ACS Publications. Most Trusted. Most Cited. Most Read
Structural Evidence for an Enolate Intermediate in GFP Fluorophore Biosynthesis
My Activity

Figure 1Loading Img
    Communication

    Structural Evidence for an Enolate Intermediate in GFP Fluorophore Biosynthesis
    Click to copy article linkArticle link copied!

    View Author Information
    Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
    Other Access Options

    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2006, 128, 10, 3166–3168
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ja0552693
    Published February 16, 2006
    Copyright © 2006 American Chemical Society

    Abstract

    Click to copy section linkSection link copied!
    Abstract Image

    The Aequorea victoria green fluorescent protein (GFP) creates a fluorophore from its component amino acids Ser65, Tyr66, and Gly67 through a remarkable post-translational modification, involving spontaneous peptide backbone cyclization, dehydration, and oxidation reactions. Here we test and extend the understanding of fluorophore biosynthesis by coupling chemical reduction and anaerobic methodologies with kinetic analyses and protein structure determination. Two high-resolution structures of dithionite-treated GFP variants reveal a previously uncharacterized enolate intermediate form of the chromophore that is viable in generating a fluorophore (t1/2 = 39 min-1) upon exposure to air. Isolation of this enolate intermediate will now allow specific probing of the rate-limiting oxidation step for fluorophore biosynthesis in GFP and its red fluorescent protein homologues. Such targeted characterizations may lead to the design of faster maturing proteins with enhanced applications in biotechnology and cell biology. Moreover, our results reveal how the GFP protein environment mimics enzyme systems, by stabilizing an otherwise high energy enolate intermediate to achieve its post-translational modification.

    Copyright © 2006 American Chemical Society

    Read this article

    To access this article, please review the available access options below.

    Get instant access

    Purchase Access

    Read this article for 48 hours. Check out below using your ACS ID or as a guest.

    Recommended

    Access through Your Institution

    You may have access to this article through your institution.

    Your institution does not have access to this content. Add or change your institution or let them know you’d like them to include access.

    *

    In papers with more than one author, the asterisk indicates the name of the author to whom inquiries about the paper should be addressed.

    Cited By

    Click to copy section linkSection link copied!

    This article is cited by 49 publications.

    1. Ismael A. Elayan, Alex Brown. Non-Degenerate Two-Photon Absorption of Fluorescent Protein Chromophores. The Journal of Physical Chemistry A 2024, 128 (36) , 7511-7523. https://doi.org/10.1021/acs.jpca.3c08402
    2. Sanjeev Kumar, M. Achanna Venkatesha, Padmanabhan Balaram. Mechanistic Investigations on N–Cα Bond Cleavages in Dibasic Peptides Containing Internal Lys and Arg Residues. Journal of the American Society for Mass Spectrometry 2022, 33 (9) , 1598-1606. https://doi.org/10.1021/jasms.2c00055
    3. Justin Nwafor, Christian Salguero, Franceine Welcome, Sercan Durmus, Rachel N. Glasser, Marc Zimmer, Tanya L. Schneider. Why Are Gly31, Gly33, and Gly35 Highly Conserved in All Fluorescent Proteins?. Biochemistry 2021, 60 (49) , 3762-3770. https://doi.org/10.1021/acs.biochem.1c00587
    4. Alexander V. Nemukhin, Bella L. Grigorenko, Maria G. Khrenova, Anna I. Krylov. Computational Challenges in Modeling of Representative Bioimaging Proteins: GFP-Like Proteins, Flavoproteins, and Phytochromes. The Journal of Physical Chemistry B 2019, 123 (29) , 6133-6149. https://doi.org/10.1021/acs.jpcb.9b00591
    5. Bella L. Grigorenko, Anna I. Krylov, and Alexander V. Nemukhin . Molecular Modeling Clarifies the Mechanism of Chromophore Maturation in the Green Fluorescent Protein. Journal of the American Chemical Society 2017, 139 (30) , 10239-10249. https://doi.org/10.1021/jacs.7b00676
    6. Yingying Ma, Hao Zhang, Qiao Sun, and Sean C. Smith . New Insights on the Mechanism of Cyclization in Chromophore Maturation of Wild-Type Green Fluorescence Protein: A Computational Study. The Journal of Physical Chemistry B 2016, 120 (24) , 5386-5394. https://doi.org/10.1021/acs.jpcb.6b04406
    7. Yingying Ma, Qiao Sun, Zhen Li, Jian-Guo Yu, and Sean C. Smith . Theoretical Studies of Chromophore Maturation in the Wild-Type Green Fluorescent Protein: ONIOM(DFT:MM) Investigation of the Mechanism of Cyclization. The Journal of Physical Chemistry B 2012, 116 (4) , 1426-1436. https://doi.org/10.1021/jp208749v
    8. Akihiko Ishii, Yuki Yamaguchi, and Norio Nakata . Fluorescent 3-Methylene-2,3-Dihydrochalcogenophenes Incorporated in a Rigid Dibenzobarrelene Skeleton. Organic Letters 2011, 13 (14) , 3702-3705. https://doi.org/10.1021/ol2013523
    9. Yingying Ma, Qiao Sun, Hong Zhang, Liang Peng, Jian-Guo Yu and Sean C. Smith . The Mechanism of Cyclization in Chromophore Maturation of Green Fluorescent Protein: A Theoretical Study. The Journal of Physical Chemistry B 2010, 114 (29) , 9698-9705. https://doi.org/10.1021/jp1039817
    10. Rita L. Strack, Daniel E. Strongin, Laurens Mets, Benjamin S. Glick and Robert J. Keenan . Chromophore Formation in DsRed Occurs by a Branched Pathway. Journal of the American Chemical Society 2010, 132 (24) , 8496-8505. https://doi.org/10.1021/ja1030084
    11. Ai Shinobu and Noam Agmon. Mapping Proton Wires in Proteins: Carbonic Anhydrase and GFP Chromophore Biosynthesis. The Journal of Physical Chemistry A 2009, 113 (26) , 7253-7266. https://doi.org/10.1021/jp8102047
    12. Lauren J. Pouwels, Liping Zhang, Nam H. Chan, Pieter C. Dorrestein and Rebekka M. Wachter . Kinetic Isotope Effect Studies on the de Novo Rate of Chromophore Formation in Fast- and Slow-Maturing GFP Variants. Biochemistry 2008, 47 (38) , 10111-10122. https://doi.org/10.1021/bi8007164
    13. Rebekka M. Wachter. Chromogenic Cross-Link Formation in Green Fluorescent Protein. Accounts of Chemical Research 2007, 40 (2) , 120-127. https://doi.org/10.1021/ar040086r
    14. Yury A. Gubarev, Elena S. Yurina, Natalia Sh. Lebedeva. Detection of green fluorescence in serum albumin upon excitation with 375 nm light: revealing new fluorescent properties. Mendeleev Communications 2024, 34 (3) , 421-423. https://doi.org/10.1016/j.mencom.2024.04.035
    15. Rémi Hocq, Sara Bottone, Arnaud Gautier, Stefan Pflügl. A fluorescent reporter system for anaerobic thermophiles. Frontiers in Bioengineering and Biotechnology 2023, 11 https://doi.org/10.3389/fbioe.2023.1226889
    16. Konstantin M. Boyko, Maria G. Khrenova, Alena Y. Nikolaeva, Pavel V. Dorovatovskii, Anna V. Vlaskina, Oksana M. Subach, Vladimir O. Popov, Fedor V. Subach. Combined Structural and Computational Study of the mRubyFT Fluorescent Timer Locked in Its Blue Form. International Journal of Molecular Sciences 2023, 24 (9) , 7906. https://doi.org/10.3390/ijms24097906
    17. Rochelle D. Ahmed, Husam Sabah Auhim, Harley L. Worthy, D. Dafydd Jones. Fluorescent Proteins: Crystallization, Structural Determination, and Nonnatural Amino Acid Incorporation. 2023, 99-119. https://doi.org/10.1007/978-1-0716-2667-2_5
    18. Asuma Janeena, Velmurugan Nagabalaji, Prem Suresh, Kamini Numbi Ramudu, Shanmugam Venkatachalam Srinivasan, Ganesh Shanmugam, Niraikulam Ayyadurai. Engineering microbial cells with metal chelating hydroxylated unnatural amino acids for removable of synthetic pollutants from water. Chemosphere 2023, 311 , 136756. https://doi.org/10.1016/j.chemosphere.2022.136756
    19. Abigail Roldán‐Salgado, Liya Muslinkina, Sergei Pletnev, Nadya Pletneva, Vladimir Pletnev, Paul Gaytán. A novel violet fluorescent protein contains a unique oxidized tyrosine as the simplest chromophore ever reported in fluorescent proteins. Protein Science 2022, 31 (3) , 688-700. https://doi.org/10.1002/pro.4265
    20. Songtao Ye, Yuqi Tang, Xin Zhang. Principles, modulation, and applications of fluorescent protein chromophores. Chemical Physics Reviews 2022, 3 (1) https://doi.org/10.1063/5.0080417
    21. Mayilvahanan Aarthy, Augustine George, Niraikulam Ayyadurai. Beyond protein tagging: Rewiring the genetic code of fluorescent proteins – A review. International Journal of Biological Macromolecules 2021, 191 , 840-851. https://doi.org/10.1016/j.ijbiomac.2021.09.108
    22. Husam Sabah Auhim, Bella L. Grigorenko, Tessa K. Harris, Ozan E. Aksakal, Igor V. Polyakov, Colin Berry, Gabriel dos Passos Gomes, Igor V. Alabugin, Pierre J. Rizkallah, Alexander V. Nemukhin, D. Dafydd Jones. Stalling chromophore synthesis of the fluorescent protein Venus reveals the molecular basis of the final oxidation step. Chemical Science 2021, 12 (22) , 7735-7745. https://doi.org/10.1039/D0SC06693A
    23. Nadya V. Pletneva, Eugene G. Maksimov, Elena A. Protasova, Anastasia V. Mamontova, Tatiana R. Simonyan, Rustam H. Ziganshin, Konstantin A. Lukyanov, Liya Muslinkina, Sergei Pletnev, Alexey M. Bogdanov, Vladimir Z. Pletnev. Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Computational and Structural Biotechnology Journal 2021, 19 , 2950-2959. https://doi.org/10.1016/j.csbj.2021.05.017
    24. Alexey A. Pakhomov, Anastasiya Yu. Frolova, Valentin M. Tabakmakher, Anton O. Chugunov, Roman G. Efremov, Vladimir I. Martynov. Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies. Journal of Photochemistry and Photobiology B: Biology 2020, 206 , 111853. https://doi.org/10.1016/j.jphotobiol.2020.111853
    25. Jun Guo, Srinivasan Ramachandran, Ruibo Zhong, Ratnesh Lal, Feng Zhang. Generating Cyan Fluorescence with De Novo Tripeptides: An In Vitro Mutation Study on the Role of Single Amino Acid Residues and Their Sequence. ChemBioChem 2019, 20 (18) , 2324-2330. https://doi.org/10.1002/cbic.201900166
    26. N. V. Pletneva, E. A. Goryacheva, I. V. Artemyev, S. F. Arkhipova, V. Z. Pletnev. Structure of Chromophores in GFP-Like Proteins: X-Ray Data. Russian Journal of Bioorganic Chemistry 2019, 45 (3) , 187-194. https://doi.org/10.1134/S106816201903004X
    27. Liya Muslinkina, Abigail Roldán-Salgado, Paul Gaytán, Víctor R. Juárez-González, Enrique Rudiño, Nadya Pletneva, Vladimir Pletnev, Zbigniew Dauter, Sergei Pletnev. Structural Factors Enabling Successful GFP-Like Proteins with Alanine as the Third Chromophore-Forming Residue. Journal of Molecular Biology 2019, 431 (7) , 1397-1408. https://doi.org/10.1016/j.jmb.2019.02.013
    28. Bella L. Grigorenko, Ekaterina D. Kots, Anna I. Krylov, Alexander V. Nemukhin. Modeling of the glycine tripeptide cyclization in the Ser65Gly/Tyr66Gly mutant of green fluorescent protein. Mendeleev Communications 2019, 29 (2) , 187-189. https://doi.org/10.1016/j.mencom.2019.03.024
    29. Hossein Roohi, Roghayeh Nokhostin. Molecular engineering of the photo switching in the ortho chromophores of the nanostructured green fluorescence protein. Journal of Luminescence 2018, 196 , 406-424. https://doi.org/10.1016/j.jlumin.2017.12.056
    30. Teerapong Pirojsirikul, Andreas W. Götz, John Weare, Ross C. Walker, Karol Kowalski, Marat Valiev. Combined quantum‐mechanical molecular mechanics calculations with NWChem and AMBER: Excited state properties of green fluorescent protein chromophore analogue in aqueous solution. Journal of Computational Chemistry 2017, 38 (18) , 1631-1639. https://doi.org/10.1002/jcc.24804
    31. Yingying Ma, Qiao Sun, Sean C. Smith. The mechanism of oxidation in chromophore maturation of wild-type green fluorescent protein: a theoretical study. Physical Chemistry Chemical Physics 2017, 19 (20) , 12942-12952. https://doi.org/10.1039/C6CP07983K
    32. Abigail Roldán-Salgado, Celidee Sánchez-Barreto, Paul Gaytán. LanFP10-A, first functional fluorescent protein whose chromophore contains the elusive mutation G67A. Gene 2016, 592 (2) , 281-290. https://doi.org/10.1016/j.gene.2016.07.026
    33. Gregor Jung. Fluorescent Proteins: The Show Must Go On!. 2016, 55-90. https://doi.org/10.1002/9781119179320.ch4
    34. Yingying Ma, Jian-Guo Yu, Qiao Sun, Zhen Li, Sean C. Smith. The mechanism of dehydration in chromophore maturation of wild-type green fluorescent protein: A theoretical study. Chemical Physics Letters 2015, 631-632 , 42-46. https://doi.org/10.1016/j.cplett.2015.04.061
    35. Scott Classen, Greg L. Hura, James M. Holton, Robert P. Rambo, Ivan Rodic, Patrick J. McGuire, Kevin Dyer, Michal Hammel, George Meigs, Kenneth A. Frankel, John A. Tainer. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source. Journal of Applied Crystallography 2013, 46 (1) , 1-13. https://doi.org/10.1107/S0021889812048698
    36. Amit Choudhary, Kimberli J. Kamer, Ronald T. Raines. A conserved interaction with the chromophore of fluorescent proteins. Protein Science 2012, 21 (2) , 171-177. https://doi.org/10.1002/pro.762
    37. Binsen Li, Ramza Shahid, Paola Peshkepija, Marc Zimmer. Water diffusion in and out of the β-barrel of GFP and the fast maturing fluorescent protein, TurboGFP. Chemical Physics 2012, 392 (1) , 143-148. https://doi.org/10.1016/j.chemphys.2011.11.001
    38. Ryo Iizuka, Mai Yamagishi-Shirasaki, Takashi Funatsu. Kinetic study of de novo chromophore maturation of fluorescent proteins. Analytical Biochemistry 2011, 414 (2) , 173-178. https://doi.org/10.1016/j.ab.2011.03.036
    39. Jasper J. van Thor. Photoconversion of the Green Fluorescent Protein and Related Proteins. 2011, 183-216. https://doi.org/10.1007/4243_2011_20
    40. Li‐June Ming. Biological Aspects of Metal Enolates. 2010https://doi.org/10.1002/9780470682531.pat0427
    41. U. Terranova, R. Nifosı`. A role for molecular compression in the post-translational formation of the Green Fluorescent Protein chromophore. Chemical Physics 2010, 371 (1-3) , 76-83. https://doi.org/10.1016/j.chemphys.2010.04.006
    42. Nadya V. Pletneva, Vladimir Z. Pletnev, Konstantin A. Lukyanov, Nadya G. Gurskaya, Ekaterina A. Goryacheva, Vladimir I. Martynov, Alexander Wlodawer, Zbigniew Dauter, Sergei Pletnev. Structural Evidence for a Dehydrated Intermediate in Green Fluorescent Protein Chromophore Biosynthesis. Journal of Biological Chemistry 2010, 285 (21) , 15978-15984. https://doi.org/10.1074/jbc.M109.092320
    43. Fabienne Merola, Bernard Levy, Isabelle Demachy, Helene Pasquier. Photophysics and Spectroscopy of Fluorophores in the Green Fluorescent Protein Family. 2010, 347-383. https://doi.org/10.1007/978-3-642-04702-2_11
    44. Benjamin T. Andrews, Melinda Roy, Patricia A. Jennings. Chromophore Packing Leads to Hysteresis in GFP. Journal of Molecular Biology 2009, 392 (1) , 218-227. https://doi.org/10.1016/j.jmb.2009.06.072
    45. A. A. Pakhomov, V. I. Martynov. Posttranslational chemistry of proteins of the GFP family. Biochemistry (Moscow) 2009, 74 (3) , 250-259. https://doi.org/10.1134/S000629790903002X
    46. Stephen R. Meech. Excited state reactions in fluorescent proteins. Chemical Society Reviews 2009, 38 (10) , 2922. https://doi.org/10.1039/b820168b
    47. Timothy D. Craggs. Green fluorescent protein: structure, folding and chromophore maturation. Chemical Society Reviews 2009, 38 (10) , 2865. https://doi.org/10.1039/b903641p
    48. Alexey A. Pakhomov, Vladimir I. Martynov. GFP Family: Structural Insights into Spectral Tuning. Chemistry & Biology 2008, 15 (8) , 755-764. https://doi.org/10.1016/j.chembiol.2008.07.009
    49. S James Remington. Fluorescent proteins: maturation, photochemistry and photophysics. Current Opinion in Structural Biology 2006, 16 (6) , 714-721. https://doi.org/10.1016/j.sbi.2006.10.001

    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2006, 128, 10, 3166–3168
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ja0552693
    Published February 16, 2006
    Copyright © 2006 American Chemical Society

    Article Views

    1113

    Altmetric

    -

    Citations

    Learn about these metrics

    Article Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.

    Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.

    The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated.