfully crystallized by slow diffusion of chloroform (CHCl3) into a solution of TBAP dissolved in dimethylformamide (DMF). (35) In the TBAP-α structure, 2-D layers of hydrogen-bonded TBAP molecules are closely packed and interact through π–π stacking of the pyrene units, which are separated by 0.38 nm. This generates a columnar microporous structure with 1.7 nm 1-D pores and unsaturated hydrogen-bonding layers on the surfaces of the needle-shaped crystals (Figures 1b and S4). Here, we characterized TBAP-α using single-crystal X-ray diffraction (sc-XRD) (Table S1), powder X-ray diffraction (PXRD), and gas absorption analysis of the micrometer-sized needle-shaped crystals (Figure S5).

Figure 1

Figure 1. Generation of the organic semiconductor, the hydrogenase-containing carboxysome shell, and the chemical–biological hybrid nanoreactor, H–S|TBAP-α. (a) Chemical structure of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP). (b) Crystal structure of α-polymorph of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP-α). (c) Genetic organization of the α-carboxysome shell operon and hydrogenase-expressing operon for the production of recombinant shells and active [FeFe]-hydrogenases in E. coli, respectively, and a schematic model of the hydrogenase-shell nanoreactor (H–S). EP: CsoS2 C-terminus as the encapsulation peptide. The hydGXEF genes encode the crucial maturase enzymes for hydrogenase formation and activation, including HydE, HydF, and HydG. PDB ID: Ferredoxin (Fd)-[FeFe]-hydrogenase, 2N0S; ferredoxin-NADP reductase (FNR), 2XNJ. (d) 3D model representation of the H–S|TBAP-α hybrid system, in which H–S adheres to the hydrogen-bonding groups on the TBAP-α crystal surface.

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TBAP-α exhibited remarkable visible-light absorption (Figure S6) and semiconducting properties with an optical bandgap of 2.30 eV and a conduction band (C.B.) of −1.15 V (Figure S7), determined by using the Mott–Schottky technique, performing a considerable thermodynamic driving force for H2 production from water. In addition, TBAP-α favors neutralized ascorbic acid (AA) aqueous solution as the sacrificial agent, (35,38) a commonly used sacrificial agent in artificial photosynthesis due to its solubility in water and the compatibility to work in a neutral medium. (39)

Self-Association of α-Carboxysome Shells and TBAP-α

The recombinant α-carboxysome shell is composed of CsoS1 and CsoS4 paralogs, as well as the linker protein CsoS2 that is attached to the inner surface of the shell. (32,33) CsoS2 exists as two distinct isoforms in Halothiobacillus neapolitanus: the longer form CsoS2A (∼130 kDa) and the short form CsoS2B (∼85 kDa). (40) The two hexameric shell proteins, CsoS1A and CsoS1C, which show 98% similarity in amino acid sequence, represent the most abundant components on the α-carboxysome shell (23) (Table S2). To verify the physical association between α-carboxysome shells and TBAP-α, we performed molecular dynamics (MD) simulations to study the binding between CsoS1A and TBAP-α, using the crystal structure of CsoS1A (PDB: 2EWH) and TBAP-α structure determined by sc-XRD. The calculated binding free energy is −22.10 kcal mol–1 by the MM/GBSA method in AmberTool22 (41) using the last 30 ns MD trajectory (150 frames) of the TBAP-α and CsoS1A protein binding simulation. MD simulations suggest that the residues mainly in the loop regions of CsoS1A, including Thr5, Arg34, Ser86, Gly89, Asp90, Lys94, Pro96, and Glu97, form strong interactions with the net-carboxylate on the surface of TBAP-α through hydrogen-bonding and salt bridges (Figure 2a–c and Tables S3 and S4). These amino acid residues are conserved among the main hexamer shell proteins, as indicated by multiple sequence alignment (Figure S8) and structural analysis (Figure S9), suggesting that the TBAP-α crystal surface interacts with α-carboxysome shells through cooperative hydrogen-bonding interactions with the shell proteins.

Figure 2

Figure 2. Binding between the α-carboxysome shell and TBAP-α. Results of molecular dynamics simulations of CsoS1A (PDB ID: 2EWH) and TBAP-α binding equilibrium states are shown in panels (a–c). (a) Front view. (b) Side view, showing the simulated binding interface between TBAP-α and the CsoS1A hexamer. (c) Zoom-in view of the noncovalent interactions (red dotted lines) formed between amino acid residues of CsoS1A (Pro96, Thr5, Ser86, Asp90, Gly89, Lys94, Arg34, Glut97) and TBAP-α (blue = N atoms, red = O atoms). (d) ITC thermogram resulting from the titration of TBAP (50 μM) into the α-carboxysome shell (3.75 μM) in TN buffer (20 mM Tris-HCl (pH = 8.0), 150 mM NaCl). (e) Thermodynamic profile of TBAP binding to α-carboxysome shell in TN buffer. ΔG, change in Gibbs Free Energy; ΔH, change in enthalpy; T, temperature in Kelvin; ΔS, change in entropy.

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Next, the binding potential of the whole recombinant α-carboxysome shells and molecular TBAP-α was detected by using isothermal titration calorimetry (ITC) (Figure 2d). A low dissociation constant (Kd) was measured as 524 (±54.4) × 10–9 M, indicating strong affinity between α-carboxysome shells and TBAP-α. In addition, the negative ΔG value indicates that the association between α-carboxysome shells and TBAP-α is energetically favorable, while the ΔH value reveals that this process is enthalpy-driven, suggesting that hydrogen bonds and van der Waals interactions may be the main driving forces in the association process (Figure 2e). The ITC results were consistent with our computational findings.
To directly visualize the association between α-carboxysome shells and TBAP-α crystals, we generated recombinant α-carboxysome shells that encapsulate mCherry, by fusing mCherry with the encapsulation peptide CsoS2 C-terminus (mCherry-EP) and coexpressing mCherry-EP with shell proteins. This approach led to the generation of mCherry-EP-Shell (C–S) (Figures S10 and S11). The purified C–S and TBAP-α were then incubated in solution for 30 min to enable self-association. Scanning electron microscopy (SEM) confirmed the coating of C–S particles on the surfaces of needle-shaped TBAP-α crystals (Figure 3a–c). Moreover, mCherry exhibits a distinct absorption maximum (λEx = 587 nm) from that of TBAP-α (λEx = 390 nm). Confocal laser scanning microscopy (CLSM) showed that the needle-shaped TBAP-α crystals exhibit bright fluorescence when excited at 488 nm and very weak red fluorescence when excited at 561 nm (Figure 3d, top row). In contrast, strong red fluorescence was recorded along the surface of TBAP-α crystals incubated with C–S when excited at 561 nm, indicating the association of C–S with the TBAP-α crystal surface (Figure 3d, bottom row). Both SEM and CLSM results demonstrate that the surfaces of TBAP-α crystals were densely coated with C–S particles in an aqueous suspension. In comparison, a bulk sample of unfunctionalized pyrene crystals (42) was incubated with C–S using the same procedure to explore the contribution of the organized layer of unsaturated carboxylic acid groups on the TBAP-α surface. The SEM images showed no visible C–S particles on these pyrene crystals (Figure S12), indicating that unsaturated carboxylic acid groups serve as the main binding sites between TBAP-α and α-carboxysome shells.

Figure 3

Figure 3. Attachment of mCherry-encapsulated C–S shells on the surface of TBAP-α crystals. SEM images of (a) uncoated TBAP-α, (b) C–S|TBAP-α (40 × 3.6 μm2 size), and (c) zoom-in view of C–S|TBAP-α. Orange arrows show the C–S particles that were attached to the TBAP-α crystal surface. (d) Fluorescence images of TBAP-α only (top row) and the C–S|TBAP-α hybrid (bottom row). Left, excitation at 488 nm; middle, excitation at 561 nm; right, the merged channel. All fluorescence images were adjusted to have the same brightness and contrast settings.

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Construction of a Light-Driven Biomimetic Hybrid Nanoreactor for Hydrogen Production

Given the unique properties of TBAP-α for light absorption and electron–proton transfer (35) as well as the strong binding between TBAP-α crystals and α-carboxysome shells, we hypothesized that the C–S|TBAP-α hybrid may serve as a novel biomimetic photocatalyst enabling electron transfer cascade and enhanced enzymatic performance in biotechnological applications. Intriguingly, sulfate ions can be soaked into the major shell hexamers of both α- and β-carboxysomes, (43,44) indicating that the pores may act as the conduits for negatively charged metabolites. Furthermore, iron–sulfur (Fe–S) clusters have been found in catabolic BMCs, (45−48) which could potentially facilitate the transfer of electrons and protons from external TBAP-α crystals across the shell to retain the internal redox environment. (49,50)
To test the hypothesis, we chose the α-carboxysome shells that encase the oxygen-sensitive redox enzymes, hydrogenases, that bind to the TBAP-α crystals. The hydrogenase-containing shells (H–S) were generated by encapsulating [FeFe]-hydrogenase fused with the CsoS2 C-terminus (HydA-EP), ferredoxin (Fd), and ferredoxin: NADP+-oxidoreductase (FNR) into the α-carboxysome shells, along with coexpression of the crucial maturase enzymes HydE, HydF, and HydG (33) (Figure 1c). H–S has been reported to exhibit enhanced H2 evolution and O2 tolerance, taking advantage of the O2-limiting microenvironment created within the α-carboxysome shell. (32,33) The comparable ζ-potentials of empty α-carboxysome shell (S), mCherry-encapsulated α-carboxysome shell (C–S), and [FeFe]-hydrogenase-encapsulated α-carboxysome shell (H–S), as well as the more negative ζ-potentials of S, C–S, and H–S after binding with TBAP-α individually, indicated that binding of the α-carboxysome shells to the TBAP-α surface was not remarkably affected by cargo encapsulation (Figure S13). Electron microscopy further confirmed that the TBAP-α crystals were coated with H–S particles (Figures 4a and S14), consistent with the observations of C–S shells and TBAP-α crystals (Figure 3).

Figure 4

Figure 4. Characterization of the light-driven H–S|TBAP-α hybrid nanoreactor. (a) SEM image of H–S|TBAP-α. Orange arrows show the H–S particles that were attached to the TBAP-α crystal surface. (b) Photoluminescence (PL) spectrum and (c) Excited-state lifetimes of H–S|TBAP-α and TBAP-α alone in 0.1 M neutralized AA aqueous solution when excited at 390 nm.

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The H–S|TBAP-α hybrid biocatalyst (Figure 1d) was generated by dispersing freshly purified H–S and TBAP-α in nitrogen-degassed neutralized AA solution (Figures S15 and S16), followed by incubation for 30 min at room temperature. UV–vis spectroscopy was used to examine the colloidal stability of H–S|TBAP-α. No significant changes were detected, even after 19 h incubation (Figure S17). We also employed photoluminescence (PL) spectroscopy to analyze the electron–hole pair recombination performance of H–S|TBAP-α and TBAP-α. The PL emission intensity of H–S|TBAP-α was quenched greatly compared to TBAP-α alone when excited at 390 nm (Figure 4b), indicating that the recombination rate for the photogenerated electron and hole was drastically reduced. This is beneficial for the transfer of electrons to H–S for the H2 production reaction. In addition, time-correlated single-photon counting (TCSPC) showed that the average weighted lifetime of H–S|TBAP-α (τavg = 4.11 ns) was greater than that of TBAP-α (τavg = 3.51 ns) in an aqueous suspension (Table S4), suggesting that more electrons were transferred to H–S rather than recombining with holes. Moreover, TBAP-α in aqueous suspension exhibited a shorter lifetime (τavg = 2.00 ns), (35) which aligns with its remarkably lower H2 production performance, even when hybridized with H–S (0.79 mmol (g TBAP)−1 h–1, Figure 5a). Therefore, the PL quench and the extended lifetime of H–S|TBAP-α indicate that H–S facilitated the separation of electron–hole pairs.

Figure 5

Figure 5. Visible-light-driven hydrogen production of H–S|TBAP-α. (a) H2-evolution rates of TBAP-α, H–S|TBAP-α, H–Sox|TBAP-α, S|TBAP-α, and H–S|Amorphous TBAP irradiated by a solar simulator for 2 h. (b) H2 evolution of TBAP-α (black dots) and H–S|TBAP-α (blue dots) as a function of time (λ > 420 nm). (c) Schematic diagram of proposed electron transfer pathway in H–S|TBAP-α for hydrogen production. Electrons generated from TBAP-α irradiation are transferred through holes on the α-carboxysome shell to the 4Fe–4S cluster via FNR or directly for proton reduction. Ascorbic acid acts as a sacrificial agent to prevent the photogenerated hole–electron recombination. Error bars represent the SD of the mean of three independent experiments.

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The electron transfer performance of TBAP-α and H–S|TBAP-α was characterized by transient photocurrent (TPC) and electrochemical impedance spectroscopy (EIS). The transient photocurrent intensity of H–S|TBAP-α reached a value that was 30% higher than that of TBAP-α alone (Figure S18a), indicating that photogenerated electrons and holes could be separated and transferred effectively to H–S in H–S|TBAP-α. The arc radius of EIS plots varied in the order H–S|TBAP-α < TBAP-α (Figure S18b), suggesting that H–S|TBAP-α showed lower electrical resistance than the TBAP-α crystalline, likely through enhanced charge transport. These assays confirmed the effective construction of the biomimetic nanoreactor with accelerated electron transfer and promising photocatalytic potential.
High-throughput sacrificial H2 evolution measurements revealed that the mass-normalized H2 evolution rate of H–S|TBAP-α (approximately 25 wt % of H–S) was 3.97 ± 0.41 mmol (g TBAP-α)−1 h–1 during 2 h irradiation in nitrogen-degassed neutralized AA aqueous solution (0.1 M) using a solar simulator (AM1.5G, 1440 W xenon, see Methods for details). The rate is almost 5 times higher than that obtained from TBAP-α alone under the same conditions (0.79 ± 0.01 mmol (g TBAP-α)−1 h–1; Figure 5a). The H2-evolution activity of TBAP-α alone is associated with the residual palladium present in the sample, which originates from the synthesis of TBAP and acts as a cocatalyst. (35) When empty shell (S) and deactivated H–S with oxygen bubbling (H–Sox) (the deactivation of H–Sox was confirmed by sodium dithionite-methyl viologen assays shown in Figure S19a) were mixed with TBAP-α respectively, the H2-evolution rates of both the resulting S|TBAP-α and H–Sox|TBAP-α declined significantly (0.78 ± 0.15 mmol (g TBAP-α)−1 h–1 for S|TBAP-α, 0.76 ± 0.06 mmol (g TBAP-α)−1 h–1 for H–Sox|TBAP-α), which were comparable to the amount of H2 produced by TBAP-α alone (Figure 5a). These results indicated that H–S in the H–S|TBAP-α hybrid nanoreactor was enzymatically active. Furthermore, no detectable amounts of H2 were produced from H–S|TBAP-α in a dark suspension, an irradiated suspension of H–S in a neutralized AA aqueous solution (0.1 M), or an irradiated suspension of H–S|TBAP-α in pure water over 2 h. Together, these control experiments indicate that TBAP-α donated photogenerated electrons for proton reduction and AA acted effectively as the hole scavenger (Figure S19 and Table S6). When TBAP-α was associated with the α-carboxysome shells that encapsulate only hydrogenases without FNR and Fd (HydA-S), there was a 33% decrease in the H2-evolution rate compared to H–S|TBAP-α (2.68 ± 0.45 mmol (g TBAP-α)−1 h–1 for HydA-S|TBAP-α, 3.97 ± 0.41 mmol (g TBAP-α)−1 h–1 for H–S|TBAP-α) (Figure S19d). These results suggest that FNR and Fd indeed contributed to the transport of photogenerated electrons to the active sites of hydrogenases.
One advantage of crystalline photocatalysts is their ability to accelerate electron transfer through a highly ordered packing pattern. This can be verified by a larger photocurrent density and smaller EIS radius from TBAP-α compared to amorphous TBAP (Figure S20). This observation coincides with the substantially higher H2 produced when H–S was hybridized with TBAP-α compared with an amorphous powdered TBAP sample. Specifically, the crystalline TBAP-α produced 3.97 ± 0.41 mmol–1 (g TBAP-α)−1 h–1, while the amorphous TBAP sample yielded only 0.79 ± 0.15 mmol–1 (g TBAP)−1 h–1 under the same conditions (Figure 5a). Hence, the synergy between H–S and TBAP-α in the hierarchical H–S|TBAP-α assemblies appears to be critical for the attached H–S structures, ensuring electron transfer between the two components and enhanced hydrogen evolution performance. The apparent quantum efficiency (AQY) was measured at different wavelengths to evaluate the photocatalytic H2 production performance of H–S|TBAP-α. The AQY measured at 420 nm was 2.8% over a 1.5 h experiment (Figure S21).
To examine the H2-evolution performance of H–S|TBAP-α in long-term irradiation, the H–S|TBAP-α hybrid nanoreactors were exposed to visible light (300 W Xe light, λ > 420 nm). As depicted in Figure 5b, H–S|TBAP-α exhibited a constant increase in H2 production as a function of time. Under the same conditions, H–S|TBAP-α produced an H2 efficiency that was roughly comparable to the noble metal-loaded system as reference, namely, 1 wt % platinum metal cocatalyst deposited on TBAP-α (Pt|TBAP-α), after 14 h of irradiation (144.3 μmol for H–S|TBAP-α, 170.2 μmol for Pt|TBAP-α) (Figure S22). In contrast, TBAP-α, without the addition of platinum cocatalyst or H–S, produced only 31.9 μmol of H2 after 14 h irradiation (Figure S22). The H2-production ability of H–S|TBAP-α ahowed a relatively steady increase as a function of time for 30 h irradiation, with an H2-evolution rate of 1,137.8 ± 47.2 μmol (g TBAP-α)−1 h–1. Intriguingly, H–S|TBAP-α exhibited remarkable stability during 5 consecutive runs over a total reaction time of 25 h, with no notable decline in the H2-production rate observed after the 5 cycles (Figure S23). From the listed state-of-the-art photocatalyst-hydrogenase hybrids (Table S7), H–S|TBAP-α has the unique advantage of considerable stability with a promising H2 production efficiency. In the long-term H2 evolution experiments, the HydA content was measured using purified HydA as a reference (Figure S24), and the total turnover number (TON) of H–S|TBAP-α was measured as 5,411,174 mol H2 (mol H2ase)−1 on average after 24-h irradiation (Xe lamp, λ > 420 nm), which is comparable to the reported organic materials-hydrogenase hybrids (Table S7). SEM was performed to examine the morphology changes of H–S|TBAP-α after 30 h of continuous irradiation. The attachment of H–S nanoparticles on the TBAP-α surface was not as obvious as before the illumination (Figure S25). Meanwhile, cracks appeared on the crystal surface, which is consistent with the crystallinity decrease found in the PXRD pattern (Figure S26).
Overall, our findings demonstrate the catalytic efficiency and robustness of H–S|TBAP-α under irradiation and the fact that the hybrid H–S|TBAP-α system has an enhanced photocatalytic H2-evolution capacity relative to the organic semiconductor TBAP-α crystal or H–S alone. We speculate that the enhanced photocatalytic H2-evolution performance of H–S|TBAP-α is partially due to accelerated electron flux from TBAP-α, through the ion-containing pores of shell protein complexes at the biotic–abiotic interface, to the catalytically active centers ([4Fe–4S] cluster) of encapsulated [FeFe]-hydrogenases, via FNR/Fd proteins or directly (Figure 5c).

Conclusions

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We developed a bottom-up strategy for biomimetic nanoreactor construction based on the inherent structural properties of biological machinery and synthetic organic materials. A crystalline HOF, TBAP-α, acts as a visible-light-capture organic antenna and can funnel energy into a complex, multicomponent biocatalytic nanoreactor, H–S, which mimics the natural photosynthesis process. This hybrid nanoreactor performs as a light-driven photocatalyst for sacrificial H2 evolution in water, and it exhibits improved activity than H–S or TBAP-α alone and comparable activity to the TBAP-α material deposited with 1 wt % of the precious metal cocatalyst, platinum. Our study suggests that H–S|TBAP-α is attributed to the separation of the photogenerated electron and hole pairs at the TBAP-α surface and the transport of electrons into the nanoreactor interior, which enhances the catalytic performance of encapsulated hydrogenases for the production of molecular hydrogen. The construction of H–S|TBAP-α with considerable hydrogen production activity acts as a promising model system to explore the potential of combining catalytic advantages from both artificial materials and natural machinery for solar energy conversion.
The successful assembly of complex, hierarchical structured nanoreactors using multiple noncovalent hydrogen-bonding interactions on organic semiconductor surfaces opens up avenues for designing new families of chemical-biologically active hybrid systems for reactions other than H2 production. Here, we demonstrated the generality and versatility of our approach, which utilizes noncovalent hydrogen-bonding interactions between multiple proteins and the organic semiconductor surface. We coated the TBAP-α crystal surface with three different proteins, C–S, H–S, and H–Sox, each with distinct catalytic properties. We postulate that this approach could be adapted to create biocatalytic nanoreactors for more complex chemical transformations by altering the cargo enzymes within the α-carboxysome shell.

Methods

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Generation of Constructs

All assemblies between genes and linearized vectors were achieved by Gibson assembly (Gibson assembly kit, New England BioLabs, U.K.). The mCherry gene was cloned to pCDFDueT-1 linearized by EcoRI and AscI to generate the pCDFDueT-mCherry vector. The mCherry gene with the nucleotide sequence encoding EP fused at the C-terminus was cloned into pCDFDueT-1 and in the frame to create pCDFDueT-mCherry-EP, using primer pairs M-F/M-C-R and M-C-F/C-R (Table S8). The mCherry gene fused to the N-termini of these truncated CsoS2 C-terminal regions was inserted into pCDFDueT linearized by BamHI and AscI. These constructs were verified by PCR and DNA sequencing and transformed into Escherichia coli BL21(DE3) cells. Plasmid maps (Figure S27) and sequences (Table S9) are available in the Supporting Information.

Coexpression and Generation of α-Carboxysome Encapsulated with mCherry (C–S)

E. coli strains containing the pCDTDuet-mCherry-CS2 plasmid and pBAD-cso-2 plasmid were cultivated in LB medium containing 50 μg mL–1 of spectinomycin and 100 μg mL–1 of ampicillin. The mCherry expression was induced by adding 0.5 mM isopropyl β-d-1-thiogalactopyranoside (IPTG) at OD600 = 0.6–0.8. After 4 h induction of the mCherry-EP expression, the shell expression was induced by 1 mM l-Arabinose, and cells were then grown at 25 °C for 16 h with constant shaking. The mCherry induction was performed before the expression of shells to allow mCherry protein expression before shell encapsulation. The cells were then harvested by centrifugation at 5000g for 10 min. The cell pellets were washed with TN buffer (20 mM Tris-HCl pH = 8.0, 150 mM NaCl) and resuspended in TN buffer supplemented with 10% (v/v) CelLytic B cell Lysis reagent (Sigma-Aldrich) and 1% Protein Inhibitor Cocktail (100×) (Sigma-Aldrich). The cell suspensions were lysed by French Press (Stansted Fluid Power, U.K.). Cell debris was removed by centrifugation at 10,000g at 4 °C for 10 min, followed by centrifugation at 50,000g to enrich C–S at 4 °C. The pellets were resuspended in TN buffer and then loaded onto sucrose gradients (10–30% or 10–50%, w/v), followed by ultracentrifugation (Beckman, XL100K Ultracentrifuge) at 105,000g for 30 min. Each sucrose fraction was collected and stored at 4 °C. Electron microscopy, confocal microscopy, SDS-PAGE, and immunoblot analysis were performed, as described in the Supporting Information.

Expression of Mature [FeFe]-Hydrogenase and Generation of α-Carboxysome Shells with Encapsulated Hydrogenases (H–S)

[FeFe]-hydrogenase from the green alga Chlamydomonas reinhardtii was expressed and encapsulated into α-carboxysome shells (H–S) in E. coli, as reported before. (24) In summary, E. coli strains containing the pCDFDuet-hydA-CS2 (GenBank accession code AAL23572.1) plasmid and the pBAD-cso-2 plasmid were cultivated in LB medium containing 0.2 mM ferric ammonium citrate, 50 μg mL–1 spectinomycin, and 100 μg mL–1 ampicillin and degassed with N2 for 30 min at OD600 = 0.6–0.8. The hydA-EP expression was induced by the addition of 0.5 mM IPTG. After 4 h induction of the hydA-EP expression, the shell expression was induced by 1 mM l-Arabinose, and cells were then grown at 25 °C for 16 h. The purification of H–S was carried out following the method for C–S mentioned above. It should be noted that H–S should be expressed and purified under anaerobic conditions, and all of the solutions used should be degassed in advance. As a control, the plasmid for expressing hydrogenases without FNR and Fd (pCDFDuet-hydA-hydGxEF-CS2) was generated by deleting both genes encoding FNR and Fd from the pCDFDuet-hydA-CS2 plasmid. The α-carboxysome shells that encapsulate hydrogenases only without FNR and Fd (HydA-S) were generated following the same procedure as that for H–S.

TBAP-α Construction

Synthesis and characterization of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP) are described in detail in the Supporting Information. As-synthesized TBAP powder (100 mg) was dissolved in DMF (8 mL). The supernatant solutions were filtered into 25 mL vials using a 0.22 μm PTFE syringe filter to remove any particulates and then placed into larger 100 mL vials with antisolvent CHCl3. Vapor diffusion of the antisolvent into the TBAP solution was carried out for several days until the vials were nearly full of solvent. The resulting crystals were activated after the crystallization solvent was exchanged with acetone 10–12 times over a few days. The crystals were then collected by filtration and characterized by PXRD.

Generation of H–S|TBAP-α Hybrid Nanoreactors

A 2 mg portion of TBAP-α and neutralized AA aqueous solution (0.1 M, 4.5 mL) were added into sample vials and purged with N2 to eliminate oxygen in the solution and sample vials. Next, 0.5 mL of H–S solution purified by a sugar gradient strategy (20% sucrose content, thereby diluting the total protein concentration to 1 mg mL–1 as measured via the Nanodrop method) was introduced into the sample vials under an N2 gas flow. The mixture solution was incubated on a rotator at room temperature for 30 min to facilitate the association of H–S on the TBAP-α surface. The H–S|TBAP-α construction was confirmed by SEM and photocatalytic H2 evolution performance.

High-Throughput Photocatalytic H2 Production Experiments

2 mg of TBAP-α or amorphous TBAP powder and neutralized AA aqueous solution (0.1 M, 4.5 mL) were added into separate sample vials (vial size = 12.5 mL) and purged with N2 on a Chemspeed Technologies Sweigher platform for 6 h. Next, the purified H–S solution (0.5 mL in 20% sucrose, 1 mg mL–1 measured using the Nanodrop method) was added under N2 gas flow to make the total volume of 5 mL. For control samples, 0.5 mL of TN buffer was added to the vials to prepare solutions with a total volume of 5 mL.
All sample vials were irradiated using an Oriel Solar Simulator with an output of 1.0 sun (AM1.5G, Class AAA, IEC/JIS/ASTM, 1440 W xenon, 12 × 12 in., MODEL: 94123A) equipped with a rocker/roller device. The vial size was 23 × 46 mm2, and the irradiation area on the samples was 16.61 cm2. Gaseous products were analyzed on a Shimadzu GC-2010 equipped with a Shimadzu HS-20, injecting a sample from the headspace sampler via a transfer line (temperature 150 °C) onto an Rt-Msieve 5 Å column with He as the carrier gas at a flow rate of 30 mL min–1. H2 was detected with a barrier discharge ionization detector and referenced against a standard that contained a known concentration of H2. Data are represented as the mean ± standard deviation (SD) from at least three repeated measurements.

Time-Course H2 Evolution Assays

Time-course H2 evolution measurements were conducted in a 67 mL quartz flask. 10 mg of TBAP-α and 22.5 mL of neutralized AA aqueous solution (0.1 M) were added to the quartz flask and purged with N2 for 30 min, followed by the addition of purified H–S solution (2.5 mL in 20% sucrose, 1 mg mL–1 measured using the Nanodrop method) under N2 gas flow to make the final volume of 25 mL. The reaction mixture was illuminated with a 300 W Newport Xe light source (Model: 6258, Ozone-free) using a λ > 420 nm cutoff filter. The light source was cooled by water circulating through a metal jacket. Gas samples were taken with a gastight syringe and run on a Bruker 450-GC gas chromatograph. H2 was detected with a thermal conductivity detector referencing standard gas with a known concentration of H2. Data are represented as mean ± SD from at least three repeated measurements.

Molecular Dynamics (MD) Simulations

Model Setup

The TBAP-α model (1 row, 5 columns) was obtained from the published data, (35) and the structure of the CsoS1A protein was downloaded from the Protein Data Bank (PDB ID: 2EWH). (44) The CsoS1A was docked to the TBAP-α model using the HDOCK Server (http://hdock.phys.hust.edu.cn/). (51) The structures with the highest scores were manually screened. The best-fit conformation was selected for molecular dynamic simulation using the AMBER20 software package. (52) The ff14SB (53) force field generated the protein parameters. The Generalized Amber Force field (GAFF) force field (54) is used to create the force field of the TBAP molecule. The atomic charges of the TBAP molecule were calculated by the restricted electrostatic potential (RESP) method with B3LYP/6-31G(d) (55,56) level of theory by the Gaussian 09 program. After examining the protonation state of the protein and adding hydrogen atoms, the system was solvated in a truncated octahedral box of the TIP3P water model (57) with a buffer of 35.0 Å. Na+ and Cl– (58) were added to neutralize the system and achieve a physiological salt concentration of 150 mM. The resulting system comprised 465,869 atoms.

MD Simulations

The system was minimized by 1000 steps of the fastest descent algorithm and 1000 steps of the conjugation gradient algorithm. Then, the system was heated to 300 K in 1 ns, and 300 ns of simulations were performed with 40 ns of NVT simulations and 260 ns of NPT simulation. The electrostatic interactions were calculated using the particle mesh Ewald (PME) (59) method, and the periodic boundary conditions were used. The Langevin thermostat method (60) is used to control the temperature, and the Berendsen barostat method (61) was used to control the system’s pressure. To mimic the environment of carboxysomes, a restraint of 10 kcal mol–1 Å–2 was applied to the backbone of the protein and TBAP-α during the simulation. The trajectory of the last 30 ns was selected as a production run for analysis.

Analysis of Simulations

The root-mean-square deviation (RMSD) of the trajectory of molecular dynamics simulations is calculated by the RMSD Trajectory Tool in VMD. (62) The hydrogen bond and salt bridge analysis used the PLIP web tool (57) (https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index). The maximum distance of the hydrogen bond was set to 4.1 Å, and the minimum angle of a hydrogen bond was 100°. The cutoff of the salt bridge interaction is 5.5 Å.

Supporting Information

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The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acscatal.4c03672.

  • Chemical synthesis pathway of TBAP (Scheme S1); NMR spectrum of TBAP (Figures S1 and S2); FI-IR spectrum of TBAP (Figure S3); crystal model of TBAP-α and 3D model of α-carboxysome shell (Figure S4); PXRD patterns of TBAP phases, nitrogen adsorption isotherm and desorption isotherm for activated TBAP-α and amorphous TBAP, and SEM images of amorphous TBAP (Figure S5); solid UV–vis absorption spectrum of amorphous TBAP and TBAP-α (Figure S6); (αhν)1/2 versus hν curve and Mott–Schottky plot, diagram of conduction band and valence band of amorphous TBAP and TBAP-α, and cyclic voltammetry plot of TBAP-α (Figure S7); amino acid sequence alignment of α-carboxysome shell proteins (Figure S8); front and side views of the structures of α-carboxysome shell proteins (Figure S9); confocal microscopy images of E. coli cells expressing mCherry-CsoS2C (mCherry-EP) and coexpressing shells and mCherry-csoS2C (C–S) and SDS-PAGE of purified C–S (Figure S10); TEM image of C–S (Figure S11); SEM and confocal microscopy images of pyrene crystals and pyrene crystals with C–S (Figure S12); ζ-potentials of TBAP-α and α-carboxysome shell-encasing proteins (Figure S13); size distribution of H–S revealed by SEM (Figure S14); SDS-PAGE result of H–S purification (Figure S15); immunoblot analysis of purified H–S (Figure S16); colloidal stability of H–S|TBAP-α (Figure S17); photocurrent responses and EIS analysis for TBAP-α and H–S|TBAP-α (Figure S18); H2 production condition optimization of H–S|TBAP-α (Figure S19); photocurrent response and EIS analysis for amorphous TBAP and TBAP-α (Figure S20); wavelength-dependent AQY value of H–S|TBAP-α (Figure S21); H2 evolution of TBAP-α, H–S|TBAP-α, and 1 wt % Pt|TBAP-α (λ > 420 nm) as a function of time (Figure S22); cycling measurements for the photocatalytic hydrogen evolution of H–S|TBAP-α (Figure S23); immunoblot analysis of purified HydA (Fd-HydA-EP) (Figure S24); SEM images (Figure S25) and PXRD pattern (Figure S26) of H–S|TBAP-α after 30 h irradiation; gene maps of used plasmids (Figure S27); crystal data and structure refinement of TBAP-α (Table S1); protein components in recombinant α-carboxysomes from E. coli (Table S2); statistics of residues for TBAP-α and CsoS1A protein binding calculated by MD simulations (Tables S3 and S4); estimated fluorescence lifetimes of TBAP-α and H–S|TBAP-α (Table S5); a list of hydrogen evolution reaction conditions in this work (Table S6); a comparison of the H–S|TBAP-α assembly performance with the related state-of-the-art photocatalysts (Table S7); primers used for pCDFDuet-mCherry-CS2 plasmid construction (Table S8); and gene sequences of used plasmids (Table S9). (PDF)

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Author Information

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  • Corresponding Authors
  • Authors
    • Jing Yang - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.;  Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
    • Qiuyao Jiang - Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
    • Yu Chen - Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
    • Quan Wen - Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
    • Xingwu Ge - Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
    • Qiang Zhu - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    • Wei Zhao - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.;  Orcidhttps://orcid.org/0000-0003-0265-2590
    • Oluwatobi Adegbite - Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, U.K.
    • Haofan Yang - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    • Liang Luo - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    • Hang Qu - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    • Veronica Del-Angel-Hernandez - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    • Rob Clowes - Materials Innovation Factory and Department of Chemistry, University of Liverpool, Liverpool L7 3NY, U.K.
    • Jun Gao - Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;  Orcidhttps://orcid.org/0000-0002-6692-1828
  • Author Contributions

    L.-N.L. and A.I.C. devised and supervised the project. M.A.L. helped supervise the project and contributed to the design of experiments and data interpretation. J.Y. designed and carried out the experiments and led the experimental work. Q.J. assisted with the construction of protein. X.G. helped with confocal microscopy. Y.C. assisted with plasmid design and preparation. Q.W. and J.G. performed molecular dynamics simulations and analysis. Q.Z. and H.Q. helped with PXRD and gas absorption measurements. W.Z., L.L., H.Y., and V.D.-A.-H. assisted with photoelectrochemical measurements. O.A. helped with the ITC measurement. R.C. assisted with high-throughput photocatalytic H2 production experiments. J.Y., M.A.L., A.I.C., and L.-N.L. wrote the manuscript with all authors’ contributions.

  • Notes
    The authors declare no competing financial interest.

Acknowledgments

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The authors thank the Liverpool Biomedical Electron Microscopy Unit and Centre for Cell Imaging for technical assistance and provision for microscopic imaging and the Materials Innovation Factory (MIF) for the provision of analytical equipment. This work was supported by the National Key R&D Program of China (2021YFA0909600), the National Natural Science Foundation of China (32070109), the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/Y008308/1, BB/Y01135X/1), the Royal Society (URF\R\180030, RGF\EA\181061, RGF\EA\180233), and the Leverhulme Trust (RPG-2021-286). The authors acknowledge financial support from the Leverhulme Trust via the Leverhulme Research Centre for Functional Materials Design.

References

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This article references 62 other publications.

  1. 1
    Tachibana, Y.; Vayssieres, L.; Durrant, J. R. Artificial photosynthesis for solar water-splitting. Nat. Photonics 2012, 6, 511– 518,  DOI: 10.1038/nphoton.2012.175
    Google Scholar
    1
    Artificial photosynthesis for solar water-splitting
    Tachibana, Yasuhiro; Vayssieres, Lionel; Durrant, James R.
    Nature Photonics (2012), 6 (8), 511-518CODEN: NPAHBY; ISSN:1749-4885. (Nature Publishing Group)
    A review. Hydrogen generated from solar-driven water-splitting has the potential to be a clean, sustainable and abundant energy source. Inspired by natural photosynthesis, artificial solar water-splitting devices are now being designed and tested. Recent developments based on mol. and/or nanostructure designs have led to advances in our understanding of light-induced charge sepn. and subsequent catalytic water oxidn. and redn. reactions. Here we review some of the recent progress towards developing artificial photosynthetic devices, together with their analogies to biol. photosynthesis, including technologies that focus on the development of visible-light active hetero-nanostructures and require an understanding of the underlying interfacial carrier dynamics. Finally, we propose a vision for a future sustainable hydrogen fuel community based on artificial photosynthesis.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtFWjtLfN&md5=b98a6de15072b768fe7403a6e3f91012
  2. 2
    Blankenship, R. E.; Tiede, D. M.; Barber, J.; Brudvig, G. W.; Fleming, G.; Ghirardi, M.; Gunner, M. R.; Junge, W.; Kramer, D. M.; Melis, A.; Moore, T. A.; Moser, C. C.; Nocera, D. G.; Nozik, A. J.; Ort, D. R.; Parson, W. W.; Prince, R. C.; Sayre, R. T. Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement. Science 2011, 332, 805– 809,  DOI: 10.1126/science.1200165
    Google Scholar
    2
    Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement
    Blankenship, Robert E.; Tiede, David M.; Barber, James; Brudvig, Gary W.; Fleming, Graham; Ghirardi, Maria; Gunner, M. R.; Junge, Wolfgang; Kramer, David M.; Melis, Anastasios; Moore, Thomas A.; Moser, Christopher C.; Nocera, Daniel G.; Nozik, Arthur J.; Ort, Donald R.; Parson, William W.; Prince, Roger C.; Sayre, Richard T.
    Science (Washington, DC, United States) (2011), 332 (6031), 805-809CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    A review. Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chem. fuels in the case of natural photosynthesis and non-stored elec. current in the case of photovoltaics. To find common ground for evaluating energy-conversion efficiency, the authors compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. Opportunities in which the frontiers of synthetic biol. might be used to enhance natural photosynthesis for improved solar energy conversion efficiency are considered.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXlslylsLk%253D&md5=4b251dbb2f5d29cd9033f5c16085baf1
  3. 3
    Wang, Y.; Vogel, A.; Sachs, M.; Sprick, R. S.; Wilbraham, L.; Moniz, S. J. A.; Godin, R.; Zwijnenburg, M. A.; Durrant, J. R.; Cooper, A. I.; Tang, J. Current understanding and challenges of solar-driven hydrogen generation using polymeric photocatalysts. Nat. Energy 2019, 4, 746– 760,  DOI: 10.1038/s41560-019-0456-5
    Google Scholar
    3
    Current understanding and challenges of solar-driven hydrogen generation using polymeric photocatalysts
    Wang, Yiou; Vogel, Anastasia; Sachs, Michael; Sprick, Reiner Sebastian; Wilbraham, Liam; Moniz, Savio J. A.; Godin, Robert; Zwijnenburg, Martijn A.; Durrant, James R.; Cooper, Andrew I.; Tang, Junwang
    Nature Energy (2019), 4 (9), 746-760CODEN: NEANFD; ISSN:2058-7546. (Nature Research)
    A review. The use of hydrogen as a fuel, when generated from water using semiconductor photocatalysts and driven by sunlight, is a sustainable alternative to fossil fuels. Polymeric photocatalysts are based on Earth-abundant elements and have the advantage over their inorg. counterparts in that their electronic properties are easily tuneable through mol. engineering. Polymeric photocatalysts have developed rapidly over the past decade, resulting in the discovery of many active materials. However, our understanding of the key properties underlying their photoinitiated redox processes has not kept pace, and this impedes further progress to generate cost-competitive technologies. Here, we discuss state-of-the-art polymeric photocatalysts and our microscopic understanding of their activities. We conclude with a discussion of five outstanding challenges in this field: non-standardized reporting of activities, limited photochem. stability, insufficient knowledge of reaction mechanisms, balancing charge carrier lifetimes with catalysis timescales and the use of unsustainable sacrificial reagents.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsleltL3I&md5=181c014c5903e1b9185990dfc929cca0
  4. 4
    Barber, J. Photosynthetic energy conversion: Natural and artificial. Chem. Soc. Rev. 2009, 38, 185– 196,  DOI: 10.1039/B802262N
    Google Scholar
    4
    Photosynthetic energy conversion: Natural and artificial
    Barber, James
    Chemical Society Reviews (2009), 38 (1), 185-196CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. Photosystem II (PSII) is the water splitting enzyme of photosynthesis. Its appearance during evolution dramatically changed the chem. compn. of our planet and set in motion an unprecedented explosion in biol. activity. Powered by sunlight, PSII supplies biol. with the hydrogen' needed to convert carbon dioxide into org. mols. The questions now are can we continue to exploit this photosynthetic process through increased use of biomass as an energy source and, more importantly, can we address the energy/CO2 problem by developing new photochem. technologies which mimic the natural system.
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  5. 5
    Zhang, J. Z.; Reisner, E. Advancing photosystem II photoelectrochemistry for semi-artificial photosynthesis. Nat. Rev. Chem. 2020, 4, 6– 21,  DOI: 10.1038/s41570-019-0149-4
    Google Scholar
    5
    Advancing photosystem II photoelectrochemistry for semi-artificial photosynthesis
    Zhang, Jenny Z.; Reisner, Erwin
    Nature Reviews Chemistry (2020), 4 (1), 6-21CODEN: NRCAF7; ISSN:2397-3358. (Nature Research)
    A review. Oxygenic photosynthesis is the primary solar energy-conversion process that supports much of life on Earth. It is initiated by photosystem II (PSII), an enzyme that exts. electrons from H2O and feeds them into an electron-transport chain to result in chem. synthesis using the input of solar energy. PSII can be immobilized onto electrodes for photoelectrochem. studies, in which electrons photogenerated from PSII are harnessed for enzyme characterization, and to drive fuel-forming reactions by electrochem. coupling the PSII to a suitable (bio)catalyst. Research in PSII photoelectrochem. has recently made substantial strides in electrode design and unravelling charge-transfer pathways at the bio-material interface. In turn, these efforts have opened up possibilities in the field of bio-photoelectrochem., expanding the range of biocatalysts that can be systematically interrogated, including biofilms of whole photosynthetic cells. Furthermore, these studies have accelerated the development of semi-artificial photosynthesis to afford autonomous, solar-driven, fuel-forming biohybrid devices. This Review summarizes the latest advancements in PSII photoelectrochem. with respect to electrode design and understanding of the bio-material interface, on both the protein and cellular level. We also discuss the role of biol. photosynthetic systems in present and future semi-artificial photosynthesis.
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  6. 6
    Pi, X.; Zhao, S.; Wang, W.; Liu, D.; Xu, C.; Han, G.; Kuang, T.; Sui, S. F.; Shen, J. R. The pigment-protein network of a diatom photosystem II–light-harvesting antenna supercomplex. Science 2019, 365, 447– 457,  DOI: 10.1126/science.aax4406
    Google Scholar
    There is no corresponding record for this reference.
  7. 7
    Vayghan, H. S.; Nawrocki, W. J.; Schiphorst, C.; Tolleter, D.; Hu, C.; Douet, V.; Glauser, G.; Finazzi, G.; Croce, R.; Wientjes, E.; Longoni, F. Photosynthetic Light Harvesting and Thylakoid Organization in a CRISPR/Cas9 Arabidopsis Thaliana LHCB1 Knockout Mutant. Front. Plant Sci. 2022, 13, 833032– 833050,  DOI: 10.3389/fpls.2022.833032
    Google Scholar
    There is no corresponding record for this reference.
  8. 8
    Koepf, M.; Teillout, A.-L.; Llansola-Portoles, M. J. Artificial Photosynthesis: An Approach for a Sustainable Future. In Handbook of Ecomaterials; Martínez, L. M. T.; Kharissova, O. V.; Kharisov, B. I., Eds.; Springer International Publishing: Cham, 2017; pp 1– 25.
    Google Scholar
    There is no corresponding record for this reference.
  9. 9
    Guo, Y.; Zhou, Q.; Nan, J.; Shi, W.; Cui, F.; Zhu, Y. Perylenetetracarboxylic acid nanosheets with internal electric fields and anisotropic charge migration for photocatalytic hydrogen evolution. Nat. Commun. 2022, 13, 2067  DOI: 10.1038/s41467-022-29826-z
    Google Scholar
    9
    Perylenetetracarboxylic acid nanosheets with internal electric fields and anisotropic charge migration for photocatalytic hydrogen evolution
    Guo, Yan; Zhou, Qixin; Nan, Jun; Shi, Wenxin; Cui, Fuyi; Zhu, Yongfa
    Nature Communications (2022), 13 (1), 2067CODEN: NCAOBW; ISSN:2041-1723. (Nature Portfolio)
    Highly efficient hydrogen evolution reactions carried out via photocatalysis using solar light remain a formidable challenge. Herein, perylenetetracarboxylic acid nanosheets with a monolayer thickness of ∼1.5 nm were synthesized and shown to be active hydrogen evolution photocatalysts with prodn. rates of 118.9 mmol g-1 h-1. The carboxyl groups increased the intensity of the internal elec. fields of perylenetetracarboxylic acid from the perylene center to the carboxyl border by 10.3 times to promote charge-carrier sepn. The photogenerated electrons and holes migrated to the edge and plane, resp., to weaken charge-carrier recombination. Moreover, the perylenetetracarboxylic acid redn. potential increases from -0.47 V to -1.13 V due to the decreased mol. conjugation and enhances the redn. ability. In addn., the carboxyl groups created hydrophilic sites. This work provides a strategy to engineer the mol. structures of future efficient photocatalysts.
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  10. 10
    Kosco, J.; Bidwell, M.; Cha, H.; Martin, T.; Howells, C. T.; Sachs, M.; Anjum, D. H.; Gonzalez Lopez, S.; Zou, L.; Wadsworth, A.; Zhang, W.; Zhang, L.; Tellam, J.; Sougrat, R.; Laquai, F.; DeLongchamp, D. M.; Durrant, J. R.; McCulloch, I. Enhanced photocatalytic hydrogen evolution from organic semiconductor heterojunction nanoparticles. Nat. Mater. 2020, 19, 559– 565,  DOI: 10.1038/s41563-019-0591-1
    Google Scholar
    10
    Enhanced photocatalytic hydrogen evolution from organic semiconductor heterojunction nanoparticles
    Kosco, Jan; Bidwell, Matthew; Cha, Hyojung; Martin, Tyler; Howells, Calvyn T.; Sachs, Michael; Anjum, Dalaver H.; Gonzalez Lopez, Sandra; Zou, Lingyu; Wadsworth, Andrew; Zhang, Weimin; Zhang, Lisheng; Tellam, James; Sougrat, Rachid; Laquai, Frederic; De Longchamp, Dean M.; Durrant, James R.; McCulloch, Iain
    Nature Materials (2020), 19 (5), 559-565CODEN: NMAACR; ISSN:1476-1122. (Nature Research)
    Photocatalysts formed from a single org. semiconductor typically suffer from inefficient intrinsic charge generation, which leads to low photocatalytic activities. It is demonstrated that incorporating a heterojunction between a donor polymer (PTB7-Th) and non-fullerene acceptor (EH-IDTBR) in org. nanoparticles (NPs) can result in hydrogen evolution photocatalysts with greatly enhanced photocatalytic activity. Control of the nanomorphol. of these NPs was achieved by varying the stabilizing surfactant employed during NP fabrication, converting it from a core-shell structure to an intermixed donor/acceptor blend and increasing H2 evolution by an order of magnitude. The resulting photocatalysts display an unprecedentedly high H2 evolution rate of over 60,000μmol h-1 g-1 under 350-800 nm illumination, and external quantum efficiencies > 6% in the region of max. solar photon flux.
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  11. 11
    Wang, Q.; Domen, K. Particulate Photocatalysts for Light-Driven Water Splitting: Mechanisms, Challenges, and Design Strategies. Chem. Rev. 2020, 120, 919– 985,  DOI: 10.1021/acs.chemrev.9b00201
    Google Scholar
    11
    Particulate Photocatalysts for Light-Driven Water Splitting: Mechanisms, Challenges, and Design Strategies
    Wang, Qian; Domen, Kazunari
    Chemical Reviews (Washington, DC, United States) (2020), 120 (2), 919-985CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. Solar-driven water splitting provides a leading approach to store the abundant yet intermittent solar energy and produce hydrogen as a clean and sustainable energy carrier. A straightforward route to light-driven water splitting is to apply self-supported particulate photocatalysts, which is expected to allow solar hydrogen to be competitive with fossil-fuel-derived hydrogen on a levelized cost basis. More importantly, the powder-based systems can lend themselves to making functional panels on a large scale while retaining the intrinsic activity of the photocatalyst. However, all attempts to generate hydrogen via powder-based solar water-splitting systems to date have unfortunately fallen short of the efficiency values required for practical applications. Photocatalysis on photocatalyst particles involves three sequential steps, absorption of photons with higher energies than the bandgap of the photocatalysts, leading to the excitation of electron-hole pairs in the particles, charge sepn. and migration of these photoexcited carriers, and surface chem. reactions based on these carriers. In this review, the focus is on the challenges of each step and summarize material design strategies to overcome the obstacles and limitations. This review illustrates that it is possible to employ the fundamental principles underlying photosynthesis and the tools of chem. and materials science to design and prep. photocatalysts for overall water splitting.
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  12. 12
    Takata, T.; Jiang, J.; Sakata, Y.; Nakabayashi, M.; Shibata, N.; Nandal, V.; Seki, K.; Hisatomi, T.; Domen, K. Photocatalytic water splitting with a quantum efficiency of almost unity. Nature 2020, 581, 411– 414,  DOI: 10.1038/s41586-020-2278-9
    Google Scholar
    12
    Photocatalytic water splitting with a quantum efficiency of almost unity
    Takata, Tsuyoshi; Jiang, Junzhe; Sakata, Yoshihisa; Nakabayashi, Mamiko; Shibata, Naoya; Nandal, Vikas; Seki, Kazuhiko; Hisatomi, Takashi; Domen, Kazunari
    Nature (London, United Kingdom) (2020), 581 (7809), 411-414CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
    Overall water splitting, evolving hydrogen and oxygen in a 2:1 stoichiometric ratio, using particulate photocatalysts is a potential means of achieving scalable and economically viable solar hydrogen prodn. To obtain high solar energy conversion efficiency, the quantum efficiency of the photocatalytic reaction must be increased over a wide range of wavelengths and semiconductors with narrow bandgaps need to be designed. However, the quantum efficiency assocd. with overall water splitting using existing photocatalysts is typically lower than ten per cent1,2. Thus, whether a particulate photocatalyst can enable a quantum efficiency of 100 per cent for the greatly endergonic water-splitting reaction remains an open question. Here we demonstrate overall water splitting at an external quantum efficiency of up to 96 per cent at wavelengths between 350 and 360 nm, which is equiv. to an internal quantum efficiency of almost unity, using a modified aluminum-doped strontium titanate (SrTiO3:Al) photocatalyst3,4. This enabled multiple consecutive forward charge transfers without backward charge transfer, reaching the upper limit of quantum efficiency for overall water splitting. Our work demonstrates the feasibility of overall water splitting free from charge recombination losses and introduces an ideal cocatalyst/photocatalyst structure for efficient water splitting.
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  13. 13
    Searle, N. Z.; Hirt, R. C. Ultraviolet Spectral Energy Distribution of Sunlight. J. Opt. Soc. Am. 1965, 55, 1413– 1421,  DOI: 10.1364/JOSA.55.001413
    Google Scholar
    There is no corresponding record for this reference.
  14. 14
    Cestellos-Blanco, S.; Zhang, H.; Kim, J. M.; Shen, Yx.; Yang, P. Photosynthetic semiconductor biohybrids for solar-driven biocatalysis. Nat. Catal. 2020, 3, 245– 255,  DOI: 10.1038/s41929-020-0428-y
    Google Scholar
    14
    Photosynthetic semiconductor biohybrids for solar-driven biocatalysis
    Cestellos-Blanco, Stefano; Zhang, Hao; Kim, Ji Min; Shen, Yue-xiao; Yang, Peidong
    Nature Catalysis (2020), 3 (3), 245-255CODEN: NCAACP; ISSN:2520-1158. (Nature Research)
    A review. Abstr.: Photosynthetic semiconductor biohybrids integrate the best attributes of biol. whole-cell catalysts and semiconducting nanomaterials. Enzymic machinery enveloped in its native cellular environment offers exquisite product selectivity and low substrate activation barriers while semiconducting nanomaterials harvest light energy stably and efficiently. In this Review Article, we illustrate the evolution and advances of photosynthetic semiconductor biohybrids focusing on the conversion of CO2 to value-added chems. We begin by considering the potential of this nascent field to meet global energy challenges while comparing it to alternate approaches. This is followed by a discussion of the advantageous coupling of electrotrophic organisms with light-active electrodes for solar-to-chem. conversion. We detail the dynamic investigation of photosensitized microorganisms creating direct light harvesting within unicellular organisms while describing complementary developments in the understanding of charge transfer mechanisms and cytoprotection. Lastly, we focus on trends and improvements needed in photosynthetic semiconductor biohybrids in order to address future challenges and enhance their widespread adoption for the prodn. of solar chems.
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  15. 15
    Kornienko, N.; Zhang, J. Z.; Sakimoto, K. K.; Yang, P.; Reisner, E. Interfacing nature’s catalytic machinery with synthetic materials for semi-artificial photosynthesis. Nat. Nanotechnol. 2018, 13, 890– 899,  DOI: 10.1038/s41565-018-0251-7
    Google Scholar
    15
    Interfacing nature's catalytic machinery with synthetic materials for semi-artificial photosynthesis
    Kornienko, Nikolay; Zhang, Jenny Z.; Sakimoto, Kelsey K.; Yang, Peidong; Reisner, Erwin
    Nature Nanotechnology (2018), 13 (10), 890-899CODEN: NNAABX; ISSN:1748-3387. (Nature Research)
    Semi-artificial photosynthetic systems aim to overcome the limitations of natural and artificial photosynthesis while providing an opportunity to investigate their resp. functionality. The progress and studies of these hybrid systems is the focus of this forward-looking perspective. In this Review, we discuss how enzymes have been interfaced with synthetic materials and employed for semi-artificial fuel prodn. In parallel, we examine how more complex living cellular systems can be recruited for in vivo fuel and chem. prodn. in an approach where inorg. nanostructures are hybridized with photosynthetic and non-photosynthetic microorganisms. Side-by-side comparisons reveal strengths and limitations of enzyme- and microorganism-based hybrid systems, and how lessons extd. from studying enzyme hybrids can be applied to investigations of microorganism-hybrid devices. We conclude by putting semi-artificial photosynthesis in the context of its own ambitions and discuss how it can help address the grand challenges facing artificial systems for the efficient generation of solar fuels and chems.
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  16. 16
    Özgen, F. F.; Runda, M. E.; Schmidt, S. Photo-biocatalytic Cascades: Combining Chemical and Enzymatic Transformations Fueled by Light. ChemBioChem 2021, 22, 790– 806,  DOI: 10.1002/cbic.202000587
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    16
    Photo-biocatalytic Cascades: Combining Chemical and Enzymatic Transformations Fueled by Light
    Ozgen Fatma Feyza; Runda Michael E; Schmidt Sandy
    Chembiochem : a European journal of chemical biology (2021), 22 (5), 790-806 ISSN:.
    In the field of green chemistry, light - an attractive natural agent - has received particular attention for driving biocatalytic reactions. Moreover, the implementation of light to drive (chemo)enzymatic cascade reactions opens up a golden window of opportunities. However, there are limitations to many current examples, mostly associated with incompatibility between the enzyme and the photocatalyst. Additionally, the formation of reactive radicals upon illumination and the loss of catalytic activities in the presence of required additives are common observations. As outlined in this review, the main question is how to overcome current challenges to the exploitation of light to drive (chemo)enzymatic transformations. First, we highlight general concepts in photo-biocatalysis, then give various examples of photo-chemoenzymatic (PCE) cascades, further summarize current synthetic examples of PCE cascades and discuss strategies to address the limitations.
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  17. 17
    Schmermund, L.; Jurkaš, V.; Özgen, F. F.; Barone, G. D.; Büchsenschütz, H. C.; Winkler, C. K.; Schmidt, S.; Kourist, R.; Kroutil, W. Photo-Biocatalysis: Biotransformations in the Presence of Light. ACS Catal. 2019, 9, 4115– 4144,  DOI: 10.1021/acscatal.9b00656
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    17
    Photo-Biocatalysis: Biotransformations in the Presence of Light
    Schmermund, Luca; Jurkas, Valentina; Oezgen, F. Feyza; Barone, Giovanni D.; Buechsenschuetz, Hanna C.; Winkler, Christoph K.; Schmidt, Sandy; Kourist, Robert; Kroutil, Wolfgang
    ACS Catalysis (2019), 9 (5), 4115-4144CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
    A review. Light has received increased attention for various chem. reactions but also in combination with biocatalytic reactions. Because currently only a few enzymic reactions are known, which per se require light, most transformations involving light and a biocatalyst exploit light either for providing the cosubstrate or cofactor in an appropriate redox state for the biotransformation. In selected cases, a promiscuous activity of known enzymes in the presence of light could be induced. In other approaches, light-induced chem. reactions have been combined with a biocatalytic step, or light-induced biocatalytic reactions were combined with chem. reactions in a linear cascade. Finally, enzymes with a light switchable moiety have been investigated to turn off/on or tune the actual reaction. This Review gives an overview of the various approaches for using light in biocatalysis.
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  18. 18
    Holá, K.; Pavliuk, M. V.; Németh, B.; Huang, P.; Zdražil, L.; Land, H.; Berggren, G.; Tian, H. Carbon Dots and [FeFe] Hydrogenase Biohybrid Assemblies for Efficient Light-Driven Hydrogen Evolution. ACS Catal. 2020, 10, 9943– 9952,  DOI: 10.1021/acscatal.0c02474
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    18
    Carbon Dots and [FeFe] Hydrogenase Biohybrid Assemblies for Efficient Light-Driven Hydrogen Evolution
    Hola, Katerina; Pavliuk, Mariia V.; Nemeth, Brigitta; Huang, Ping; Zdrazil, Lukas; Land, Henrik; Berggren, Gustav; Tian, Haining
    ACS Catalysis (2020), 10 (17), 9943-9952CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
    Artificial photosynthesis is seen as a path to convert and store solar energy into chem. energy for our society. In this work, highly fluorescent aspartic acid-based carbon dots (CDs) are synthesized and employed as a photosensitizer to drive photocatalytic hydrogen evolution with an [FeFe] hydrogenase (CrHydA1). The direct interaction in CDs from L-aspartic acid (AspCDs)/CrHydA1 self-assembly systems, which is visualized from native gel electrophoresis, has been systematically investigated to understand the electron-transfer dynamics and its impact on photocatalytic efficiency. The study discloses the significant influence of the electrostatic surrounding generated by sacrificial electron donors on the intimate interplay within the oppositely charged subunits of the biohybrid assembly as well as the overall photocatalytic performance. The system reaches an external quantum efficiency of 1.7% at 420 nm and an initial activity of 1.73μmol(H2) mg-1(hydrogenase) min-1 under favorable electrostatic conditions. Owing to the ability of the synthesized AspCDs to operate efficiently under visible light, in contrast to other materials that require UV illumination, the stability of the biohybrid assembly in the presence of a redox mediator extends beyond 1 wk.
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  19. 19
    Gai, P.; Yu, W.; Zhao, H.; Qi, R.; Li, F.; Liu, L.; Lv, F.; Wang, S. Solar-Powered Organic Semiconductor-Bacteria Biohybrids for CO2 Reduction into Acetic Acid. Angew. Chem., Int. Ed. 2020, 59, 7224– 7229,  DOI: 10.1002/anie.202001047
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    19
    Solar-Powered Organic Semiconductor-Bacteria Biohybrids for CO2 Reduction into Acetic Acid
    Gai, Panpan; Yu, Wen; Zhao, Hao; Qi, Ruilian; Li, Feng; Liu, Libing; Lv, Fengting; Wang, Shu
    Angewandte Chemie, International Edition (2020), 59 (18), 7224-7229CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
    An org. semiconductor-bacteria biohybrid photosynthetic system is used to efficiently realize CO2 redn. to produce acetic acid with the non-photosynthetic bacteria Moorella thermoacetica. Perylene diimide deriv. (PDI) and poly(fluorene-co-phenylene) (PFP) were coated on the bacteria surface as photosensitizers to form a p-n heterojunction (PFP/PDI) layer, affording higher hole/electron sepn. efficiency. The π-conjugated semiconductors possess excellent light-harvesting ability and biocompatibility, and the cationic side chains of org. semiconductors could intercalate into cell membranes, ensuring efficient electron transfer to bacteria. Moorella thermoacetica can thus harvest photoexcited electrons from the PFP/PDI heterojunction, driving the Wood-Ljungdahl pathway to synthesize acetic acid from CO2 under illumination. The efficiency of this org. biohybrid is about 1.6 %, which is comparable to those of reported inorg. biohybrid systems.
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  20. 20
    Wang, X.; Saba, T.; Yiu, H. H. P.; Howe, R. F.; Anderson, J. A.; Shi, J. Cofactor NAD(P)H Regeneration Inspired by Heterogeneous Pathways. Chem 2017, 2, 621– 654,  DOI: 10.1016/j.chempr.2017.04.009
    Google Scholar
    20
    Cofactor NAD(P)H Regeneration Inspired by Heterogeneous Pathways
    Wang, Xiaodong; Saba, Tony; Yiu, Humphrey H. P.; Howe, Russell F.; Anderson, James A.; Shi, Jiafu
    Chem (2017), 2 (5), 621-654CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)
    Biocatalysis can empower chem., pharmaceutical, and energy industries, where the use of enzymes facilitates low-energy, sustainable methods of producing high-value chems. and pharmaceuticals that are otherwise impossibly troublesome or costly to obtain. One of the largest classes of enzymes (oxidoreductases, ∼25% of the total) capable of promoting bioredn. reactions is vital for the global pharmaceutical and chem. market because of their intrinsic enantioselectivity and specificity. Enzymic redn. depends on a coenzyme or cofactor as a hydride source, namely NAD (NADH) or its phosphorylated form (NADPH). Given the high cost, stoichiometric usage, and phys. instability of NAD(P)H, a suitable method for NAD(P)H regeneration is essential for practical application. This review summarizes the existing methods for NAD(P)H regeneration, including enzymic, chem., homogeneous catalytic, electrochem., photocatalytic, and heterogeneous catalytic routes. Particular focus is given to recent progress in developing heterogeneous systems with potential significance in terms of process simplicity, cleanliness, and energy and/or cost savings.
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  21. 21
    Gentil, S.; Che Mansor, S. M.; Jamet, H.; Cosnier, S.; Cavazza, C.; Le Goff, A. Oriented Immobilization of [NiFeSe] Hydrogenases on Covalently and Noncovalently Functionalized Carbon Nanotubes for H2/Air Enzymatic Fuel Cells. ACS Catal. 2018, 8, 3957– 3964,  DOI: 10.1021/acscatal.8b00708
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    21
    Oriented Immobilization of [NiFeSe] Hydrogenases on Covalently and Noncovalently Functionalized Carbon Nanotubes for H2/Air Enzymatic Fuel Cells
    Gentil, Solene; Che Mansor, Syamim Muhamad; Jamet, Helene; Cosnier, Serge; Cavazza, Christine; Le Goff, Alan
    ACS Catalysis (2018), 8 (5), 3957-3964CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
    We report the oriented immobilization of [NiFeSe] hydrogenases on both covalently and noncovalently modified carbon nanotubes (CNTs) electrodes. A specific interaction of the [NiFeSe] hydrogenase from Desulfomicrobium baculatum with hydrophobic org. mols. was probed by electrochem., quartz crystal microbalance with dissipation monitoring (QCM-D), and theor. calcns. Taking advantage of these hydrophobic interactions, the enzyme was efficiently wired on anthraquinone and adamantane-modified CNTs. Because of rational immobilization onto functionalized CNTs, the O2-tolerant [NiFeSe]-hydrogenase is able to efficiently operate in a H2/air gas-diffusion enzymic fuel cell.
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  22. 22
    Zhang, S.; Liu, S.; Sun, Y.; Li, S.; Shi, J.; Jiang, Z. Enzyme-photo-coupled catalytic systems. Chem. Soc. Rev. 2021, 50, 13449– 13466,  DOI: 10.1039/D1CS00392E
    Google Scholar
    22
    Enzyme-photo-coupled catalytic systems
    Zhang, Shaohua; Liu, Shusong; Sun, Yiying; Li, Shihao; Shi, Jiafu; Jiang, Zhongyi
    Chemical Society Reviews (2021), 50 (24), 13449-13466CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
    A review. Efficient chem. transformation in a green, low-carbon way is crucial for the sustainable development of modern society. Enzyme-photo-coupled catalytic systems (EPCS) that integrate the exceptional selectivity of enzyme catalysis and the unique reactivity of photocatalysis hold great promise in solar-driven 'mol. editing'. However, the involvement of multiple components and catalytic processes challenged the design of efficient and stable EPCS. To show a clear picture of the complex catalytic system, in this review, we analyze EPCS from the perspective of system engineering. First, we disintegrate the complex system into four elementary components, and reorganize these components into biocatalytic and photocatalytic ensembles (BE and PE). By resolving current accessible systems, we identify that connectivity and compatibility between BE and PE are two crucial factors that govern the performance of EPCS. Then, we discuss the origin of undesirable connectivity and low compatibility, and deduce the possible solns. Based on these understandings, we propose the designing principles of EPCS. Lastly, we provide a future perspective of EPCS.
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  23. 23
    Sun, Y.; Lin, Y.; Harman, V. M.; Beynon, R. J.; Johnson, J. R.; Liu, L.-N. Decoding the Absolute Stoichiometric Composition and Structural Plasticity of a-Carboxysomes. mBio 2022, 13, e03629-21  DOI: 10.1128/mbio.03629-21
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    There is no corresponding record for this reference.
  24. 24
    Gonzalez-Esquer, C. R.; Newnham, S. E.; Kerfeld, C. A. Bacterial microcompartments as metabolic modules for plant synthetic biology. Plant J. 2016, 87, 66– 75,  DOI: 10.1111/tpj.13166
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    24
    Bacterial microcompartments as metabolic modules for plant synthetic biology
    Gonzalez-Esquer, C. Raul; Newnham, Sarah E.; Kerfeld, Cheryl A.
    Plant Journal (2016), 87 (1), 66-75CODEN: PLJUED; ISSN:0960-7412. (Wiley-Blackwell)
    Bacterial microcompartments (BMCs) are megadalton-sized protein assemblies that enclose segments of metabolic pathways within cells. They increase the catalytic efficiency of the encapsulated enzymes while sequestering volatile or toxic intermediates from the bulk cytosol. The first BMCs discovered were the carboxysomes of cyanobacteria. Carboxysomes compartmentalize the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) with carbonic anhydrase. They enhance the carboxylase activity of RuBisCO by increasing the local concn. of CO2 in the vicinity of the enzyme's active site. As a metabolic module for carbon fixation, carboxysomes could be transferred to eukaryotic organisms (e.g. plants) to increase photosynthetic efficiency. Within the scope of synthetic biol., carboxysomes and other BMCs hold even greater potential when considered a source of building blocks for the development of nanoreactors or three-dimensional scaffolds to increase the efficiency of either native or heterologously expressed enzymes. The carboxysome serves as an ideal model system for testing approaches to engineering BMCs because their expression in cyanobacteria provides a sensitive screen for form (appearance of polyhedral bodies) and function (ability to grow on air). We recount recent progress in the re-engineering of the carboxysome shell and core to offer a conceptual framework for the development of BMC-based architectures for applications in plant synthetic biol.
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  25. 25
    Liu, L. N. Advances in the bacterial organelles for CO2 fixation. Trends Microbiol. 2022, 30, 567– 580,  DOI: 10.1016/j.tim.2021.10.004
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    25
    Advances in the bacterial organelles for CO2 fixation
    Liu, Lu-Ning
    Trends in Microbiology (2022), 30 (6), 567-580CODEN: TRMIEA; ISSN:0966-842X. (Elsevier Ltd.)
    Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concn. mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biol. to repurpose the metabolic module in diverse applications.
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  26. 26
    Huang, J.; Jiang, Q.; Yang, M.; Dykes, G. F.; Weetman, S. L.; Xin, W.; He, H. L.; Liu, L. N. Probing the internal pH and permeability of a carboxysome shell. Biomacromolecules 2022, 23, 4339– 4348,  DOI: 10.1021/acs.biomac.2c00781
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    26
    Probing the Internal pH and Permeability of a Carboxysome Shell
    Huang, Jiafeng; Jiang, Qiuyao; Yang, Mengru; Dykes, Gregory F.; Weetman, Samantha L.; Xin, Wei; He, Hai-Lun; Liu, Lu-Ning
    Biomacromolecules (2022), 23 (10), 4339-4348CODEN: BOMAF6; ISSN:1525-7797. (American Chemical Society)
    The carboxysome is a protein-based nanoscale organelle in cyanobacteria and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase (CA) within a polyhedral protein shell. The intrinsic self-assembly and architectural features of carboxysomes and the semipermeability of the protein shell provide the foundation for the accumulation of CO2 within carboxysomes and enhanced carboxylation. Here, we develop an approach to det. the interior pH conditions and inorg. carbon accumulation within an α-carboxysome shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell permeability. By incorporating a pH reporter, pHluorin2, within empty α-carboxysome shells produced in Escherichia coli, we probe the interior pH of the protein shells with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells than the cytoplasmic pH and buffer pH, as well as the modulation of the interior pH in response to changes in external environments, indicating the shell permeability to bicarbonate ions and protons. We further det. the satd. HCO3- concn. of 15 mM within α-carboxysome shells and show the CA-mediated increase in the interior CO2 level. Uncovering the interior physiochem. microenvironment of carboxysomes is crucial for understanding the mechanisms underlying carboxysomal shell permeability and enhancement of Rubisco carboxylation within carboxysomes. Such fundamental knowledge may inform reprogramming carboxysomes to improve metab. and recruit foreign enzymes for enhanced catalytical performance.
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  27. 27
    Faulkner, M.; Szabó, I.; Weetman, S. L.; Sicard, F.; Huber, R. G.; Bond, P. J.; Rosta, E.; Liu, L.-N. Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein. Sci. Rep. 2020, 10, 17501  DOI: 10.1038/s41598-020-74536-5
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    27
    Molecular simulations unravel molecular principles that mediate selective permeability of carboxysome shell protein
    Faulkner, Matthew; Szabo, Istvan; Weetman, Samantha L.; Sicard, Francois; Huber, Roland G.; Bond, Peter J.; Rosta, Edina; Liu, Lu-Ning
    Scientific Reports (2020), 10 (1), 17501CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)
    Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2 fixation. How the protein shell directs influx and efflux of mols. in an effective manner has remained elusive. Here we use mol. dynamics and umbrella sampling calcns. to det. the free-energy profiles of the metabolic substrates, bicarbonate, CO2 and ribulose bisphosphate and the product 3-phosphoglycerate assocd. with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating mol. transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated exptl. by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates mol. transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biol.
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  28. 28
    Mahinthichaichan, P.; Morris, D. M.; Wang, Y.; Jensen, G. J.; Tajkhorshid, E. Selective permeability of carboxysome shell pores to anionic molecules. J. Phys. Chem. B 2018, 122, 9110– 9118,  DOI: 10.1021/acs.jpcb.8b06822
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    28
    Selective Permeability of Carboxysome Shell Pores to Anionic Molecules
    Mahinthichaichan, Paween; Morris, Dylan M.; Wang, Yi; Jensen, Grant J.; Tajkhorshid, Emad
    Journal of Physical Chemistry B (2018), 122 (39), 9110-9118CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
    Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist of small proteins that form hexameric units with semi-permeable central pores contg. binding sites for anions. This feature is thought to selectively allow access to RuBisCO enzymes inside the carboxysome by HCO3- (the dominant form of CO2 in the aq. soln. at pH 7.4) but not O2, which leads to a non-productive reaction. To test this hypothesis, here we use mol. dynamics simulations to characterize the energetics and permeability of CO2, O2, and HCO3- through the central pores of two different shell proteins, namely, CsoS1A of α-carboxysome and CcmK4 of β-carboxysome shells. We find that the central pores are in fact selectively permeable to anions such as HCO3-, as predicted by the model.
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  29. 29
    Cammack, R.; Frey, M.; Robson, R. Hydrogen as a Fuel, Learning from Nature; CRC Press, 2001.
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    There is no corresponding record for this reference.
  30. 30
    Vignais, P. M.; Billoud, B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem. Rev. 2007, 107, 4206– 4272,  DOI: 10.1021/cr050196r
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    30
    Occurrence, classification, and biological function of hydrogenases: An overview
    Vignais, Paulette M.; Billoud, Bernard
    Chemical Reviews (Washington, DC, United States) (2007), 107 (10), 4206-4272CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. The occurrence, diversity, evolutionary relations, classification, biosynthesis, and roles of hydrogenases in Nature are reviewed and discussed.
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  31. 31
    Lubitz, W.; Ogata, H.; Rudiger, O.; Reijerse, E. Hydrogenases. Chem. Rev. 2014, 114, 4081– 4148,  DOI: 10.1021/cr4005814
    Google Scholar
    31
    Hydrogenases
    Lubitz, Wolfgang; Ogata, Hideaki; Ruediger, Olaf; Reijerse, Edward
    Chemical Reviews (Washington, DC, United States) (2014), 114 (8), 4081-4148CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. The current state of knowledge on hydrogenases, esp. recent advances made in understanding the detailed structure and function of these important enzymes. The authors provide an overview of important previous achievements with the main focus on [NiFe] and [FeFe] hydrogenases, and in part also on [Fe] hydrogenases. Recent progress on biomimetic model systems for hydrogenases and devices using hydrogenases both in fuel cells and for H2 prodn. are presented with emphasis on functional aspects. The great progress made in synthesizing model systems for hydrogenases that are functionally active is promising for the future employment of such catalysts in hydrogen technologies.
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  32. 32
    Jiang, Q.; Li, T.; Yang, J.; Aitchison, C. M.; Huang, J.; Chen, Y.; Huang, F.; Wang, Q.; Cooper, A. I.; Liu, L.-N. Synthetic engineering of a new biocatalyst encapsulating [NiFe]-hydrogenases for enhanced hydrogen production. J. Mater. Chem. B 2023, 11, 2684– 2692,  DOI: 10.1039/D2TB02781J
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    32
    Synthetic engineering of a new biocatalyst encapsulating [NiFe]-hydrogenases for enhanced hydrogen production
    Jiang, Qiuyao; Li, Tianpei; Yang, Jing; Aitchison, Catherine M.; Huang, Jiafeng; Chen, Yu; Huang, Fang; Wang, Qiang; Cooper, Andrew I.; Liu, Lu-Ning
    Journal of Materials Chemistry B: Materials for Biology and Medicine (2023), 11 (12), 2684-2692CODEN: JMCBDV; ISSN:2050-7518. (Royal Society of Chemistry)
    Hydrogenases are microbial metalloenzymes capable of catalyzing the reversible interconversion between mol. hydrogen and protons with high efficiency, and have great potential in the development of new electrocatalysts for renewable fuel prodn. Here, we engineered the intact proteinaceous shell of the carboxysome, a self-assembling protein organelle for CO2 fixation in cyanobacteria and proteobacteria, and sequestered heterologously produced [NiFe]-hydrogenases into the carboxysome shell. The protein-based hybrid catalyst produced in E. coli shows substantially improved hydrogen prodn. under both aerobic and anaerobic conditions and enhanced material and functional robustness, compared to unencapsulated [NiFe]-hydrogenases. The catalytically functional nanoreactor as well as the self-assembling and encapsulation strategies provide a framework for engineering new bioinspired electrocatalysts to improve the sustainable prodn. of fuels and chems. in biotechnol. and chem. applications.
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  33. 33
    Li, T.; Jiang, Q.; Huang, J.; Aitchison, C. M.; Huang, F.; Yang, M.; Dykes, G. F.; He, H. L.; Wang, Q.; Sprick, R. S.; Cooper, A. I.; Liu, L. N. Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nat. Commun. 2020, 11, 5448  DOI: 10.1038/s41467-020-19280-0
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    33
    Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production
    Li, Tianpei; Jiang, Qiuyao; Huang, Jiafeng; Aitchison, Catherine M.; Huang, Fang; Yang, Mengru; Dykes, Gregory F.; He, Hai-Lun; Wang, Qiang; Sprick, Reiner Sebastian; Cooper, Andrew I.; Liu, Lu-Ning
    Nature Communications (2020), 11 (1), 5448CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
    Abstr.: Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biol. elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diam.) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the prodn. of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen prodn. of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.
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  34. 34
    Qin, W. K.; Tung, C. H.; Wu, L. Z. Covalent organic framework and hydrogen-bonded organic framework for solar-driven photocatalysis. J. Mater. Chem. A 2023, 11, 12521– 12538,  DOI: 10.1039/D2TA09375H
    Google Scholar
    There is no corresponding record for this reference.
  35. 35
    Aitchison, C. M.; Kane, C. M.; McMahon, D. P.; Spackman, P. R.; Pulido, A.; Wang, X.; Wilbraham, L.; Chen, L.; Clowes, R.; Zwijnenburg, M. A.; Sprick, R. S.; Little, M. A.; Day, G. M.; Cooper, A. I. Photocatalytic proton reduction by a computationally identified, molecular hydrogen-bonded framework. J. Mater. Chem. A 2020, 8, 7158– 7170,  DOI: 10.1039/D0TA00219D
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    35
    Photocatalytic proton reduction by a computationally identified, molecular hydrogen-bonded framework
    Aitchison, Catherine M.; Kane, Christopher M.; McMahon, David P.; Spackman, Peter R.; Pulido, Angeles; Wang, Xiaoyan; Wilbraham, Liam; Chen, Linjiang; Clowes, Rob; Zwijnenburg, Martijn A.; Sprick, Reiner Sebastian; Little, Marc A.; Day, Graeme M.; Cooper, Andrew I.
    Journal of Materials Chemistry A: Materials for Energy and Sustainability (2020), 8 (15), 7158-7170CODEN: JMCAET; ISSN:2050-7496. (Royal Society of Chemistry)
    We show that a hydrogen-bonded framework, TBAP-α, with extended π-stacked pyrene columns has a sacrificial photocatalytic hydrogen prodn. rate of up to 3108μmol g-1 h-1. This is the highest activity reported for a mol. org. crystal. By comparison, a chem.-identical but amorphous sample of TBAP was 20-200 times less active, depending on the reaction conditions, showing unambiguously that crystal packing in mol. crystals can dictate photocatalytic activity. Crystal structure prediction (CSP) was used to predict the solid-state structure of TBAP and other functionalised, conformationally-flexible pyrene derivs. Specifically, we show that energy-structure-function (ESF) maps can be used to identify mols. such as TBAP that are likely to form extended π-stacked columns in the solid state. This opens up a methodol. for the a priori computational design of mol. org. photocatalysts and other energy-relevant materials, such as org. electronics.
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  36. 36
    Stylianou, K. C.; Heck, R.; Chong, S. Y.; Bacsa, J.; Jones, J. T. A.; Khimyak, Y. Z.; Bradshaw, D.; Rosseinsky, M. J. A guest-responsive fluorescent 3D microporous metal-organic framework derived from a long-lifetime pyrene core. J. Am. Chem. Soc. 2010, 132, 4119– 4130,  DOI: 10.1021/ja906041f
    Google Scholar
    36
    A Guest-Responsive Fluorescent 3D Microporous Metal-Organic Framework Derived from a Long-Lifetime Pyrene Core
    Stylianou, Kyriakos C.; Heck, Romain; Chong, Samantha Y.; Bacsa, John; Jones, James T. A.; Khimyak, Yaroslav Z.; Bradshaw, Darren; Rosseinsky, Matthew J.
    Journal of the American Chemical Society (2010), 132 (12), 4119-4130CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    The carboxylate ligand pyrene-1,3,6,8-tetrakis(p-benzoic acid) (TBAPy), based on the strongly fluorescent long-lifetime pyrene core, affords a permanently microporous fluorescent metal-org. framework, [In2(OH)2(TBAPy)]·(guests) (1), displaying 54% total accessible vol. and excellent thermal stability. Fluorescence studies reveal that both 1 and TBAPy display strong emission bands at 471 and 529 nm, resp., upon excitation at 390 nm, with framework coordination of the TBAPy ligands significantly increasing the emission lifetime from 0.089 to 0.110 ms. Upon desolvation, the emission band for the framework is shifted to lower energy: however, upon re-exposure to DMF the as-made material is regenerated with reversible fluorescence behavior. Together with the lifetime, the emission intensity is strongly enhanced by spatial sepn. of the optically active ligand mols. within the MOF structure and is dependent on the amt. and chem. nature of the guest species in the pores. The quantum yield of the material is 6.7% and, coupled with the fluorescence lifetime on the millisecond time scale, begins to approach the values obsd. for Eu(III)-cryptate-derived com. sensors.
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  37. 37
    Chen, G.; Huang, S.; Shen, Y.; Kou, X.; Ma, X.; Huang, S.; Tong, Q.; Ma, K.; Chen, W.; Wang, P.; Shen, J.; Zhu, F.; Ouyang, G. Protein-directed, hydrogen-bonded biohybrid framework. Chem 2021, 7, 2722– 2742,  DOI: 10.1016/j.chempr.2021.07.003
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    37
    Protein-directed, hydrogen-bonded biohybrid framework
    Chen, Guosheng; Huang, Siming; Shen, Yong; Kou, Xiaoxue; Ma, Xiaomin; Huang, Shuyao; Tong, Qing; Ma, Kaili; Chen, Wen; Wang, Peiyi; Shen, Jun; Zhu, Fang; Ouyang, Gangfeng
    Chem (2021), 7 (10), 2722-2742CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)
    Here, we describe a versatile protein-directed assembly strategy that enables the organization of different types of proteins and org. linkers into a highly cryst. hybrid framework through hydrogen-bond interaction. The whole assembly process is protein actuated but is independent of the protein-surface property. Advanced low-electron-dose cryoelectron microscopy techniques clearly witness the crystallog. structure of hybrid framework at a single-mol. level, and we demonstrate that the proteins are independently and tightly isolated in the cryst. frameworks, with a record-high protein content in the reported biohybrid framework materials. In addn., the hybrid framework has ultrahigh chem. stability, and its aperture structure and protein confinement tightness are controllable through modulating the org. linkers. When using enzymes as the building block, the obtained enzyme framework shows significantly improved stability compared with the free enzymes and displays notable advantages for biocatalysis compared with the burgeoning enzyme-MOF biohybrids in terms of active ingredient content, robustness, and catalytic efficiency.
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  38. 38
    Zhou, Q.; Guo, Y.; Zhu, Y. Photocatalytic sacrificial H2 evolution dominated by micropore-confined exciton transfer in hydrogen-bonded organic frameworks. Nat. Catal. 2023, 6, 574– 584,  DOI: 10.1038/s41929-023-00972-x
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    38
    Photocatalytic sacrificial H2 evolution dominated by micropore-confined exciton transfer in hydrogen-bonded organic frameworks
    Zhou, Qixin; Guo, Yan; Zhu, Yongfa
    Nature Catalysis (2023), 6 (7), 574-584CODEN: NCAACP; ISSN:2520-1158. (Nature Portfolio)
    Org. semiconductors are attractive photocatalysts, but their quantum yields are limited by the transfer of photogenerated charges to the surface. A promising strategy for low-loss charge transfer is to shorten the distance from the bulk exciton coupling region to the catalyst surface. Here we employ the hydrogen-bonded org. framework 1,3,6,8-tetrakis(p-benzoic acid)pyrene (HOF-H4TBAPy) with hydrophilic one-dimensional micropore channels as a proof of concept for this approach. Under irradn., photogenerated excitons rapidly transfer to the inner surface of adjacent micropores, engendering a mere 1.88 nm transfer route, thus significantly improving exciton utilization. When the micropore channel length does not exceed 0.59μm, the sacrificial photocatalytic H2 evolution rate of HOF-H4TBAPy reaches 358 mmol h-1 g-1 and the apparent quantum yield at 420 nm is 28.6%. We further demonstrated a stable 1.03 mol day-1 m-2 H2 evolution on a 0.5 m2 HOF-H4TBAPy-loaded fiber under 1 Sun irradn.
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  39. 39
    Pellegrin, Y.; Odobel, F. Sacrificial electron donor reagents for solar fuel production. C. R. Chim. 2017, 20, 283– 295,  DOI: 10.1016/j.crci.2015.11.026
    Google Scholar
    39
    Sacrificial electron donor reagents for solar fuel production
    Pellegrin, Yann; Odobel, Fabrice
    Comptes Rendus Chimie (2017), 20 (3), 283-295CODEN: CRCOCR; ISSN:1631-0748. (Elsevier Masson SAS)
    A review is given. Although justly considered as a cumbersome component in artificial photosystems, these simple mols. are a necessary evil to drive photo-induced reactions aiming at producing high added value mols. by photo-induced redn. of low energy value substrates. This paper 1rst presents the specifications of sacrificial electron donors. Then the various families of sacrificial donors used from the early 1970s to nowadays are reviewed, such as aliph. and arom. amines, benzyl-dihydronicotinamide (BNAH), dimethylphenylbenzimidazoline (BIH), ascorbic acid, oxalate and finally thiols. Exptl. conditions (pH, solvent) are immensely versatile but important trends are given for adequate operation of a three-component system. Although literature abounds with various, very different artificial photosystems, we will realize that virtually the same sacrificial donors are used over and over again.
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  40. 40
    Baker, S. H.; Lorbach, S. C.; Rodriguez-Buey, M.; Williams, D. S.; Aldrich, H. C.; Shively, J. M. The correlation of the gene csoS2 of the carboxysome operon with two polypeptides of the carboxysome in Thiobacillus neapolitanus. Arch. Microbiol. 1999, 172, 233– 239,  DOI: 10.1007/s002030050765
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    40
    The correlation of the gene csoS2 of the carboxysome operon with two polypeptides of the carboxysome in Thiobacillus neapolitanus
    Baker, Stefanie H.; Lorbach, Stanley C.; Rodriguez-Buey, Marisa; Williams, Donna S.; Aldrich, Henry C.; Shively, Jessup M.
    Archives of Microbiology (1999), 172 (4), 233-239CODEN: AMICCW; ISSN:0302-8933. (Springer-Verlag)
    The carboxysomal polypeptides of Thiobacillus neapolitanus with apparent mol. masses of 85 and 130 kDa were isolated and subjected to N-terminal sequencing. The first 17 amino acids of the two peptides were identical. The sequence perfectly matched the deduced amino acid sequence of an open reading frame in the carboxysome operon. The gene was subsequently named csoS2. Expression of the gene in Escherichia coli resulted in the prodn. of two peptides with apparent mol. masses of 85 and 130 kDa. Immunospecific antibodies generated against the smaller peptide recognized both peptides; the peptides were named CsoS2A and CsoS2B, resp. A digoxigenin-hydrazide glycosylation assay revealed that both CsoS2A and CsoS2B are post-translationally modified by glycosylation. CsoS2 was localized to the edges of purified carboxysomes by immunogold electron microscopy using the monospecific CsoS2A antibodies. The mol. mass of CsoS2A calcd. from the nucleotide sequence was 92.3 kDa.
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  41. 41
    Case, D. A.; Aktulga, H. M.; Belfon, K.; Cerutti, D. S.; Cisneros, G. A.; Cruzeiro, V. W. D.; Forouzesh, N.; Giese, T. J.; Götz, A. W.; Gohlke, H.; Izadi, S.; Kasavajhala, K.; Kaymak, M. C.; King, E.; Kurtzman, T.; Lee, T.-S.; Li, P.; Liu, J.; Luchko, T.; Luo, R.; Manathunga, M.; Machado, M. R.; Nguyen, H. M.; O’Hearn, K. A.; Onufriev, A. V.; Pan, F.; Pantano, S.; Qi, R.; Rahnamoun, A.; Risheh, A.; Schott-Verdugo, S.; Shajan, A.; Swails, J.; Wang, J.; Wei, H.; Wu, X.; Wu, Y.; Zhang, S.; Zhao, S.; Zhu, Q.; Cheatham, T. E., III; Roe, D. R.; Roitberg, A.; Simmerling, C.; York, D. M.; Nagan, M. C.; Merz, K. M., Jr. AmberTools. J. Chem. Inf. Model. 2023, 63, 6183– 6191,  DOI: 10.1021/acs.jcim.3c01153
    Google Scholar
    41
    AmberTools
    Case, David A.; Aktulga, Hasan Metin; Belfon, Kellon; Cerutti, David S.; Cisneros, G. Andres; Cruzeiro, Vinicius Wilian D.; Forouzesh, Negin; Giese, Timothy J.; Gotz, Andreas W.; Gohlke, Holger; Izadi, Saeed; Kasavajhala, Koushik; Kaymak, Mehmet C.; King, Edward; Kurtzman, Tom; Lee, Tai-Sung; Li, Pengfei; Liu, Jian; Luchko, Tyler; Luo, Ray; Manathunga, Madushanka; Machado, Matias R.; Nguyen, Hai Minh; O.bxsolid.Hearn, Kurt A.; Onufriev, Alexey V.; Pan, Feng; Pantano, Sergio; Qi, Ruxi; Rahnamoun, Ali; Risheh, Ali; Schott-Verdugo, Stephan; Shajan, Akhil; Swails, Jason; Wang, Junmei; Wei, Haixin; Wu, Xiongwu; Wu, Yongxian; Zhang, Shi; Zhao, Shiji; Zhu, Qiang; Cheatham III, Thomas E.; Roe, Daniel R.; Roitberg, Adrian; Simmerling, Carlos; York, Darrin M.; Nagan, Maria C.; Merz Jr., Kenneth M.
    Journal of Chemical Information and Modeling (2023), 63 (20), 6183-6191CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
    AmberTools is a free and open-source collection of programs used to set up, run, and analyze mol. simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
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  42. 42
    Karthi, N.; Venkatachalam, M. Growth and Characterization Novel Organic Nonlinear Optical Crystal of Pyrene. Int. J. Sci. 2013, 1, 8– 12
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    There is no corresponding record for this reference.
  43. 43
    Tanaka, S.; Kerfeld, C. A.; Sawaya, M. R.; Cai, F.; Heinhorst, S.; Cannon, G. C.; Yeates, T. O. Atomic-level models of the bacterial carboxysome shell. Science 2008, 319, 1083– 1086,  DOI: 10.1126/science.1151458
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    43
    Atomic-Level Models of the Bacterial Carboxysome Shell
    Tanaka, Shiho; Kerfeld, Cheryl A.; Sawaya, Michael R.; Cai, Fei; Heinhorst, Sabine; Cannon, Gordon C.; Yeates, Todd O.
    Science (Washington, DC, United States) (2008), 319 (5866), 1083-1086CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
    The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diam. and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into mol. layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolns. of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary at. models for the carboxysome shell.
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  44. 44
    Tsai, Y.; Sawaya, M. R.; Cannon, G. C.; Cai, F.; Williams, E. B.; Heinhorst, S.; Kerfeld, C. A.; Yeates, T. O. Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol. 2007, 5, e144,  DOI: 10.1371/journal.pbio.0050144
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    There is no corresponding record for this reference.
  45. 45
    Parsons, J. B.; Dinesh, S. D.; Deery, E.; Leech, H. K.; Brindley, A. A.; Heldt, D.; Frank, S.; Smales, C. M.; Lünsdorf, H.; Rambach, A.; Gass, M. H.; Bleloch, A.; McClean, K. J.; Munro, A. W.; Rigby, S. E. J.; Warren, M. J.; Prentice, M. B. Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis. J. Biol. Chem. 2008, 283, 14366– 14375,  DOI: 10.1074/jbc.M709214200
    Google Scholar
    45
    Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis
    Parsons, Joshua B.; Dinesh, Sriramulu D.; Deery, Evelyne; Leech, Helen K.; Brindley, Amanda A.; Heldt, Dana; Frank, Steffanie; Smales, C. Mark; Luensdorf, Heinrich; Rambach, Alain; Gass, Mhairi H.; Bleloch, Andrew; McClean, Kirsty J.; Munro, Andrew W.; Rigby, Stephen E. J.; Warren, Martin J.; Prentice, Michael B.
    Journal of Biological Chemistry (2008), 283 (21), 14366-14375CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
    Many heterotrophic bacteria have the ability to make polyhedral structures contg. metabolic enzymes that are bounded by a unilamellar protein shell (metabolosomes or enterosomes). These bacterial organelles contain enzymes assocd. with a specific metabolic process (e.g., 1,2-propanediol or ethanolamine utilization). The authors show that the 21 gene regulon specifying the pdu organelle and propanediol utilization enzymes from Citrobacter freundii is fully functional when cloned in Escherichia coli, both producing metabolosomes and allowing propanediol utilization. Genetic manipulation of the level of specific shell proteins resulted in the formation of aberrantly shaped metabolosomes, providing evidence for their involvement as delimiting entities in the organelle. This is the first demonstration of complete recombinant metabolosome activity transferred in a single step and supports phylogenetic evidence that the pdu genes are readily horizontally transmissible. One of the predicted shell proteins (PduT) was found to have a novel Fe-S center formed between four protein subunits. The recombinant model will facilitate future expts. establishing the structure and assembly of these multiprotein assemblages and their fate when the specific metabolic function is no longer required.
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  46. 46
    Parsons, J. B.; Lawrence, A. D.; McLean, K. J.; Munro, A. W.; Rigby, S. E. J.; Warren, M. J. Characterisation of PduS, the pdu Metabolosome Corrin Reductase, and Evidence of Substructural Organisation within the Bacterial Microcompartment. PLoS One 2010, 5, e14009,  DOI: 10.1371/journal.pone.0014009
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    There is no corresponding record for this reference.
  47. 47
    Silva, D. A.; Yu, S.; Ulge, U. Y.; Spangler, J. B.; Jude, K. M.; Labão-Almeida, C.; Ali, L. R.; Quijano-Rubio, A.; Ruterbusch, M.; Leung, I.; Biary, T.; Crowley, S. J.; Marcos, E.; Walkey, C. D.; Weitzner, B. D.; Pardo-Avila, F.; Castellanos, J.; Carter, L.; Stewart, L.; Riddell, S. R.; Pepper, M.; Bernardes, G. J. L.; Dougan, M.; Garcia, K. C.; Baker, D. De novo design of potent and selective mimics of IL-2 and IL-15. Nature 2019, 565, 186– 191,  DOI: 10.1038/s41586-018-0830-7
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    47
    De novo design of potent and selective mimics of IL-2 and IL-15
    Silva, Daniel-Adriano; Yu, Shawn; Ulge, Umut Y.; Spangler, Jamie B.; Jude, Kevin M.; Labao-Almeida, Carlos; Ali, Lestat R.; Quijano-Rubio, Alfredo; Ruterbusch, Mikel; Leung, Isabel; Biary, Tamara; Crowley, Stephanie J.; Marcos, Enrique; Walkey, Carl D.; Weitzner, Brian D.; Pardo-Avila, Fatima; Castellanos, Javier; Carter, Lauren; Stewart, Lance; Riddell, Stanley R.; Pepper, Marion; Bernardes, Goncalo J. L.; Dougan, Michael; Garcia, K. Christopher; Baker, David
    Nature (London, United Kingdom) (2019), 565 (7738), 186-191CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
    We describe a de novo computational approach for designing proteins that recapitulate the binding sites of natural cytokines, but are otherwise unrelated in topol. or amino acid sequence. We use this strategy to design mimics of the central immune cytokine interleukin-2 (IL-2) that bind to the IL-2 receptor βγc heterodimer (IL-2Rβγc) but have no binding site for IL-2Rα (also called CD25) or IL-15Rα (also known as CD215). The designs are hyper-stable, bind human and mouse IL-2Rβγc with higher affinity than the natural cytokines, and elicit downstream cell signalling independently of IL-2Rα and IL-15Rα. Crystal structures of the optimized design neoleukin-2/15 (Neo-2/15), both alone and in complex with IL-2Rβγc, are very similar to the designed model. Neo-2/15 has superior therapeutic activity to IL-2 in mouse models of melanoma and colon cancer, with reduced toxicity and undetectable immunogenicity. Our strategy for building hyper-stable de novo mimetics could be applied generally to signalling proteins, enabling the creation of superior therapeutic candidates.
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  48. 48
    Thompson, M. C.; Wheatley, N. M.; Jorda, J.; Sawaya, M. R.; Gidaniyan, S. D.; Ahmed, H.; Yang, Z.; McCarty, K. N.; Whitelegge, J. P.; Yeates, T. O. Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein. J. Mol. Biol. 2014, 426, 3287– 3304,  DOI: 10.1016/j.jmb.2014.07.018
    Google Scholar
    There is no corresponding record for this reference.
  49. 49
    Zeng, Z.; Boeren, S.; Bhandula, V.; Light, S. H.; Smid, E. J.; Notebaart, R. A.; Abee, T. Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes. mSystems 2021, 6, e01349-20  DOI: 10.1128/msystems.01349-20
    Google Scholar
    There is no corresponding record for this reference.
  50. 50
    Ferlez, B.; Markus, S.; Kerfeld, C. A. Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles. mBio 2019, 10, e02327-18  DOI: 10.1128/mBio.02327-18
    Google Scholar
    There is no corresponding record for this reference.
  51. 51
    Yan, Y. M.; Tao, H. Y.; He, J. H.; Huang, S.-Y. The HDOCK server for integrated protein–protein docking. Nat. Protoc. 2020, 15, 1829– 1852,  DOI: 10.1038/s41596-020-0312-x
    Google Scholar
    51
    The HDOCK server for integrated protein-protein docking
    Yan, Yumeng; Tao, Huanyu; He, Jiahua; Huang, Sheng-You
    Nature Protocols (2020), 15 (5), 1829-1852CODEN: NPARDW; ISSN:1750-2799. (Nature Research)
    The HDOCK server is a highly integrated suite of homol. search, template-based modeling, structure prediction, macromol. docking, biol. information incorporation and job management for robust and fast protein-protein docking. With input information for receptor and ligand mols. (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which exptl. information about the protein-protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein-RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two mols. and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min.
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  52. 52
    Case, A. D.; Belfon, K.; Ido, B.-S.; Scott, R. B.; Cerutti, D. S.; Cheatham, T. E., III; Cruzeiro, V. W. D.; Darden, T. A.; Duke, R. E.; Giambasu, G.; Gilson, M. K.; Gohlke, H.; Goetz, A. W.; Harris, R.; Izadi, S.; Izmailov, S. A.; Kasavajhala, K.; Kovalenko, A.; Krasny, R.; Kurtzman, T.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.; L, J.; Luchko, T.; Luo, R.; Man, V.; Merz, K. M.; Miao, Y.; Mikhailovskii, O.; Monard, G.; Nguyen, H.; Onufriev, A.; Pan, F.; Pantano, S.; Qi, R.; Roe, D. R.; Roitberg, A.; Sagui, C.; Schott-Verdugo, S.; Shen, J.; Simmerling, C. L.; Skrynnikov, N. R.; Smith, J.; Swails, J.; Walker, R. C.; Wang, J.; Wilson, L.; Wolf, R. M.; Wu, X.; Xiong, Y.; Xue, Y.; D M AMBER 2020; University of California: New York, 2020.
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    There is no corresponding record for this reference.
  53. 53
    Maier, J. A.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K. E.; Simmerling, C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J. Chem. Theory Comput. 2015, 11, 3696– 3713,  DOI: 10.1021/acs.jctc.5b00255
    Google Scholar
    53
    ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
    Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik; Wickstrom, Lauren; Hauser, Kevin E.; Simmerling, Carlos
    Journal of Chemical Theory and Computation (2015), 11 (8), 3696-3713CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
    Mol. mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Av. errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a phys. motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reprodn. of NMR χ1 scalar coupling measurements for proteins in soln. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
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  54. 54
    Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25, 1157– 1174,  DOI: 10.1002/jcc.20035
    Google Scholar
    54
    Development and testing of a general Amber force field
    Wang, Junmei; Wolf, Romain M.; Caldwell, James W.; Kollman, Peter A.; Case, David A.
    Journal of Computational Chemistry (2004), 25 (9), 1157-1174CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
    We describe here a general Amber force field (GAFF) for org. mols. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most org. and pharmaceutical mols. that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited no. of atom types, but incorporates both empirical and heuristic models to est. force consts. and partial at. charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallog. structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, resp.). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermol. energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, resp. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, resp.), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to expt.) is about 0.5 kcal/mol. GAFF can be applied to wide range of mols. in an automatic fashion, making it suitable for rational drug design and database searching.
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  55. 55
    Wang, Z.; Li, J.; Liu, J.; Wang, L.; Lu, Y.; Liu, J. P. Molecular insight into the selective binding between human telomere G-quadruplex and a negatively charged stabilizer. Clin. Exp. Pharmacol. Physiol. 2020, 47, 892– 902,  DOI: 10.1111/1440-1681.13249
    Google Scholar
    There is no corresponding record for this reference.
  56. 56
    Kim, M.; Kreig, A.; Lee, C. Y.; Rube, H. T.; Calvert, J.; Song, J. S.; Myong, S. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Res. 2016, 44, 4807– 4817,  DOI: 10.1093/nar/gkw272
    Google Scholar
    56
    Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA
    Kim, Minji; Kreig, Alex; Lee, Chun-Ying; Rube, H. Tomas; Calvert, Jacob; Song, Jun S.; Myong, Sua
    Nucleic Acids Research (2016), 44 (10), 4807-4817CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
    G-quadruplex (GQ) is a four-stranded DNA structure that can be formed in guanine-rich sequences. GQ structures have been proposed to regulate diverse biol. processes including transcription, replication, translation and telomere maintenance. Recent studies have demonstrated the existence of GQ DNA in live mammalian cells and a significant no. of potential GQ forming sequences in the human genome. We present a systematic and quant. anal. of GQ folding propensity on a large set of 438 GQ forming sequences in double-stranded DNA by integrating fluorescence measurement, single mol. imaging and computational modeling. We find that short min. loop length and the thymine base are two main factors that lead to high GQ folding propensity. Linear and Gaussian process regression models further validate that the GQ folding potential can be predicted with high accuracy based on the loop length distribution and the nucleotide content of the loop sequences. Our study provides important new parameters that can inform the evaluation and classification of putative GQ sequences in the human genome.
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  57. 57
    Price, D. J.; Charles, L. B. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 2004, 121, 10096– 10103,  DOI: 10.1063/1.1808117
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    57
    A modified TIP3P water potential for simulation with Ewald summation
    Price, Daniel J.; Brooks, Charles L., III
    Journal of Chemical Physics (2004), 121 (20), 10096-10103CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
    The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for mol. dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calcn. of nonbonded, heteroat. interaction energies, and limiting the no. of Lennard-Jones calcns. required. Under these conditions, this model provides accurate d. (ρ = 0.997 g/mL) and heat of vaporization (ΔHvap = 10.53 kcal/mol) at 25 °C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielec. const. (.vepsiln.0 = 89) and the diffusion coeff. (D = 4.0×10-5 cm2/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temp. d. max. Several similar models are considered with the addnl. constraint of trying to match the performance of the optimized potentials for liq. simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compds., phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielec. const. (.vepsiln.0 = 76), however, the improvement in this est. is on the same order as the uncertainty in the calcn.
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  58. 58
    Li, P. F.; Merz, K. Metal ion modeling using classical mechanics. Chem. Rev. 2017, 117, 1564– 1686,  DOI: 10.1021/acs.chemrev.6b00440
    Google Scholar
    58
    Metal Ion Modeling Using Classical Mechanics
    Li, Pengfei; Merz, Kenneth M., Jr.
    Chemical Reviews (Washington, DC, United States) (2017), 117 (3), 1564-1686CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
    A review. Metal ions play significant roles in numerous fields including chem., geochem., biochem. and materials science. With computational tools increasingly becoming important in chem. research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aq. and solid phases. Herein we review both quantum and classical modeling strategies for metal ion contg. systems that have been developed over the past few decades. This review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond based models. Quantum mech. studies of metal ion contg. systems at the semiempirical, ab initio and d. functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion contg. systems.
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  59. 59
    Cheatham, T. E. I.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins. J. Am. Chem. Soc. 1995, 117, 4193– 4194,  DOI: 10.1021/ja00119a045
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    59
    Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
    Cheatham, T. E. III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A.
    Journal of the American Chemical Society (1995), 117 (14), 4193-4CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
    Results from mol. dynamics simulations with AMBER 4.1 of three different, fully solvated, fully charged, macromol. structures-- x-ray derived structures of d(CCAACGTTGG)2 DNA and ubiquitin and an NMR derived r(UUCG) RNA hairpin loop and stem structure-- are presented. We compare the use of the Particle Mesh Ewald (PME) method for the treatment of long range electrostatic interactions to std. charge group based truncation cutoff methods. All of the simulations with PME remain closer to the obsd. structures while maintaining reasonable at. positional fluctuations.
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  60. 60
    Loncharich, R. J.; Brooks, R. B.; Pastor, W. R. Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers 1992, 32, 523– 535,  DOI: 10.1002/bip.360320508
    Google Scholar
    60
    Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide
    Loncharich, Richard J.; Brooks, Bernard R.; Pastor, Richard W.
    Biopolymers (1992), 32 (5), 523-35CODEN: BIPMAA; ISSN:0006-3525.
    The rate const. for the transition between the equatorial and axial conformations of N-acetylalanyl-N'-methylamide has been detd. from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is max. at collision frequency γ = 2 ps-1, shows diffusive character for γ ≥ 10 ps-1, but does not approach zero even at γ = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., γ ≈ 2 ps-1). This method is expected to be more efficient than either mol. dynamics in vacuo (which corresponds to LD with γ = 0) or mol. dynamics in solvent (where dynamics is largely diffusive).
    >> More from SciFinder ®
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  61. 61
    Berendsen, H. J. C.; Postma, J. P. M.; Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684– 3690,  DOI: 10.1063/1.448118
    Google Scholar
    61
    Molecular dynamics with coupling to an external bath
    Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R.
    Journal of Chemical Physics (1984), 81 (8), 3684-90CODEN: JCPSA6; ISSN:0021-9606.
    In mol. dynamics (MD) simulations, the need often arises to maintain such parameters as temp. or pressure rather than energy and vol., or to impose gradients for studying transport properties in nonequil. MD. A method is described to realize coupling to an external bath with const. temp. or pressure with adjustable time consts. for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyat. mols. involving internal constraints. The influence of coupling time consts. on dynamical variables is evaluated. A leap-frog algorithm is presented for the general case involving constraints with coupling to both a const. temp. and a const. pressure bath.
    >> More from SciFinder ®
    https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADyaL2cXmtlGksbY%253D&md5=5510dc00297d63b91ee3a7a4ae5aacb1
  62. 62
    Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graphics 1996, 14, 33– 38,  DOI: 10.1016/0263-7855(96)00018-5
    Google Scholar
    62
    VDM: visual molecular dynamics
    Humphrey, William; Dalke, Andrew; Schulten, Klaus
    Journal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)
    VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
    >> More from SciFinder ®
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  • Abstract

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    Figure 1

    Figure 1. Generation of the organic semiconductor, the hydrogenase-containing carboxysome shell, and the chemical–biological hybrid nanoreactor, H–S|TBAP-α. (a) Chemical structure of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP). (b) Crystal structure of α-polymorph of 1,3,6,8-tetra(4′-carboxyphenyl)pyrene (TBAP-α). (c) Genetic organization of the α-carboxysome shell operon and hydrogenase-expressing operon for the production of recombinant shells and active [FeFe]-hydrogenases in E. coli, respectively, and a schematic model of the hydrogenase-shell nanoreactor (H–S). EP: CsoS2 C-terminus as the encapsulation peptide. The hydGXEF genes encode the crucial maturase enzymes for hydrogenase formation and activation, including HydE, HydF, and HydG. PDB ID: Ferredoxin (Fd)-[FeFe]-hydrogenase, 2N0S; ferredoxin-NADP reductase (FNR), 2XNJ. (d) 3D model representation of the H–S|TBAP-α hybrid system, in which H–S adheres to the hydrogen-bonding groups on the TBAP-α crystal surface.

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    Figure 2

    Figure 2. Binding between the α-carboxysome shell and TBAP-α. Results of molecular dynamics simulations of CsoS1A (PDB ID: 2EWH) and TBAP-α binding equilibrium states are shown in panels (a–c). (a) Front view. (b) Side view, showing the simulated binding interface between TBAP-α and the CsoS1A hexamer. (c) Zoom-in view of the noncovalent interactions (red dotted lines) formed between amino acid residues of CsoS1A (Pro96, Thr5, Ser86, Asp90, Gly89, Lys94, Arg34, Glut97) and TBAP-α (blue = N atoms, red = O atoms). (d) ITC thermogram resulting from the titration of TBAP (50 μM) into the α-carboxysome shell (3.75 μM) in TN buffer (20 mM Tris-HCl (pH = 8.0), 150 mM NaCl). (e) Thermodynamic profile of TBAP binding to α-carboxysome shell in TN buffer. ΔG, change in Gibbs Free Energy; ΔH, change in enthalpy; T, temperature in Kelvin; ΔS, change in entropy.

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    Figure 3

    Figure 3. Attachment of mCherry-encapsulated C–S shells on the surface of TBAP-α crystals. SEM images of (a) uncoated TBAP-α, (b) C–S|TBAP-α (40 × 3.6 μm2 size), and (c) zoom-in view of C–S|TBAP-α. Orange arrows show the C–S particles that were attached to the TBAP-α crystal surface. (d) Fluorescence images of TBAP-α only (top row) and the C–S|TBAP-α hybrid (bottom row). Left, excitation at 488 nm; middle, excitation at 561 nm; right, the merged channel. All fluorescence images were adjusted to have the same brightness and contrast settings.

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    Figure 4

    Figure 4. Characterization of the light-driven H–S|TBAP-α hybrid nanoreactor. (a) SEM image of H–S|TBAP-α. Orange arrows show the H–S particles that were attached to the TBAP-α crystal surface. (b) Photoluminescence (PL) spectrum and (c) Excited-state lifetimes of H–S|TBAP-α and TBAP-α alone in 0.1 M neutralized AA aqueous solution when excited at 390 nm.

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    Figure 5

    Figure 5. Visible-light-driven hydrogen production of H–S|TBAP-α. (a) H2-evolution rates of TBAP-α, H–S|TBAP-α, H–Sox|TBAP-α, S|TBAP-α, and H–S|Amorphous TBAP irradiated by a solar simulator for 2 h. (b) H2 evolution of TBAP-α (black dots) and H–S|TBAP-α (blue dots) as a function of time (λ > 420 nm). (c) Schematic diagram of proposed electron transfer pathway in H–S|TBAP-α for hydrogen production. Electrons generated from TBAP-α irradiation are transferred through holes on the α-carboxysome shell to the 4Fe–4S cluster via FNR or directly for proton reduction. Ascorbic acid acts as a sacrificial agent to prevent the photogenerated hole–electron recombination. Error bars represent the SD of the mean of three independent experiments.

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  • References

    This article references 62 other publications.

    1. 1
      Tachibana, Y.; Vayssieres, L.; Durrant, J. R. Artificial photosynthesis for solar water-splitting. Nat. Photonics 2012, 6, 511– 518,  DOI: 10.1038/nphoton.2012.175
      1
      Artificial photosynthesis for solar water-splitting
      Tachibana, Yasuhiro; Vayssieres, Lionel; Durrant, James R.
      Nature Photonics (2012), 6 (8), 511-518CODEN: NPAHBY; ISSN:1749-4885. (Nature Publishing Group)
      A review. Hydrogen generated from solar-driven water-splitting has the potential to be a clean, sustainable and abundant energy source. Inspired by natural photosynthesis, artificial solar water-splitting devices are now being designed and tested. Recent developments based on mol. and/or nanostructure designs have led to advances in our understanding of light-induced charge sepn. and subsequent catalytic water oxidn. and redn. reactions. Here we review some of the recent progress towards developing artificial photosynthetic devices, together with their analogies to biol. photosynthesis, including technologies that focus on the development of visible-light active hetero-nanostructures and require an understanding of the underlying interfacial carrier dynamics. Finally, we propose a vision for a future sustainable hydrogen fuel community based on artificial photosynthesis.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XhtFWjtLfN&md5=b98a6de15072b768fe7403a6e3f91012
    2. 2
      Blankenship, R. E.; Tiede, D. M.; Barber, J.; Brudvig, G. W.; Fleming, G.; Ghirardi, M.; Gunner, M. R.; Junge, W.; Kramer, D. M.; Melis, A.; Moore, T. A.; Moser, C. C.; Nocera, D. G.; Nozik, A. J.; Ort, D. R.; Parson, W. W.; Prince, R. C.; Sayre, R. T. Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement. Science 2011, 332, 805– 809,  DOI: 10.1126/science.1200165
      2
      Comparing Photosynthetic and Photovoltaic Efficiencies and Recognizing the Potential for Improvement
      Blankenship, Robert E.; Tiede, David M.; Barber, James; Brudvig, Gary W.; Fleming, Graham; Ghirardi, Maria; Gunner, M. R.; Junge, Wolfgang; Kramer, David M.; Melis, Anastasios; Moore, Thomas A.; Moser, Christopher C.; Nocera, Daniel G.; Nozik, Arthur J.; Ort, Donald R.; Parson, William W.; Prince, Roger C.; Sayre, Richard T.
      Science (Washington, DC, United States) (2011), 332 (6031), 805-809CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      A review. Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chem. fuels in the case of natural photosynthesis and non-stored elec. current in the case of photovoltaics. To find common ground for evaluating energy-conversion efficiency, the authors compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. Opportunities in which the frontiers of synthetic biol. might be used to enhance natural photosynthesis for improved solar energy conversion efficiency are considered.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXlslylsLk%253D&md5=4b251dbb2f5d29cd9033f5c16085baf1
    3. 3
      Wang, Y.; Vogel, A.; Sachs, M.; Sprick, R. S.; Wilbraham, L.; Moniz, S. J. A.; Godin, R.; Zwijnenburg, M. A.; Durrant, J. R.; Cooper, A. I.; Tang, J. Current understanding and challenges of solar-driven hydrogen generation using polymeric photocatalysts. Nat. Energy 2019, 4, 746– 760,  DOI: 10.1038/s41560-019-0456-5
      3
      Current understanding and challenges of solar-driven hydrogen generation using polymeric photocatalysts
      Wang, Yiou; Vogel, Anastasia; Sachs, Michael; Sprick, Reiner Sebastian; Wilbraham, Liam; Moniz, Savio J. A.; Godin, Robert; Zwijnenburg, Martijn A.; Durrant, James R.; Cooper, Andrew I.; Tang, Junwang
      Nature Energy (2019), 4 (9), 746-760CODEN: NEANFD; ISSN:2058-7546. (Nature Research)
      A review. The use of hydrogen as a fuel, when generated from water using semiconductor photocatalysts and driven by sunlight, is a sustainable alternative to fossil fuels. Polymeric photocatalysts are based on Earth-abundant elements and have the advantage over their inorg. counterparts in that their electronic properties are easily tuneable through mol. engineering. Polymeric photocatalysts have developed rapidly over the past decade, resulting in the discovery of many active materials. However, our understanding of the key properties underlying their photoinitiated redox processes has not kept pace, and this impedes further progress to generate cost-competitive technologies. Here, we discuss state-of-the-art polymeric photocatalysts and our microscopic understanding of their activities. We conclude with a discussion of five outstanding challenges in this field: non-standardized reporting of activities, limited photochem. stability, insufficient knowledge of reaction mechanisms, balancing charge carrier lifetimes with catalysis timescales and the use of unsustainable sacrificial reagents.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhsleltL3I&md5=181c014c5903e1b9185990dfc929cca0
    4. 4
      Barber, J. Photosynthetic energy conversion: Natural and artificial. Chem. Soc. Rev. 2009, 38, 185– 196,  DOI: 10.1039/B802262N
      4
      Photosynthetic energy conversion: Natural and artificial
      Barber, James
      Chemical Society Reviews (2009), 38 (1), 185-196CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      A review. Photosystem II (PSII) is the water splitting enzyme of photosynthesis. Its appearance during evolution dramatically changed the chem. compn. of our planet and set in motion an unprecedented explosion in biol. activity. Powered by sunlight, PSII supplies biol. with the hydrogen' needed to convert carbon dioxide into org. mols. The questions now are can we continue to exploit this photosynthetic process through increased use of biomass as an energy source and, more importantly, can we address the energy/CO2 problem by developing new photochem. technologies which mimic the natural system.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhsFWjtL3F&md5=40b98cc87b09ed53202cd635be7c4994
    5. 5
      Zhang, J. Z.; Reisner, E. Advancing photosystem II photoelectrochemistry for semi-artificial photosynthesis. Nat. Rev. Chem. 2020, 4, 6– 21,  DOI: 10.1038/s41570-019-0149-4
      5
      Advancing photosystem II photoelectrochemistry for semi-artificial photosynthesis
      Zhang, Jenny Z.; Reisner, Erwin
      Nature Reviews Chemistry (2020), 4 (1), 6-21CODEN: NRCAF7; ISSN:2397-3358. (Nature Research)
      A review. Oxygenic photosynthesis is the primary solar energy-conversion process that supports much of life on Earth. It is initiated by photosystem II (PSII), an enzyme that exts. electrons from H2O and feeds them into an electron-transport chain to result in chem. synthesis using the input of solar energy. PSII can be immobilized onto electrodes for photoelectrochem. studies, in which electrons photogenerated from PSII are harnessed for enzyme characterization, and to drive fuel-forming reactions by electrochem. coupling the PSII to a suitable (bio)catalyst. Research in PSII photoelectrochem. has recently made substantial strides in electrode design and unravelling charge-transfer pathways at the bio-material interface. In turn, these efforts have opened up possibilities in the field of bio-photoelectrochem., expanding the range of biocatalysts that can be systematically interrogated, including biofilms of whole photosynthetic cells. Furthermore, these studies have accelerated the development of semi-artificial photosynthesis to afford autonomous, solar-driven, fuel-forming biohybrid devices. This Review summarizes the latest advancements in PSII photoelectrochem. with respect to electrode design and understanding of the bio-material interface, on both the protein and cellular level. We also discuss the role of biol. photosynthetic systems in present and future semi-artificial photosynthesis.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXisVygu7%252FM&md5=1d091975debb2fba3c4e26ca24100335
    6. 6
      Pi, X.; Zhao, S.; Wang, W.; Liu, D.; Xu, C.; Han, G.; Kuang, T.; Sui, S. F.; Shen, J. R. The pigment-protein network of a diatom photosystem II–light-harvesting antenna supercomplex. Science 2019, 365, 447– 457,  DOI: 10.1126/science.aax4406
      There is no corresponding record for this reference.
    7. 7
      Vayghan, H. S.; Nawrocki, W. J.; Schiphorst, C.; Tolleter, D.; Hu, C.; Douet, V.; Glauser, G.; Finazzi, G.; Croce, R.; Wientjes, E.; Longoni, F. Photosynthetic Light Harvesting and Thylakoid Organization in a CRISPR/Cas9 Arabidopsis Thaliana LHCB1 Knockout Mutant. Front. Plant Sci. 2022, 13, 833032– 833050,  DOI: 10.3389/fpls.2022.833032
      There is no corresponding record for this reference.
    8. 8
      Koepf, M.; Teillout, A.-L.; Llansola-Portoles, M. J. Artificial Photosynthesis: An Approach for a Sustainable Future. In Handbook of Ecomaterials; Martínez, L. M. T.; Kharissova, O. V.; Kharisov, B. I., Eds.; Springer International Publishing: Cham, 2017; pp 1– 25.
      There is no corresponding record for this reference.
    9. 9
      Guo, Y.; Zhou, Q.; Nan, J.; Shi, W.; Cui, F.; Zhu, Y. Perylenetetracarboxylic acid nanosheets with internal electric fields and anisotropic charge migration for photocatalytic hydrogen evolution. Nat. Commun. 2022, 13, 2067  DOI: 10.1038/s41467-022-29826-z
      9
      Perylenetetracarboxylic acid nanosheets with internal electric fields and anisotropic charge migration for photocatalytic hydrogen evolution
      Guo, Yan; Zhou, Qixin; Nan, Jun; Shi, Wenxin; Cui, Fuyi; Zhu, Yongfa
      Nature Communications (2022), 13 (1), 2067CODEN: NCAOBW; ISSN:2041-1723. (Nature Portfolio)
      Highly efficient hydrogen evolution reactions carried out via photocatalysis using solar light remain a formidable challenge. Herein, perylenetetracarboxylic acid nanosheets with a monolayer thickness of ∼1.5 nm were synthesized and shown to be active hydrogen evolution photocatalysts with prodn. rates of 118.9 mmol g-1 h-1. The carboxyl groups increased the intensity of the internal elec. fields of perylenetetracarboxylic acid from the perylene center to the carboxyl border by 10.3 times to promote charge-carrier sepn. The photogenerated electrons and holes migrated to the edge and plane, resp., to weaken charge-carrier recombination. Moreover, the perylenetetracarboxylic acid redn. potential increases from -0.47 V to -1.13 V due to the decreased mol. conjugation and enhances the redn. ability. In addn., the carboxyl groups created hydrophilic sites. This work provides a strategy to engineer the mol. structures of future efficient photocatalysts.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XhtVGht73E&md5=f8c29ac315efe8c28b049245041368d4
    10. 10
      Kosco, J.; Bidwell, M.; Cha, H.; Martin, T.; Howells, C. T.; Sachs, M.; Anjum, D. H.; Gonzalez Lopez, S.; Zou, L.; Wadsworth, A.; Zhang, W.; Zhang, L.; Tellam, J.; Sougrat, R.; Laquai, F.; DeLongchamp, D. M.; Durrant, J. R.; McCulloch, I. Enhanced photocatalytic hydrogen evolution from organic semiconductor heterojunction nanoparticles. Nat. Mater. 2020, 19, 559– 565,  DOI: 10.1038/s41563-019-0591-1
      10
      Enhanced photocatalytic hydrogen evolution from organic semiconductor heterojunction nanoparticles
      Kosco, Jan; Bidwell, Matthew; Cha, Hyojung; Martin, Tyler; Howells, Calvyn T.; Sachs, Michael; Anjum, Dalaver H.; Gonzalez Lopez, Sandra; Zou, Lingyu; Wadsworth, Andrew; Zhang, Weimin; Zhang, Lisheng; Tellam, James; Sougrat, Rachid; Laquai, Frederic; De Longchamp, Dean M.; Durrant, James R.; McCulloch, Iain
      Nature Materials (2020), 19 (5), 559-565CODEN: NMAACR; ISSN:1476-1122. (Nature Research)
      Photocatalysts formed from a single org. semiconductor typically suffer from inefficient intrinsic charge generation, which leads to low photocatalytic activities. It is demonstrated that incorporating a heterojunction between a donor polymer (PTB7-Th) and non-fullerene acceptor (EH-IDTBR) in org. nanoparticles (NPs) can result in hydrogen evolution photocatalysts with greatly enhanced photocatalytic activity. Control of the nanomorphol. of these NPs was achieved by varying the stabilizing surfactant employed during NP fabrication, converting it from a core-shell structure to an intermixed donor/acceptor blend and increasing H2 evolution by an order of magnitude. The resulting photocatalysts display an unprecedentedly high H2 evolution rate of over 60,000μmol h-1 g-1 under 350-800 nm illumination, and external quantum efficiencies > 6% in the region of max. solar photon flux.
      >> More from SciFinder ®
      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitlCgtbo%253D&md5=6ecc9f643dd2bbae4d3905129ec2e2dd
    11. 11
      Wang, Q.; Domen, K. Particulate Photocatalysts for Light-Driven Water Splitting: Mechanisms, Challenges, and Design Strategies. Chem. Rev. 2020, 120, 919– 985,  DOI: 10.1021/acs.chemrev.9b00201
      11
      Particulate Photocatalysts for Light-Driven Water Splitting: Mechanisms, Challenges, and Design Strategies
      Wang, Qian; Domen, Kazunari
      Chemical Reviews (Washington, DC, United States) (2020), 120 (2), 919-985CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. Solar-driven water splitting provides a leading approach to store the abundant yet intermittent solar energy and produce hydrogen as a clean and sustainable energy carrier. A straightforward route to light-driven water splitting is to apply self-supported particulate photocatalysts, which is expected to allow solar hydrogen to be competitive with fossil-fuel-derived hydrogen on a levelized cost basis. More importantly, the powder-based systems can lend themselves to making functional panels on a large scale while retaining the intrinsic activity of the photocatalyst. However, all attempts to generate hydrogen via powder-based solar water-splitting systems to date have unfortunately fallen short of the efficiency values required for practical applications. Photocatalysis on photocatalyst particles involves three sequential steps, absorption of photons with higher energies than the bandgap of the photocatalysts, leading to the excitation of electron-hole pairs in the particles, charge sepn. and migration of these photoexcited carriers, and surface chem. reactions based on these carriers. In this review, the focus is on the challenges of each step and summarize material design strategies to overcome the obstacles and limitations. This review illustrates that it is possible to employ the fundamental principles underlying photosynthesis and the tools of chem. and materials science to design and prep. photocatalysts for overall water splitting.
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    12. 12
      Takata, T.; Jiang, J.; Sakata, Y.; Nakabayashi, M.; Shibata, N.; Nandal, V.; Seki, K.; Hisatomi, T.; Domen, K. Photocatalytic water splitting with a quantum efficiency of almost unity. Nature 2020, 581, 411– 414,  DOI: 10.1038/s41586-020-2278-9
      12
      Photocatalytic water splitting with a quantum efficiency of almost unity
      Takata, Tsuyoshi; Jiang, Junzhe; Sakata, Yoshihisa; Nakabayashi, Mamiko; Shibata, Naoya; Nandal, Vikas; Seki, Kazuhiko; Hisatomi, Takashi; Domen, Kazunari
      Nature (London, United Kingdom) (2020), 581 (7809), 411-414CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
      Overall water splitting, evolving hydrogen and oxygen in a 2:1 stoichiometric ratio, using particulate photocatalysts is a potential means of achieving scalable and economically viable solar hydrogen prodn. To obtain high solar energy conversion efficiency, the quantum efficiency of the photocatalytic reaction must be increased over a wide range of wavelengths and semiconductors with narrow bandgaps need to be designed. However, the quantum efficiency assocd. with overall water splitting using existing photocatalysts is typically lower than ten per cent1,2. Thus, whether a particulate photocatalyst can enable a quantum efficiency of 100 per cent for the greatly endergonic water-splitting reaction remains an open question. Here we demonstrate overall water splitting at an external quantum efficiency of up to 96 per cent at wavelengths between 350 and 360 nm, which is equiv. to an internal quantum efficiency of almost unity, using a modified aluminum-doped strontium titanate (SrTiO3:Al) photocatalyst3,4. This enabled multiple consecutive forward charge transfers without backward charge transfer, reaching the upper limit of quantum efficiency for overall water splitting. Our work demonstrates the feasibility of overall water splitting free from charge recombination losses and introduces an ideal cocatalyst/photocatalyst structure for efficient water splitting.
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    13. 13
      Searle, N. Z.; Hirt, R. C. Ultraviolet Spectral Energy Distribution of Sunlight. J. Opt. Soc. Am. 1965, 55, 1413– 1421,  DOI: 10.1364/JOSA.55.001413
      There is no corresponding record for this reference.
    14. 14
      Cestellos-Blanco, S.; Zhang, H.; Kim, J. M.; Shen, Yx.; Yang, P. Photosynthetic semiconductor biohybrids for solar-driven biocatalysis. Nat. Catal. 2020, 3, 245– 255,  DOI: 10.1038/s41929-020-0428-y
      14
      Photosynthetic semiconductor biohybrids for solar-driven biocatalysis
      Cestellos-Blanco, Stefano; Zhang, Hao; Kim, Ji Min; Shen, Yue-xiao; Yang, Peidong
      Nature Catalysis (2020), 3 (3), 245-255CODEN: NCAACP; ISSN:2520-1158. (Nature Research)
      A review. Abstr.: Photosynthetic semiconductor biohybrids integrate the best attributes of biol. whole-cell catalysts and semiconducting nanomaterials. Enzymic machinery enveloped in its native cellular environment offers exquisite product selectivity and low substrate activation barriers while semiconducting nanomaterials harvest light energy stably and efficiently. In this Review Article, we illustrate the evolution and advances of photosynthetic semiconductor biohybrids focusing on the conversion of CO2 to value-added chems. We begin by considering the potential of this nascent field to meet global energy challenges while comparing it to alternate approaches. This is followed by a discussion of the advantageous coupling of electrotrophic organisms with light-active electrodes for solar-to-chem. conversion. We detail the dynamic investigation of photosensitized microorganisms creating direct light harvesting within unicellular organisms while describing complementary developments in the understanding of charge transfer mechanisms and cytoprotection. Lastly, we focus on trends and improvements needed in photosynthetic semiconductor biohybrids in order to address future challenges and enhance their widespread adoption for the prodn. of solar chems.
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    15. 15
      Kornienko, N.; Zhang, J. Z.; Sakimoto, K. K.; Yang, P.; Reisner, E. Interfacing nature’s catalytic machinery with synthetic materials for semi-artificial photosynthesis. Nat. Nanotechnol. 2018, 13, 890– 899,  DOI: 10.1038/s41565-018-0251-7
      15
      Interfacing nature's catalytic machinery with synthetic materials for semi-artificial photosynthesis
      Kornienko, Nikolay; Zhang, Jenny Z.; Sakimoto, Kelsey K.; Yang, Peidong; Reisner, Erwin
      Nature Nanotechnology (2018), 13 (10), 890-899CODEN: NNAABX; ISSN:1748-3387. (Nature Research)
      Semi-artificial photosynthetic systems aim to overcome the limitations of natural and artificial photosynthesis while providing an opportunity to investigate their resp. functionality. The progress and studies of these hybrid systems is the focus of this forward-looking perspective. In this Review, we discuss how enzymes have been interfaced with synthetic materials and employed for semi-artificial fuel prodn. In parallel, we examine how more complex living cellular systems can be recruited for in vivo fuel and chem. prodn. in an approach where inorg. nanostructures are hybridized with photosynthetic and non-photosynthetic microorganisms. Side-by-side comparisons reveal strengths and limitations of enzyme- and microorganism-based hybrid systems, and how lessons extd. from studying enzyme hybrids can be applied to investigations of microorganism-hybrid devices. We conclude by putting semi-artificial photosynthesis in the context of its own ambitions and discuss how it can help address the grand challenges facing artificial systems for the efficient generation of solar fuels and chems.
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    16. 16
      Özgen, F. F.; Runda, M. E.; Schmidt, S. Photo-biocatalytic Cascades: Combining Chemical and Enzymatic Transformations Fueled by Light. ChemBioChem 2021, 22, 790– 806,  DOI: 10.1002/cbic.202000587
      16
      Photo-biocatalytic Cascades: Combining Chemical and Enzymatic Transformations Fueled by Light
      Ozgen Fatma Feyza; Runda Michael E; Schmidt Sandy
      Chembiochem : a European journal of chemical biology (2021), 22 (5), 790-806 ISSN:.
      In the field of green chemistry, light - an attractive natural agent - has received particular attention for driving biocatalytic reactions. Moreover, the implementation of light to drive (chemo)enzymatic cascade reactions opens up a golden window of opportunities. However, there are limitations to many current examples, mostly associated with incompatibility between the enzyme and the photocatalyst. Additionally, the formation of reactive radicals upon illumination and the loss of catalytic activities in the presence of required additives are common observations. As outlined in this review, the main question is how to overcome current challenges to the exploitation of light to drive (chemo)enzymatic transformations. First, we highlight general concepts in photo-biocatalysis, then give various examples of photo-chemoenzymatic (PCE) cascades, further summarize current synthetic examples of PCE cascades and discuss strategies to address the limitations.
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    17. 17
      Schmermund, L.; Jurkaš, V.; Özgen, F. F.; Barone, G. D.; Büchsenschütz, H. C.; Winkler, C. K.; Schmidt, S.; Kourist, R.; Kroutil, W. Photo-Biocatalysis: Biotransformations in the Presence of Light. ACS Catal. 2019, 9, 4115– 4144,  DOI: 10.1021/acscatal.9b00656
      17
      Photo-Biocatalysis: Biotransformations in the Presence of Light
      Schmermund, Luca; Jurkas, Valentina; Oezgen, F. Feyza; Barone, Giovanni D.; Buechsenschuetz, Hanna C.; Winkler, Christoph K.; Schmidt, Sandy; Kourist, Robert; Kroutil, Wolfgang
      ACS Catalysis (2019), 9 (5), 4115-4144CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
      A review. Light has received increased attention for various chem. reactions but also in combination with biocatalytic reactions. Because currently only a few enzymic reactions are known, which per se require light, most transformations involving light and a biocatalyst exploit light either for providing the cosubstrate or cofactor in an appropriate redox state for the biotransformation. In selected cases, a promiscuous activity of known enzymes in the presence of light could be induced. In other approaches, light-induced chem. reactions have been combined with a biocatalytic step, or light-induced biocatalytic reactions were combined with chem. reactions in a linear cascade. Finally, enzymes with a light switchable moiety have been investigated to turn off/on or tune the actual reaction. This Review gives an overview of the various approaches for using light in biocatalysis.
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    18. 18
      Holá, K.; Pavliuk, M. V.; Németh, B.; Huang, P.; Zdražil, L.; Land, H.; Berggren, G.; Tian, H. Carbon Dots and [FeFe] Hydrogenase Biohybrid Assemblies for Efficient Light-Driven Hydrogen Evolution. ACS Catal. 2020, 10, 9943– 9952,  DOI: 10.1021/acscatal.0c02474
      18
      Carbon Dots and [FeFe] Hydrogenase Biohybrid Assemblies for Efficient Light-Driven Hydrogen Evolution
      Hola, Katerina; Pavliuk, Mariia V.; Nemeth, Brigitta; Huang, Ping; Zdrazil, Lukas; Land, Henrik; Berggren, Gustav; Tian, Haining
      ACS Catalysis (2020), 10 (17), 9943-9952CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
      Artificial photosynthesis is seen as a path to convert and store solar energy into chem. energy for our society. In this work, highly fluorescent aspartic acid-based carbon dots (CDs) are synthesized and employed as a photosensitizer to drive photocatalytic hydrogen evolution with an [FeFe] hydrogenase (CrHydA1). The direct interaction in CDs from L-aspartic acid (AspCDs)/CrHydA1 self-assembly systems, which is visualized from native gel electrophoresis, has been systematically investigated to understand the electron-transfer dynamics and its impact on photocatalytic efficiency. The study discloses the significant influence of the electrostatic surrounding generated by sacrificial electron donors on the intimate interplay within the oppositely charged subunits of the biohybrid assembly as well as the overall photocatalytic performance. The system reaches an external quantum efficiency of 1.7% at 420 nm and an initial activity of 1.73μmol(H2) mg-1(hydrogenase) min-1 under favorable electrostatic conditions. Owing to the ability of the synthesized AspCDs to operate efficiently under visible light, in contrast to other materials that require UV illumination, the stability of the biohybrid assembly in the presence of a redox mediator extends beyond 1 wk.
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    19. 19
      Gai, P.; Yu, W.; Zhao, H.; Qi, R.; Li, F.; Liu, L.; Lv, F.; Wang, S. Solar-Powered Organic Semiconductor-Bacteria Biohybrids for CO2 Reduction into Acetic Acid. Angew. Chem., Int. Ed. 2020, 59, 7224– 7229,  DOI: 10.1002/anie.202001047
      19
      Solar-Powered Organic Semiconductor-Bacteria Biohybrids for CO2 Reduction into Acetic Acid
      Gai, Panpan; Yu, Wen; Zhao, Hao; Qi, Ruilian; Li, Feng; Liu, Libing; Lv, Fengting; Wang, Shu
      Angewandte Chemie, International Edition (2020), 59 (18), 7224-7229CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)
      An org. semiconductor-bacteria biohybrid photosynthetic system is used to efficiently realize CO2 redn. to produce acetic acid with the non-photosynthetic bacteria Moorella thermoacetica. Perylene diimide deriv. (PDI) and poly(fluorene-co-phenylene) (PFP) were coated on the bacteria surface as photosensitizers to form a p-n heterojunction (PFP/PDI) layer, affording higher hole/electron sepn. efficiency. The π-conjugated semiconductors possess excellent light-harvesting ability and biocompatibility, and the cationic side chains of org. semiconductors could intercalate into cell membranes, ensuring efficient electron transfer to bacteria. Moorella thermoacetica can thus harvest photoexcited electrons from the PFP/PDI heterojunction, driving the Wood-Ljungdahl pathway to synthesize acetic acid from CO2 under illumination. The efficiency of this org. biohybrid is about 1.6 %, which is comparable to those of reported inorg. biohybrid systems.
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    20. 20
      Wang, X.; Saba, T.; Yiu, H. H. P.; Howe, R. F.; Anderson, J. A.; Shi, J. Cofactor NAD(P)H Regeneration Inspired by Heterogeneous Pathways. Chem 2017, 2, 621– 654,  DOI: 10.1016/j.chempr.2017.04.009
      20
      Cofactor NAD(P)H Regeneration Inspired by Heterogeneous Pathways
      Wang, Xiaodong; Saba, Tony; Yiu, Humphrey H. P.; Howe, Russell F.; Anderson, James A.; Shi, Jiafu
      Chem (2017), 2 (5), 621-654CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)
      Biocatalysis can empower chem., pharmaceutical, and energy industries, where the use of enzymes facilitates low-energy, sustainable methods of producing high-value chems. and pharmaceuticals that are otherwise impossibly troublesome or costly to obtain. One of the largest classes of enzymes (oxidoreductases, ∼25% of the total) capable of promoting bioredn. reactions is vital for the global pharmaceutical and chem. market because of their intrinsic enantioselectivity and specificity. Enzymic redn. depends on a coenzyme or cofactor as a hydride source, namely NAD (NADH) or its phosphorylated form (NADPH). Given the high cost, stoichiometric usage, and phys. instability of NAD(P)H, a suitable method for NAD(P)H regeneration is essential for practical application. This review summarizes the existing methods for NAD(P)H regeneration, including enzymic, chem., homogeneous catalytic, electrochem., photocatalytic, and heterogeneous catalytic routes. Particular focus is given to recent progress in developing heterogeneous systems with potential significance in terms of process simplicity, cleanliness, and energy and/or cost savings.
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    21. 21
      Gentil, S.; Che Mansor, S. M.; Jamet, H.; Cosnier, S.; Cavazza, C.; Le Goff, A. Oriented Immobilization of [NiFeSe] Hydrogenases on Covalently and Noncovalently Functionalized Carbon Nanotubes for H2/Air Enzymatic Fuel Cells. ACS Catal. 2018, 8, 3957– 3964,  DOI: 10.1021/acscatal.8b00708
      21
      Oriented Immobilization of [NiFeSe] Hydrogenases on Covalently and Noncovalently Functionalized Carbon Nanotubes for H2/Air Enzymatic Fuel Cells
      Gentil, Solene; Che Mansor, Syamim Muhamad; Jamet, Helene; Cosnier, Serge; Cavazza, Christine; Le Goff, Alan
      ACS Catalysis (2018), 8 (5), 3957-3964CODEN: ACCACS; ISSN:2155-5435. (American Chemical Society)
      We report the oriented immobilization of [NiFeSe] hydrogenases on both covalently and noncovalently modified carbon nanotubes (CNTs) electrodes. A specific interaction of the [NiFeSe] hydrogenase from Desulfomicrobium baculatum with hydrophobic org. mols. was probed by electrochem., quartz crystal microbalance with dissipation monitoring (QCM-D), and theor. calcns. Taking advantage of these hydrophobic interactions, the enzyme was efficiently wired on anthraquinone and adamantane-modified CNTs. Because of rational immobilization onto functionalized CNTs, the O2-tolerant [NiFeSe]-hydrogenase is able to efficiently operate in a H2/air gas-diffusion enzymic fuel cell.
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    22. 22
      Zhang, S.; Liu, S.; Sun, Y.; Li, S.; Shi, J.; Jiang, Z. Enzyme-photo-coupled catalytic systems. Chem. Soc. Rev. 2021, 50, 13449– 13466,  DOI: 10.1039/D1CS00392E
      22
      Enzyme-photo-coupled catalytic systems
      Zhang, Shaohua; Liu, Shusong; Sun, Yiying; Li, Shihao; Shi, Jiafu; Jiang, Zhongyi
      Chemical Society Reviews (2021), 50 (24), 13449-13466CODEN: CSRVBR; ISSN:0306-0012. (Royal Society of Chemistry)
      A review. Efficient chem. transformation in a green, low-carbon way is crucial for the sustainable development of modern society. Enzyme-photo-coupled catalytic systems (EPCS) that integrate the exceptional selectivity of enzyme catalysis and the unique reactivity of photocatalysis hold great promise in solar-driven 'mol. editing'. However, the involvement of multiple components and catalytic processes challenged the design of efficient and stable EPCS. To show a clear picture of the complex catalytic system, in this review, we analyze EPCS from the perspective of system engineering. First, we disintegrate the complex system into four elementary components, and reorganize these components into biocatalytic and photocatalytic ensembles (BE and PE). By resolving current accessible systems, we identify that connectivity and compatibility between BE and PE are two crucial factors that govern the performance of EPCS. Then, we discuss the origin of undesirable connectivity and low compatibility, and deduce the possible solns. Based on these understandings, we propose the designing principles of EPCS. Lastly, we provide a future perspective of EPCS.
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    23. 23
      Sun, Y.; Lin, Y.; Harman, V. M.; Beynon, R. J.; Johnson, J. R.; Liu, L.-N. Decoding the Absolute Stoichiometric Composition and Structural Plasticity of a-Carboxysomes. mBio 2022, 13, e03629-21  DOI: 10.1128/mbio.03629-21
      There is no corresponding record for this reference.
    24. 24
      Gonzalez-Esquer, C. R.; Newnham, S. E.; Kerfeld, C. A. Bacterial microcompartments as metabolic modules for plant synthetic biology. Plant J. 2016, 87, 66– 75,  DOI: 10.1111/tpj.13166
      24
      Bacterial microcompartments as metabolic modules for plant synthetic biology
      Gonzalez-Esquer, C. Raul; Newnham, Sarah E.; Kerfeld, Cheryl A.
      Plant Journal (2016), 87 (1), 66-75CODEN: PLJUED; ISSN:0960-7412. (Wiley-Blackwell)
      Bacterial microcompartments (BMCs) are megadalton-sized protein assemblies that enclose segments of metabolic pathways within cells. They increase the catalytic efficiency of the encapsulated enzymes while sequestering volatile or toxic intermediates from the bulk cytosol. The first BMCs discovered were the carboxysomes of cyanobacteria. Carboxysomes compartmentalize the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) with carbonic anhydrase. They enhance the carboxylase activity of RuBisCO by increasing the local concn. of CO2 in the vicinity of the enzyme's active site. As a metabolic module for carbon fixation, carboxysomes could be transferred to eukaryotic organisms (e.g. plants) to increase photosynthetic efficiency. Within the scope of synthetic biol., carboxysomes and other BMCs hold even greater potential when considered a source of building blocks for the development of nanoreactors or three-dimensional scaffolds to increase the efficiency of either native or heterologously expressed enzymes. The carboxysome serves as an ideal model system for testing approaches to engineering BMCs because their expression in cyanobacteria provides a sensitive screen for form (appearance of polyhedral bodies) and function (ability to grow on air). We recount recent progress in the re-engineering of the carboxysome shell and core to offer a conceptual framework for the development of BMC-based architectures for applications in plant synthetic biol.
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    25. 25
      Liu, L. N. Advances in the bacterial organelles for CO2 fixation. Trends Microbiol. 2022, 30, 567– 580,  DOI: 10.1016/j.tim.2021.10.004
      25
      Advances in the bacterial organelles for CO2 fixation
      Liu, Lu-Ning
      Trends in Microbiology (2022), 30 (6), 567-580CODEN: TRMIEA; ISSN:0966-842X. (Elsevier Ltd.)
      Carboxysomes are a family of bacterial microcompartments (BMCs), present in all cyanobacteria and some proteobacteria, which encapsulate the primary CO2-fixing enzyme, Rubisco, within a virus-like polyhedral protein shell. Carboxysomes provide significantly elevated levels of CO2 around Rubisco to maximize carboxylation and reduce wasteful photorespiration, thus functioning as the central CO2-fixation organelles of bacterial CO2-concn. mechanisms. Their intriguing architectural features allow carboxysomes to make a vast contribution to carbon assimilation on a global scale. In this review, we discuss recent research progress that provides new insights into the mechanisms of how carboxysomes are assembled and functionally maintained in bacteria and recent advances in synthetic biol. to repurpose the metabolic module in diverse applications.
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    26. 26
      Huang, J.; Jiang, Q.; Yang, M.; Dykes, G. F.; Weetman, S. L.; Xin, W.; He, H. L.; Liu, L. N. Probing the internal pH and permeability of a carboxysome shell. Biomacromolecules 2022, 23, 4339– 4348,  DOI: 10.1021/acs.biomac.2c00781
      26
      Probing the Internal pH and Permeability of a Carboxysome Shell
      Huang, Jiafeng; Jiang, Qiuyao; Yang, Mengru; Dykes, Gregory F.; Weetman, Samantha L.; Xin, Wei; He, Hai-Lun; Liu, Lu-Ning
      Biomacromolecules (2022), 23 (10), 4339-4348CODEN: BOMAF6; ISSN:1525-7797. (American Chemical Society)
      The carboxysome is a protein-based nanoscale organelle in cyanobacteria and many proteobacteria, which encapsulates the key CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase (CA) within a polyhedral protein shell. The intrinsic self-assembly and architectural features of carboxysomes and the semipermeability of the protein shell provide the foundation for the accumulation of CO2 within carboxysomes and enhanced carboxylation. Here, we develop an approach to det. the interior pH conditions and inorg. carbon accumulation within an α-carboxysome shell derived from a chemoautotrophic proteobacterium Halothiobacillus neapolitanus and evaluate the shell permeability. By incorporating a pH reporter, pHluorin2, within empty α-carboxysome shells produced in Escherichia coli, we probe the interior pH of the protein shells with and without CA. Our in vivo and in vitro results demonstrate a lower interior pH of α-carboxysome shells than the cytoplasmic pH and buffer pH, as well as the modulation of the interior pH in response to changes in external environments, indicating the shell permeability to bicarbonate ions and protons. We further det. the satd. HCO3- concn. of 15 mM within α-carboxysome shells and show the CA-mediated increase in the interior CO2 level. Uncovering the interior physiochem. microenvironment of carboxysomes is crucial for understanding the mechanisms underlying carboxysomal shell permeability and enhancement of Rubisco carboxylation within carboxysomes. Such fundamental knowledge may inform reprogramming carboxysomes to improve metab. and recruit foreign enzymes for enhanced catalytical performance.
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    27. 27
      Faulkner, M.; Szabó, I.; Weetman, S. L.; Sicard, F.; Huber, R. G.; Bond, P. J.; Rosta, E.; Liu, L.-N. Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein. Sci. Rep. 2020, 10, 17501  DOI: 10.1038/s41598-020-74536-5
      27
      Molecular simulations unravel molecular principles that mediate selective permeability of carboxysome shell protein
      Faulkner, Matthew; Szabo, Istvan; Weetman, Samantha L.; Sicard, Francois; Huber, Roland G.; Bond, Peter J.; Rosta, Edina; Liu, Lu-Ning
      Scientific Reports (2020), 10 (1), 17501CODEN: SRCEC3; ISSN:2045-2322. (Nature Research)
      Bacterial microcompartments (BMCs) are nanoscale proteinaceous organelles that encapsulate enzymes from the cytoplasm using an icosahedral protein shell that resembles viral capsids. Of particular interest are the carboxysomes (CBs), which sequester the CO2-fixing enzymes ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) to enhance carbon assimilation. The carboxysome shell serves as a semi-permeable barrier for passage of metabolites in and out of the carboxysome to enhance CO2 fixation. How the protein shell directs influx and efflux of mols. in an effective manner has remained elusive. Here we use mol. dynamics and umbrella sampling calcns. to det. the free-energy profiles of the metabolic substrates, bicarbonate, CO2 and ribulose bisphosphate and the product 3-phosphoglycerate assocd. with their transition through the major carboxysome shell protein CcmK2. We elucidate the electrostatic charge-based permeability and key amino acid residues of CcmK2 functioning in mediating mol. transit through the central pore. Conformational changes of the loops forming the central pore may also be required for transit of specific metabolites. The importance of these in-silico findings is validated exptl. by site-directed mutagenesis of the key CcmK2 residue Serine 39. This study provides insight into the mechanism that mediates mol. transport through the shells of carboxysomes, applicable to other BMCs. It also offers a predictive approach to investigate and manipulate the shell permeability, with the intent of engineering BMC-based metabolic modules for new functions in synthetic biol.
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    28. 28
      Mahinthichaichan, P.; Morris, D. M.; Wang, Y.; Jensen, G. J.; Tajkhorshid, E. Selective permeability of carboxysome shell pores to anionic molecules. J. Phys. Chem. B 2018, 122, 9110– 9118,  DOI: 10.1021/acs.jpcb.8b06822
      28
      Selective Permeability of Carboxysome Shell Pores to Anionic Molecules
      Mahinthichaichan, Paween; Morris, Dylan M.; Wang, Yi; Jensen, Grant J.; Tajkhorshid, Emad
      Journal of Physical Chemistry B (2018), 122 (39), 9110-9118CODEN: JPCBFK; ISSN:1520-5207. (American Chemical Society)
      Carboxysomes are closed polyhedral cellular microcompartments that increase the efficiency of carbon fixation in autotrophic bacteria. Carboxysome shells consist of small proteins that form hexameric units with semi-permeable central pores contg. binding sites for anions. This feature is thought to selectively allow access to RuBisCO enzymes inside the carboxysome by HCO3- (the dominant form of CO2 in the aq. soln. at pH 7.4) but not O2, which leads to a non-productive reaction. To test this hypothesis, here we use mol. dynamics simulations to characterize the energetics and permeability of CO2, O2, and HCO3- through the central pores of two different shell proteins, namely, CsoS1A of α-carboxysome and CcmK4 of β-carboxysome shells. We find that the central pores are in fact selectively permeable to anions such as HCO3-, as predicted by the model.
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    29. 29
      Cammack, R.; Frey, M.; Robson, R. Hydrogen as a Fuel, Learning from Nature; CRC Press, 2001.
      There is no corresponding record for this reference.
    30. 30
      Vignais, P. M.; Billoud, B. Occurrence, Classification, and Biological Function of Hydrogenases: An Overview. Chem. Rev. 2007, 107, 4206– 4272,  DOI: 10.1021/cr050196r
      30
      Occurrence, classification, and biological function of hydrogenases: An overview
      Vignais, Paulette M.; Billoud, Bernard
      Chemical Reviews (Washington, DC, United States) (2007), 107 (10), 4206-4272CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. The occurrence, diversity, evolutionary relations, classification, biosynthesis, and roles of hydrogenases in Nature are reviewed and discussed.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtFehu7rO&md5=aaa7289d7ad7340e59d6f3ed1e2ce1a7
    31. 31
      Lubitz, W.; Ogata, H.; Rudiger, O.; Reijerse, E. Hydrogenases. Chem. Rev. 2014, 114, 4081– 4148,  DOI: 10.1021/cr4005814
      31
      Hydrogenases
      Lubitz, Wolfgang; Ogata, Hideaki; Ruediger, Olaf; Reijerse, Edward
      Chemical Reviews (Washington, DC, United States) (2014), 114 (8), 4081-4148CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. The current state of knowledge on hydrogenases, esp. recent advances made in understanding the detailed structure and function of these important enzymes. The authors provide an overview of important previous achievements with the main focus on [NiFe] and [FeFe] hydrogenases, and in part also on [Fe] hydrogenases. Recent progress on biomimetic model systems for hydrogenases and devices using hydrogenases both in fuel cells and for H2 prodn. are presented with emphasis on functional aspects. The great progress made in synthesizing model systems for hydrogenases that are functionally active is promising for the future employment of such catalysts in hydrogen technologies.
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    32. 32
      Jiang, Q.; Li, T.; Yang, J.; Aitchison, C. M.; Huang, J.; Chen, Y.; Huang, F.; Wang, Q.; Cooper, A. I.; Liu, L.-N. Synthetic engineering of a new biocatalyst encapsulating [NiFe]-hydrogenases for enhanced hydrogen production. J. Mater. Chem. B 2023, 11, 2684– 2692,  DOI: 10.1039/D2TB02781J
      32
      Synthetic engineering of a new biocatalyst encapsulating [NiFe]-hydrogenases for enhanced hydrogen production
      Jiang, Qiuyao; Li, Tianpei; Yang, Jing; Aitchison, Catherine M.; Huang, Jiafeng; Chen, Yu; Huang, Fang; Wang, Qiang; Cooper, Andrew I.; Liu, Lu-Ning
      Journal of Materials Chemistry B: Materials for Biology and Medicine (2023), 11 (12), 2684-2692CODEN: JMCBDV; ISSN:2050-7518. (Royal Society of Chemistry)
      Hydrogenases are microbial metalloenzymes capable of catalyzing the reversible interconversion between mol. hydrogen and protons with high efficiency, and have great potential in the development of new electrocatalysts for renewable fuel prodn. Here, we engineered the intact proteinaceous shell of the carboxysome, a self-assembling protein organelle for CO2 fixation in cyanobacteria and proteobacteria, and sequestered heterologously produced [NiFe]-hydrogenases into the carboxysome shell. The protein-based hybrid catalyst produced in E. coli shows substantially improved hydrogen prodn. under both aerobic and anaerobic conditions and enhanced material and functional robustness, compared to unencapsulated [NiFe]-hydrogenases. The catalytically functional nanoreactor as well as the self-assembling and encapsulation strategies provide a framework for engineering new bioinspired electrocatalysts to improve the sustainable prodn. of fuels and chems. in biotechnol. and chem. applications.
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    33. 33
      Li, T.; Jiang, Q.; Huang, J.; Aitchison, C. M.; Huang, F.; Yang, M.; Dykes, G. F.; He, H. L.; Wang, Q.; Sprick, R. S.; Cooper, A. I.; Liu, L. N. Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production. Nat. Commun. 2020, 11, 5448  DOI: 10.1038/s41467-020-19280-0
      33
      Reprogramming bacterial protein organelles as a nanoreactor for hydrogen production
      Li, Tianpei; Jiang, Qiuyao; Huang, Jiafeng; Aitchison, Catherine M.; Huang, Fang; Yang, Mengru; Dykes, Gregory F.; He, Hai-Lun; Wang, Qiang; Sprick, Reiner Sebastian; Cooper, Andrew I.; Liu, Lu-Ning
      Nature Communications (2020), 11 (1), 5448CODEN: NCAOBW; ISSN:2041-1723. (Nature Research)
      Abstr.: Compartmentalization is a ubiquitous building principle in cells, which permits segregation of biol. elements and reactions. The carboxysome is a specialized bacterial organelle that encapsulates enzymes into a virus-like protein shell and plays essential roles in photosynthetic carbon fixation. The naturally designed architecture, semi-permeability, and catalytic improvement of carboxysomes have inspired rational design and engineering of new nanomaterials to incorporate desired enzymes into the protein shell for enhanced catalytic performance. Here, we build large, intact carboxysome shells (over 90 nm in diam.) in the industrial microorganism Escherichia coli by expressing a set of carboxysome protein-encoding genes. We develop strategies for enzyme activation, shell self-assembly, and cargo encapsulation to construct a robust nanoreactor that incorporates catalytically active [FeFe]-hydrogenases and functional partners within the empty shell for the prodn. of hydrogen. We show that shell encapsulation and the internal microenvironment of the new catalyst facilitate hydrogen prodn. of the encapsulated oxygen-sensitive hydrogenases. The study provides insights into the assembly and formation of carboxysomes and paves the way for engineering carboxysome shell-based nanoreactors to recruit specific enzymes for diverse catalytic reactions.
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    34. 34
      Qin, W. K.; Tung, C. H.; Wu, L. Z. Covalent organic framework and hydrogen-bonded organic framework for solar-driven photocatalysis. J. Mater. Chem. A 2023, 11, 12521– 12538,  DOI: 10.1039/D2TA09375H
      There is no corresponding record for this reference.
    35. 35
      Aitchison, C. M.; Kane, C. M.; McMahon, D. P.; Spackman, P. R.; Pulido, A.; Wang, X.; Wilbraham, L.; Chen, L.; Clowes, R.; Zwijnenburg, M. A.; Sprick, R. S.; Little, M. A.; Day, G. M.; Cooper, A. I. Photocatalytic proton reduction by a computationally identified, molecular hydrogen-bonded framework. J. Mater. Chem. A 2020, 8, 7158– 7170,  DOI: 10.1039/D0TA00219D
      35
      Photocatalytic proton reduction by a computationally identified, molecular hydrogen-bonded framework
      Aitchison, Catherine M.; Kane, Christopher M.; McMahon, David P.; Spackman, Peter R.; Pulido, Angeles; Wang, Xiaoyan; Wilbraham, Liam; Chen, Linjiang; Clowes, Rob; Zwijnenburg, Martijn A.; Sprick, Reiner Sebastian; Little, Marc A.; Day, Graeme M.; Cooper, Andrew I.
      Journal of Materials Chemistry A: Materials for Energy and Sustainability (2020), 8 (15), 7158-7170CODEN: JMCAET; ISSN:2050-7496. (Royal Society of Chemistry)
      We show that a hydrogen-bonded framework, TBAP-α, with extended π-stacked pyrene columns has a sacrificial photocatalytic hydrogen prodn. rate of up to 3108μmol g-1 h-1. This is the highest activity reported for a mol. org. crystal. By comparison, a chem.-identical but amorphous sample of TBAP was 20-200 times less active, depending on the reaction conditions, showing unambiguously that crystal packing in mol. crystals can dictate photocatalytic activity. Crystal structure prediction (CSP) was used to predict the solid-state structure of TBAP and other functionalised, conformationally-flexible pyrene derivs. Specifically, we show that energy-structure-function (ESF) maps can be used to identify mols. such as TBAP that are likely to form extended π-stacked columns in the solid state. This opens up a methodol. for the a priori computational design of mol. org. photocatalysts and other energy-relevant materials, such as org. electronics.
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    36. 36
      Stylianou, K. C.; Heck, R.; Chong, S. Y.; Bacsa, J.; Jones, J. T. A.; Khimyak, Y. Z.; Bradshaw, D.; Rosseinsky, M. J. A guest-responsive fluorescent 3D microporous metal-organic framework derived from a long-lifetime pyrene core. J. Am. Chem. Soc. 2010, 132, 4119– 4130,  DOI: 10.1021/ja906041f
      36
      A Guest-Responsive Fluorescent 3D Microporous Metal-Organic Framework Derived from a Long-Lifetime Pyrene Core
      Stylianou, Kyriakos C.; Heck, Romain; Chong, Samantha Y.; Bacsa, John; Jones, James T. A.; Khimyak, Yaroslav Z.; Bradshaw, Darren; Rosseinsky, Matthew J.
      Journal of the American Chemical Society (2010), 132 (12), 4119-4130CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      The carboxylate ligand pyrene-1,3,6,8-tetrakis(p-benzoic acid) (TBAPy), based on the strongly fluorescent long-lifetime pyrene core, affords a permanently microporous fluorescent metal-org. framework, [In2(OH)2(TBAPy)]·(guests) (1), displaying 54% total accessible vol. and excellent thermal stability. Fluorescence studies reveal that both 1 and TBAPy display strong emission bands at 471 and 529 nm, resp., upon excitation at 390 nm, with framework coordination of the TBAPy ligands significantly increasing the emission lifetime from 0.089 to 0.110 ms. Upon desolvation, the emission band for the framework is shifted to lower energy: however, upon re-exposure to DMF the as-made material is regenerated with reversible fluorescence behavior. Together with the lifetime, the emission intensity is strongly enhanced by spatial sepn. of the optically active ligand mols. within the MOF structure and is dependent on the amt. and chem. nature of the guest species in the pores. The quantum yield of the material is 6.7% and, coupled with the fluorescence lifetime on the millisecond time scale, begins to approach the values obsd. for Eu(III)-cryptate-derived com. sensors.
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    37. 37
      Chen, G.; Huang, S.; Shen, Y.; Kou, X.; Ma, X.; Huang, S.; Tong, Q.; Ma, K.; Chen, W.; Wang, P.; Shen, J.; Zhu, F.; Ouyang, G. Protein-directed, hydrogen-bonded biohybrid framework. Chem 2021, 7, 2722– 2742,  DOI: 10.1016/j.chempr.2021.07.003
      37
      Protein-directed, hydrogen-bonded biohybrid framework
      Chen, Guosheng; Huang, Siming; Shen, Yong; Kou, Xiaoxue; Ma, Xiaomin; Huang, Shuyao; Tong, Qing; Ma, Kaili; Chen, Wen; Wang, Peiyi; Shen, Jun; Zhu, Fang; Ouyang, Gangfeng
      Chem (2021), 7 (10), 2722-2742CODEN: CHEMVE; ISSN:2451-9294. (Cell Press)
      Here, we describe a versatile protein-directed assembly strategy that enables the organization of different types of proteins and org. linkers into a highly cryst. hybrid framework through hydrogen-bond interaction. The whole assembly process is protein actuated but is independent of the protein-surface property. Advanced low-electron-dose cryoelectron microscopy techniques clearly witness the crystallog. structure of hybrid framework at a single-mol. level, and we demonstrate that the proteins are independently and tightly isolated in the cryst. frameworks, with a record-high protein content in the reported biohybrid framework materials. In addn., the hybrid framework has ultrahigh chem. stability, and its aperture structure and protein confinement tightness are controllable through modulating the org. linkers. When using enzymes as the building block, the obtained enzyme framework shows significantly improved stability compared with the free enzymes and displays notable advantages for biocatalysis compared with the burgeoning enzyme-MOF biohybrids in terms of active ingredient content, robustness, and catalytic efficiency.
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    38. 38
      Zhou, Q.; Guo, Y.; Zhu, Y. Photocatalytic sacrificial H2 evolution dominated by micropore-confined exciton transfer in hydrogen-bonded organic frameworks. Nat. Catal. 2023, 6, 574– 584,  DOI: 10.1038/s41929-023-00972-x
      38
      Photocatalytic sacrificial H2 evolution dominated by micropore-confined exciton transfer in hydrogen-bonded organic frameworks
      Zhou, Qixin; Guo, Yan; Zhu, Yongfa
      Nature Catalysis (2023), 6 (7), 574-584CODEN: NCAACP; ISSN:2520-1158. (Nature Portfolio)
      Org. semiconductors are attractive photocatalysts, but their quantum yields are limited by the transfer of photogenerated charges to the surface. A promising strategy for low-loss charge transfer is to shorten the distance from the bulk exciton coupling region to the catalyst surface. Here we employ the hydrogen-bonded org. framework 1,3,6,8-tetrakis(p-benzoic acid)pyrene (HOF-H4TBAPy) with hydrophilic one-dimensional micropore channels as a proof of concept for this approach. Under irradn., photogenerated excitons rapidly transfer to the inner surface of adjacent micropores, engendering a mere 1.88 nm transfer route, thus significantly improving exciton utilization. When the micropore channel length does not exceed 0.59μm, the sacrificial photocatalytic H2 evolution rate of HOF-H4TBAPy reaches 358 mmol h-1 g-1 and the apparent quantum yield at 420 nm is 28.6%. We further demonstrated a stable 1.03 mol day-1 m-2 H2 evolution on a 0.5 m2 HOF-H4TBAPy-loaded fiber under 1 Sun irradn.
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    39. 39
      Pellegrin, Y.; Odobel, F. Sacrificial electron donor reagents for solar fuel production. C. R. Chim. 2017, 20, 283– 295,  DOI: 10.1016/j.crci.2015.11.026
      39
      Sacrificial electron donor reagents for solar fuel production
      Pellegrin, Yann; Odobel, Fabrice
      Comptes Rendus Chimie (2017), 20 (3), 283-295CODEN: CRCOCR; ISSN:1631-0748. (Elsevier Masson SAS)
      A review is given. Although justly considered as a cumbersome component in artificial photosystems, these simple mols. are a necessary evil to drive photo-induced reactions aiming at producing high added value mols. by photo-induced redn. of low energy value substrates. This paper 1rst presents the specifications of sacrificial electron donors. Then the various families of sacrificial donors used from the early 1970s to nowadays are reviewed, such as aliph. and arom. amines, benzyl-dihydronicotinamide (BNAH), dimethylphenylbenzimidazoline (BIH), ascorbic acid, oxalate and finally thiols. Exptl. conditions (pH, solvent) are immensely versatile but important trends are given for adequate operation of a three-component system. Although literature abounds with various, very different artificial photosystems, we will realize that virtually the same sacrificial donors are used over and over again.
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    40. 40
      Baker, S. H.; Lorbach, S. C.; Rodriguez-Buey, M.; Williams, D. S.; Aldrich, H. C.; Shively, J. M. The correlation of the gene csoS2 of the carboxysome operon with two polypeptides of the carboxysome in Thiobacillus neapolitanus. Arch. Microbiol. 1999, 172, 233– 239,  DOI: 10.1007/s002030050765
      40
      The correlation of the gene csoS2 of the carboxysome operon with two polypeptides of the carboxysome in Thiobacillus neapolitanus
      Baker, Stefanie H.; Lorbach, Stanley C.; Rodriguez-Buey, Marisa; Williams, Donna S.; Aldrich, Henry C.; Shively, Jessup M.
      Archives of Microbiology (1999), 172 (4), 233-239CODEN: AMICCW; ISSN:0302-8933. (Springer-Verlag)
      The carboxysomal polypeptides of Thiobacillus neapolitanus with apparent mol. masses of 85 and 130 kDa were isolated and subjected to N-terminal sequencing. The first 17 amino acids of the two peptides were identical. The sequence perfectly matched the deduced amino acid sequence of an open reading frame in the carboxysome operon. The gene was subsequently named csoS2. Expression of the gene in Escherichia coli resulted in the prodn. of two peptides with apparent mol. masses of 85 and 130 kDa. Immunospecific antibodies generated against the smaller peptide recognized both peptides; the peptides were named CsoS2A and CsoS2B, resp. A digoxigenin-hydrazide glycosylation assay revealed that both CsoS2A and CsoS2B are post-translationally modified by glycosylation. CsoS2 was localized to the edges of purified carboxysomes by immunogold electron microscopy using the monospecific CsoS2A antibodies. The mol. mass of CsoS2A calcd. from the nucleotide sequence was 92.3 kDa.
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    41. 41
      Case, D. A.; Aktulga, H. M.; Belfon, K.; Cerutti, D. S.; Cisneros, G. A.; Cruzeiro, V. W. D.; Forouzesh, N.; Giese, T. J.; Götz, A. W.; Gohlke, H.; Izadi, S.; Kasavajhala, K.; Kaymak, M. C.; King, E.; Kurtzman, T.; Lee, T.-S.; Li, P.; Liu, J.; Luchko, T.; Luo, R.; Manathunga, M.; Machado, M. R.; Nguyen, H. M.; O’Hearn, K. A.; Onufriev, A. V.; Pan, F.; Pantano, S.; Qi, R.; Rahnamoun, A.; Risheh, A.; Schott-Verdugo, S.; Shajan, A.; Swails, J.; Wang, J.; Wei, H.; Wu, X.; Wu, Y.; Zhang, S.; Zhao, S.; Zhu, Q.; Cheatham, T. E., III; Roe, D. R.; Roitberg, A.; Simmerling, C.; York, D. M.; Nagan, M. C.; Merz, K. M., Jr. AmberTools. J. Chem. Inf. Model. 2023, 63, 6183– 6191,  DOI: 10.1021/acs.jcim.3c01153
      41
      AmberTools
      Case, David A.; Aktulga, Hasan Metin; Belfon, Kellon; Cerutti, David S.; Cisneros, G. Andres; Cruzeiro, Vinicius Wilian D.; Forouzesh, Negin; Giese, Timothy J.; Gotz, Andreas W.; Gohlke, Holger; Izadi, Saeed; Kasavajhala, Koushik; Kaymak, Mehmet C.; King, Edward; Kurtzman, Tom; Lee, Tai-Sung; Li, Pengfei; Liu, Jian; Luchko, Tyler; Luo, Ray; Manathunga, Madushanka; Machado, Matias R.; Nguyen, Hai Minh; O.bxsolid.Hearn, Kurt A.; Onufriev, Alexey V.; Pan, Feng; Pantano, Sergio; Qi, Ruxi; Rahnamoun, Ali; Risheh, Ali; Schott-Verdugo, Stephan; Shajan, Akhil; Swails, Jason; Wang, Junmei; Wei, Haixin; Wu, Xiongwu; Wu, Yongxian; Zhang, Shi; Zhao, Shiji; Zhu, Qiang; Cheatham III, Thomas E.; Roe, Daniel R.; Roitberg, Adrian; Simmerling, Carlos; York, Darrin M.; Nagan, Maria C.; Merz Jr., Kenneth M.
      Journal of Chemical Information and Modeling (2023), 63 (20), 6183-6191CODEN: JCISD8; ISSN:1549-9596. (American Chemical Society)
      AmberTools is a free and open-source collection of programs used to set up, run, and analyze mol. simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
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    42. 42
      Karthi, N.; Venkatachalam, M. Growth and Characterization Novel Organic Nonlinear Optical Crystal of Pyrene. Int. J. Sci. 2013, 1, 8– 12
      There is no corresponding record for this reference.
    43. 43
      Tanaka, S.; Kerfeld, C. A.; Sawaya, M. R.; Cai, F.; Heinhorst, S.; Cannon, G. C.; Yeates, T. O. Atomic-level models of the bacterial carboxysome shell. Science 2008, 319, 1083– 1086,  DOI: 10.1126/science.1151458
      43
      Atomic-Level Models of the Bacterial Carboxysome Shell
      Tanaka, Shiho; Kerfeld, Cheryl A.; Sawaya, Michael R.; Cai, Fei; Heinhorst, Sabine; Cannon, Gordon C.; Yeates, Todd O.
      Science (Washington, DC, United States) (2008), 319 (5866), 1083-1086CODEN: SCIEAS; ISSN:0036-8075. (American Association for the Advancement of Science)
      The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation. The carboxysome shell is roughly 800 to 1400 angstroms in diam. and is assembled from several thousand protein subunits. Previous studies have revealed the three-dimensional structures of hexameric carboxysome shell proteins, which self-assemble into mol. layers that most likely constitute the facets of the polyhedral shell. Here, we report the three-dimensional structures of two proteins of previously unknown function, CcmL and OrfA (or CsoS4A), from the two known classes of carboxysomes, at resolns. of 2.4 and 2.15 angstroms. Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell. Combining these pentamers with the hexamers previously elucidated gives two plausible, preliminary at. models for the carboxysome shell.
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    44. 44
      Tsai, Y.; Sawaya, M. R.; Cannon, G. C.; Cai, F.; Williams, E. B.; Heinhorst, S.; Kerfeld, C. A.; Yeates, T. O. Structural analysis of CsoS1A and the protein shell of the Halothiobacillus neapolitanus carboxysome. PLoS Biol. 2007, 5, e144,  DOI: 10.1371/journal.pbio.0050144
      There is no corresponding record for this reference.
    45. 45
      Parsons, J. B.; Dinesh, S. D.; Deery, E.; Leech, H. K.; Brindley, A. A.; Heldt, D.; Frank, S.; Smales, C. M.; Lünsdorf, H.; Rambach, A.; Gass, M. H.; Bleloch, A.; McClean, K. J.; Munro, A. W.; Rigby, S. E. J.; Warren, M. J.; Prentice, M. B. Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis. J. Biol. Chem. 2008, 283, 14366– 14375,  DOI: 10.1074/jbc.M709214200
      45
      Biochemical and Structural Insights into Bacterial Organelle Form and Biogenesis
      Parsons, Joshua B.; Dinesh, Sriramulu D.; Deery, Evelyne; Leech, Helen K.; Brindley, Amanda A.; Heldt, Dana; Frank, Steffanie; Smales, C. Mark; Luensdorf, Heinrich; Rambach, Alain; Gass, Mhairi H.; Bleloch, Andrew; McClean, Kirsty J.; Munro, Andrew W.; Rigby, Stephen E. J.; Warren, Martin J.; Prentice, Michael B.
      Journal of Biological Chemistry (2008), 283 (21), 14366-14375CODEN: JBCHA3; ISSN:0021-9258. (American Society for Biochemistry and Molecular Biology)
      Many heterotrophic bacteria have the ability to make polyhedral structures contg. metabolic enzymes that are bounded by a unilamellar protein shell (metabolosomes or enterosomes). These bacterial organelles contain enzymes assocd. with a specific metabolic process (e.g., 1,2-propanediol or ethanolamine utilization). The authors show that the 21 gene regulon specifying the pdu organelle and propanediol utilization enzymes from Citrobacter freundii is fully functional when cloned in Escherichia coli, both producing metabolosomes and allowing propanediol utilization. Genetic manipulation of the level of specific shell proteins resulted in the formation of aberrantly shaped metabolosomes, providing evidence for their involvement as delimiting entities in the organelle. This is the first demonstration of complete recombinant metabolosome activity transferred in a single step and supports phylogenetic evidence that the pdu genes are readily horizontally transmissible. One of the predicted shell proteins (PduT) was found to have a novel Fe-S center formed between four protein subunits. The recombinant model will facilitate future expts. establishing the structure and assembly of these multiprotein assemblages and their fate when the specific metabolic function is no longer required.
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    46. 46
      Parsons, J. B.; Lawrence, A. D.; McLean, K. J.; Munro, A. W.; Rigby, S. E. J.; Warren, M. J. Characterisation of PduS, the pdu Metabolosome Corrin Reductase, and Evidence of Substructural Organisation within the Bacterial Microcompartment. PLoS One 2010, 5, e14009,  DOI: 10.1371/journal.pone.0014009
      There is no corresponding record for this reference.
    47. 47
      Silva, D. A.; Yu, S.; Ulge, U. Y.; Spangler, J. B.; Jude, K. M.; Labão-Almeida, C.; Ali, L. R.; Quijano-Rubio, A.; Ruterbusch, M.; Leung, I.; Biary, T.; Crowley, S. J.; Marcos, E.; Walkey, C. D.; Weitzner, B. D.; Pardo-Avila, F.; Castellanos, J.; Carter, L.; Stewart, L.; Riddell, S. R.; Pepper, M.; Bernardes, G. J. L.; Dougan, M.; Garcia, K. C.; Baker, D. De novo design of potent and selective mimics of IL-2 and IL-15. Nature 2019, 565, 186– 191,  DOI: 10.1038/s41586-018-0830-7
      47
      De novo design of potent and selective mimics of IL-2 and IL-15
      Silva, Daniel-Adriano; Yu, Shawn; Ulge, Umut Y.; Spangler, Jamie B.; Jude, Kevin M.; Labao-Almeida, Carlos; Ali, Lestat R.; Quijano-Rubio, Alfredo; Ruterbusch, Mikel; Leung, Isabel; Biary, Tamara; Crowley, Stephanie J.; Marcos, Enrique; Walkey, Carl D.; Weitzner, Brian D.; Pardo-Avila, Fatima; Castellanos, Javier; Carter, Lauren; Stewart, Lance; Riddell, Stanley R.; Pepper, Marion; Bernardes, Goncalo J. L.; Dougan, Michael; Garcia, K. Christopher; Baker, David
      Nature (London, United Kingdom) (2019), 565 (7738), 186-191CODEN: NATUAS; ISSN:0028-0836. (Nature Research)
      We describe a de novo computational approach for designing proteins that recapitulate the binding sites of natural cytokines, but are otherwise unrelated in topol. or amino acid sequence. We use this strategy to design mimics of the central immune cytokine interleukin-2 (IL-2) that bind to the IL-2 receptor βγc heterodimer (IL-2Rβγc) but have no binding site for IL-2Rα (also called CD25) or IL-15Rα (also known as CD215). The designs are hyper-stable, bind human and mouse IL-2Rβγc with higher affinity than the natural cytokines, and elicit downstream cell signalling independently of IL-2Rα and IL-15Rα. Crystal structures of the optimized design neoleukin-2/15 (Neo-2/15), both alone and in complex with IL-2Rβγc, are very similar to the designed model. Neo-2/15 has superior therapeutic activity to IL-2 in mouse models of melanoma and colon cancer, with reduced toxicity and undetectable immunogenicity. Our strategy for building hyper-stable de novo mimetics could be applied generally to signalling proteins, enabling the creation of superior therapeutic candidates.
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      https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXmvFWjsL4%253D&md5=b0438f16407dbaec2fc813e7caba9887
    48. 48
      Thompson, M. C.; Wheatley, N. M.; Jorda, J.; Sawaya, M. R.; Gidaniyan, S. D.; Ahmed, H.; Yang, Z.; McCarty, K. N.; Whitelegge, J. P.; Yeates, T. O. Identification of a Unique Fe-S Cluster Binding Site in a Glycyl-Radical Type Microcompartment Shell Protein. J. Mol. Biol. 2014, 426, 3287– 3304,  DOI: 10.1016/j.jmb.2014.07.018
      There is no corresponding record for this reference.
    49. 49
      Zeng, Z.; Boeren, S.; Bhandula, V.; Light, S. H.; Smid, E. J.; Notebaart, R. A.; Abee, T. Bacterial Microcompartments Coupled with Extracellular Electron Transfer Drive the Anaerobic Utilization of Ethanolamine in Listeria monocytogenes. mSystems 2021, 6, e01349-20  DOI: 10.1128/msystems.01349-20
      There is no corresponding record for this reference.
    50. 50
      Ferlez, B.; Markus, S.; Kerfeld, C. A. Glycyl Radical Enzyme-Associated Microcompartments: Redox-Replete Bacterial Organelles. mBio 2019, 10, e02327-18  DOI: 10.1128/mBio.02327-18
      There is no corresponding record for this reference.
    51. 51
      Yan, Y. M.; Tao, H. Y.; He, J. H.; Huang, S.-Y. The HDOCK server for integrated protein–protein docking. Nat. Protoc. 2020, 15, 1829– 1852,  DOI: 10.1038/s41596-020-0312-x
      51
      The HDOCK server for integrated protein-protein docking
      Yan, Yumeng; Tao, Huanyu; He, Jiahua; Huang, Sheng-You
      Nature Protocols (2020), 15 (5), 1829-1852CODEN: NPARDW; ISSN:1750-2799. (Nature Research)
      The HDOCK server is a highly integrated suite of homol. search, template-based modeling, structure prediction, macromol. docking, biol. information incorporation and job management for robust and fast protein-protein docking. With input information for receptor and ligand mols. (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which exptl. information about the protein-protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein-RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two mols. and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min.
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    52. 52
      Case, A. D.; Belfon, K.; Ido, B.-S.; Scott, R. B.; Cerutti, D. S.; Cheatham, T. E., III; Cruzeiro, V. W. D.; Darden, T. A.; Duke, R. E.; Giambasu, G.; Gilson, M. K.; Gohlke, H.; Goetz, A. W.; Harris, R.; Izadi, S.; Izmailov, S. A.; Kasavajhala, K.; Kovalenko, A.; Krasny, R.; Kurtzman, T.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.; L, J.; Luchko, T.; Luo, R.; Man, V.; Merz, K. M.; Miao, Y.; Mikhailovskii, O.; Monard, G.; Nguyen, H.; Onufriev, A.; Pan, F.; Pantano, S.; Qi, R.; Roe, D. R.; Roitberg, A.; Sagui, C.; Schott-Verdugo, S.; Shen, J.; Simmerling, C. L.; Skrynnikov, N. R.; Smith, J.; Swails, J.; Walker, R. C.; Wang, J.; Wilson, L.; Wolf, R. M.; Wu, X.; Xiong, Y.; Xue, Y.; D M AMBER 2020; University of California: New York, 2020.
      There is no corresponding record for this reference.
    53. 53
      Maier, J. A.; Martinez, C.; Kasavajhala, K.; Wickstrom, L.; Hauser, K. E.; Simmerling, C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. J. Chem. Theory Comput. 2015, 11, 3696– 3713,  DOI: 10.1021/acs.jctc.5b00255
      53
      ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
      Maier, James A.; Martinez, Carmenza; Kasavajhala, Koushik; Wickstrom, Lauren; Hauser, Kevin E.; Simmerling, Carlos
      Journal of Chemical Theory and Computation (2015), 11 (8), 3696-3713CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)
      Mol. mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Av. errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a phys. motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reprodn. of NMR χ1 scalar coupling measurements for proteins in soln. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
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    54. 54
      Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25, 1157– 1174,  DOI: 10.1002/jcc.20035
      54
      Development and testing of a general Amber force field
      Wang, Junmei; Wolf, Romain M.; Caldwell, James W.; Kollman, Peter A.; Case, David A.
      Journal of Computational Chemistry (2004), 25 (9), 1157-1174CODEN: JCCHDD; ISSN:0192-8651. (John Wiley & Sons, Inc.)
      We describe here a general Amber force field (GAFF) for org. mols. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most org. and pharmaceutical mols. that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited no. of atom types, but incorporates both empirical and heuristic models to est. force consts. and partial at. charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallog. structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 Å, which is comparable to that of the Tripos 5.2 force field (0.25 Å) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 Å, resp.). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermol. energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 Å and 1.2 kcal/mol, resp. These data are comparable to results from Parm99/RESP (0.16 Å and 1.18 kcal/mol, resp.), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to expt.) is about 0.5 kcal/mol. GAFF can be applied to wide range of mols. in an automatic fashion, making it suitable for rational drug design and database searching.
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    55. 55
      Wang, Z.; Li, J.; Liu, J.; Wang, L.; Lu, Y.; Liu, J. P. Molecular insight into the selective binding between human telomere G-quadruplex and a negatively charged stabilizer. Clin. Exp. Pharmacol. Physiol. 2020, 47, 892– 902,  DOI: 10.1111/1440-1681.13249
      There is no corresponding record for this reference.
    56. 56
      Kim, M.; Kreig, A.; Lee, C. Y.; Rube, H. T.; Calvert, J.; Song, J. S.; Myong, S. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Res. 2016, 44, 4807– 4817,  DOI: 10.1093/nar/gkw272
      56
      Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA
      Kim, Minji; Kreig, Alex; Lee, Chun-Ying; Rube, H. Tomas; Calvert, Jacob; Song, Jun S.; Myong, Sua
      Nucleic Acids Research (2016), 44 (10), 4807-4817CODEN: NARHAD; ISSN:0305-1048. (Oxford University Press)
      G-quadruplex (GQ) is a four-stranded DNA structure that can be formed in guanine-rich sequences. GQ structures have been proposed to regulate diverse biol. processes including transcription, replication, translation and telomere maintenance. Recent studies have demonstrated the existence of GQ DNA in live mammalian cells and a significant no. of potential GQ forming sequences in the human genome. We present a systematic and quant. anal. of GQ folding propensity on a large set of 438 GQ forming sequences in double-stranded DNA by integrating fluorescence measurement, single mol. imaging and computational modeling. We find that short min. loop length and the thymine base are two main factors that lead to high GQ folding propensity. Linear and Gaussian process regression models further validate that the GQ folding potential can be predicted with high accuracy based on the loop length distribution and the nucleotide content of the loop sequences. Our study provides important new parameters that can inform the evaluation and classification of putative GQ sequences in the human genome.
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    57. 57
      Price, D. J.; Charles, L. B. A modified TIP3P water potential for simulation with Ewald summation. J. Chem. Phys. 2004, 121, 10096– 10103,  DOI: 10.1063/1.1808117
      57
      A modified TIP3P water potential for simulation with Ewald summation
      Price, Daniel J.; Brooks, Charles L., III
      Journal of Chemical Physics (2004), 121 (20), 10096-10103CODEN: JCPSA6; ISSN:0021-9606. (American Institute of Physics)
      The charges and Lennard-Jones parameters of the TIP3P water potential have been modified to improve its performance under the common condition for mol. dynamics simulations of using Ewald summation in lieu of relatively short nonbonded truncation schemes. These parameters were optimized under the condition that the hydrogen atoms do not have Lennard-Jones parameters, thus making the model independent of the combining rules used for the calcn. of nonbonded, heteroat. interaction energies, and limiting the no. of Lennard-Jones calcns. required. Under these conditions, this model provides accurate d. (ρ = 0.997 g/mL) and heat of vaporization (ΔHvap = 10.53 kcal/mol) at 25 °C and 1 atm, but also provides improved structure in the second peak of the O-O radial distribution function and improved values for the dielec. const. (.vepsiln.0 = 89) and the diffusion coeff. (D = 4.0×10-5 cm2/s) relative to the original parametrization. Like the original parameterization, however, this model does not show a temp. d. max. Several similar models are considered with the addnl. constraint of trying to match the performance of the optimized potentials for liq. simulation atom force field to that obtained when using the simulation conditions under which it was originally designed, but no model was entirely satisfactory in reproducing the relative difference in free energies of hydration between the model compds., phenol and benzene. Finally, a model that incorporates a long-range correction for truncated Lennard-Jones interactions is presented, which provides a very accurate dielec. const. (.vepsiln.0 = 76), however, the improvement in this est. is on the same order as the uncertainty in the calcn.
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    58. 58
      Li, P. F.; Merz, K. Metal ion modeling using classical mechanics. Chem. Rev. 2017, 117, 1564– 1686,  DOI: 10.1021/acs.chemrev.6b00440
      58
      Metal Ion Modeling Using Classical Mechanics
      Li, Pengfei; Merz, Kenneth M., Jr.
      Chemical Reviews (Washington, DC, United States) (2017), 117 (3), 1564-1686CODEN: CHREAY; ISSN:0009-2665. (American Chemical Society)
      A review. Metal ions play significant roles in numerous fields including chem., geochem., biochem. and materials science. With computational tools increasingly becoming important in chem. research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aq. and solid phases. Herein we review both quantum and classical modeling strategies for metal ion contg. systems that have been developed over the past few decades. This review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond based models. Quantum mech. studies of metal ion contg. systems at the semiempirical, ab initio and d. functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion contg. systems.
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    59. 59
      Cheatham, T. E. I.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins. J. Am. Chem. Soc. 1995, 117, 4193– 4194,  DOI: 10.1021/ja00119a045
      59
      Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins
      Cheatham, T. E. III; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A.
      Journal of the American Chemical Society (1995), 117 (14), 4193-4CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)
      Results from mol. dynamics simulations with AMBER 4.1 of three different, fully solvated, fully charged, macromol. structures-- x-ray derived structures of d(CCAACGTTGG)2 DNA and ubiquitin and an NMR derived r(UUCG) RNA hairpin loop and stem structure-- are presented. We compare the use of the Particle Mesh Ewald (PME) method for the treatment of long range electrostatic interactions to std. charge group based truncation cutoff methods. All of the simulations with PME remain closer to the obsd. structures while maintaining reasonable at. positional fluctuations.
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    60. 60
      Loncharich, R. J.; Brooks, R. B.; Pastor, W. R. Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N′-methylamide. Biopolymers 1992, 32, 523– 535,  DOI: 10.1002/bip.360320508
      60
      Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide
      Loncharich, Richard J.; Brooks, Bernard R.; Pastor, Richard W.
      Biopolymers (1992), 32 (5), 523-35CODEN: BIPMAA; ISSN:0006-3525.
      The rate const. for the transition between the equatorial and axial conformations of N-acetylalanyl-N'-methylamide has been detd. from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is max. at collision frequency γ = 2 ps-1, shows diffusive character for γ ≥ 10 ps-1, but does not approach zero even at γ = 0.01 ps-1. This behavior differs from that found for a one-dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., γ ≈ 2 ps-1). This method is expected to be more efficient than either mol. dynamics in vacuo (which corresponds to LD with γ = 0) or mol. dynamics in solvent (where dynamics is largely diffusive).
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    61. 61
      Berendsen, H. J. C.; Postma, J. P. M.; Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 81, 3684– 3690,  DOI: 10.1063/1.448118
      61
      Molecular dynamics with coupling to an external bath
      Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; DiNola, A.; Haak, J. R.
      Journal of Chemical Physics (1984), 81 (8), 3684-90CODEN: JCPSA6; ISSN:0021-9606.
      In mol. dynamics (MD) simulations, the need often arises to maintain such parameters as temp. or pressure rather than energy and vol., or to impose gradients for studying transport properties in nonequil. MD. A method is described to realize coupling to an external bath with const. temp. or pressure with adjustable time consts. for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyat. mols. involving internal constraints. The influence of coupling time consts. on dynamical variables is evaluated. A leap-frog algorithm is presented for the general case involving constraints with coupling to both a const. temp. and a const. pressure bath.
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    62. 62
      Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J. Mol. Graphics 1996, 14, 33– 38,  DOI: 10.1016/0263-7855(96)00018-5
      62
      VDM: visual molecular dynamics
      Humphrey, William; Dalke, Andrew; Schulten, Klaus
      Journal of Molecular Graphics (1996), 14 (1), 33-8, plates, 27-28CODEN: JMGRDV; ISSN:0263-7855. (Elsevier)
      VMD is a mol. graphics program designed for the display and anal. of mol. assemblies, in particular, biopolymers such as proteins and nucleic acids. VMD can simultaneously display any no. of structures using a wide variety of rendering styles and coloring methods. Mols. are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resoln. raster images of displayed mols. may be produced by generating input scripts for use by a no. of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate mol. dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biol., which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs, VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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  • Supporting Information

    Supporting Information

    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acscatal.4c03672.

    • Chemical synthesis pathway of TBAP (Scheme S1); NMR spectrum of TBAP (Figures S1 and S2); FI-IR spectrum of TBAP (Figure S3); crystal model of TBAP-α and 3D model of α-carboxysome shell (Figure S4); PXRD patterns of TBAP phases, nitrogen adsorption isotherm and desorption isotherm for activated TBAP-α and amorphous TBAP, and SEM images of amorphous TBAP (Figure S5); solid UV–vis absorption spectrum of amorphous TBAP and TBAP-α (Figure S6); (αhν)1/2 versus hν curve and Mott–Schottky plot, diagram of conduction band and valence band of amorphous TBAP and TBAP-α, and cyclic voltammetry plot of TBAP-α (Figure S7); amino acid sequence alignment of α-carboxysome shell proteins (Figure S8); front and side views of the structures of α-carboxysome shell proteins (Figure S9); confocal microscopy images of E. coli cells expressing mCherry-CsoS2C (mCherry-EP) and coexpressing shells and mCherry-csoS2C (C–S) and SDS-PAGE of purified C–S (Figure S10); TEM image of C–S (Figure S11); SEM and confocal microscopy images of pyrene crystals and pyrene crystals with C–S (Figure S12); ζ-potentials of TBAP-α and α-carboxysome shell-encasing proteins (Figure S13); size distribution of H–S revealed by SEM (Figure S14); SDS-PAGE result of H–S purification (Figure S15); immunoblot analysis of purified H–S (Figure S16); colloidal stability of H–S|TBAP-α (Figure S17); photocurrent responses and EIS analysis for TBAP-α and H–S|TBAP-α (Figure S18); H2 production condition optimization of H–S|TBAP-α (Figure S19); photocurrent response and EIS analysis for amorphous TBAP and TBAP-α (Figure S20); wavelength-dependent AQY value of H–S|TBAP-α (Figure S21); H2 evolution of TBAP-α, H–S|TBAP-α, and 1 wt % Pt|TBAP-α (λ > 420 nm) as a function of time (Figure S22); cycling measurements for the photocatalytic hydrogen evolution of H–S|TBAP-α (Figure S23); immunoblot analysis of purified HydA (Fd-HydA-EP) (Figure S24); SEM images (Figure S25) and PXRD pattern (Figure S26) of H–S|TBAP-α after 30 h irradiation; gene maps of used plasmids (Figure S27); crystal data and structure refinement of TBAP-α (Table S1); protein components in recombinant α-carboxysomes from E. coli (Table S2); statistics of residues for TBAP-α and CsoS1A protein binding calculated by MD simulations (Tables S3 and S4); estimated fluorescence lifetimes of TBAP-α and H–S|TBAP-α (Table S5); a list of hydrogen evolution reaction conditions in this work (Table S6); a comparison of the H–S|TBAP-α assembly performance with the related state-of-the-art photocatalysts (Table S7); primers used for pCDFDuet-mCherry-CS2 plasmid construction (Table S8); and gene sequences of used plasmids (Table S9). (PDF)


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