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    Theoretical Studies of Short Polyproline Systems: Recalibration of a Molecular Ruler†
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    Quantum Theory Project, University of Florida, P.O. Box 118435, Gainesville, Florida 32611-8435, Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, and Department of Chemistry, Hope College, Holland, Michigan 49422-9000
    †Part of the “George C. Schatz Festschrift”.
    * Address correspondence to this author.
    ‡Quantum Theory Project, University of Florida.
    §Department of Chemistry, University of Florida.
    ⊥Department of Chemistry, Hope College.
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    The Journal of Physical Chemistry A

    Cite this: J. Phys. Chem. A 2009, 113, 16, 4639–4646
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    https://doi.org/10.1021/jp811395r
    Published March 5, 2009
    Copyright © 2009 American Chemical Society
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    Abstract

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    FRET experiments enable studies of the chemical and physical properties of individual molecules, which has long been a dream of chemists. However, these modern experimental techniques are still limited by the lack of information about the dynamic behavior of the fluorescent labels as well as by the use of dipole−dipole approximation even at short donor-to-acceptor distances. Our results help to suggest that these assumptions need to be carefully considered when designing experiments. We show that at short donor−acceptor separation, dipole−dipole approximation breaks down and Förster theory fails and cannot be used to obtain correct distances. We also explicitly demonstrate that dyes’ linkers allow for a lot of flexibility in the fluorescent label orientation and position resulting in distances much shorter than assumed earlier.

    Copyright © 2009 American Chemical Society

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    Supporting Information

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    Tables of the dye force field parameters and charges. This material is available free of charge via the Internet at http://pubs.acs.org.

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    This article is cited by 36 publications.

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    3. Ying-Chen Lai, Chih-Ying Lin, Meng-Ru Chung, Pei-Yu Hung, Jia-Cherng Horng, I-Chia Chen, and Li-Kang Chu . Distance-Dependent Excited-State Electron Transfer from Tryptophan to Gold Nanoparticles through Polyproline Helices. The Journal of Physical Chemistry C 2017, 121 (9) , 4882-4890. https://doi.org/10.1021/acs.jpcc.6b12640
    4. Yuko Otani, Satoshi Watanabe, Tomohiko Ohwada, and Akio Kitao . Molecular Dynamics Study of Nitrogen-Pyramidalized Bicyclic β-Proline Oligomers: Length-Dependent Convergence to Organized Structures. The Journal of Physical Chemistry B 2017, 121 (1) , 100-109. https://doi.org/10.1021/acs.jpcb.6b10668
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    6. Gary Beane, Klaus Boldt, Nicholas Kirkwood, and Paul Mulvaney . Energy Transfer between Quantum Dots and Conjugated Dye Molecules. The Journal of Physical Chemistry C 2014, 118 (31) , 18079-18086. https://doi.org/10.1021/jp502033d
    7. Siyuan Wang, Yuko Otani, Xin Liu, Masatoshi Kawahata, Kentaro Yamaguchi, and Tomohiko Ohwada . Robust trans-Amide Helical Structure of Oligomers of Bicyclic Mimics of β-Proline: Impact of Positional Switching of Bridgehead Substituent on Amide cis–trans Equilibrium. The Journal of Organic Chemistry 2014, 79 (11) , 5287-5300. https://doi.org/10.1021/jo500916j
    8. Simon Sindbert, Stanislav Kalinin, Hien Nguyen, Andrea Kienzler, Lilia Clima, Willi Bannwarth, Bettina Appel, Sabine Müller, and Claus A. M. Seidel . Accurate Distance Determination of Nucleic Acids via Förster Resonance Energy Transfer: Implications of Dye Linker Length and Rigidity. Journal of the American Chemical Society 2011, 133 (8) , 2463-2480. https://doi.org/10.1021/ja105725e
    9. Francis O. Talbot, Anthony Rullo, Huihui Yao, and Rebecca A. Jockusch. Fluorescence Resonance Energy Transfer in Gaseous, Mass-Selected Polyproline Peptides. Journal of the American Chemical Society 2010, 132 (45) , 16156-16164. https://doi.org/10.1021/ja1067405
    10. Charles E. Wickersham, Kevin J. Cash, Shawn H. Pfeil, Irina Bruck, Daniel L. Kaplan, Kevin W. Plaxco and Everett A. Lipman . Tracking a Molecular Motor with a Nanoscale Optical Encoder. Nano Letters 2010, 10 (3) , 1022-1027. https://doi.org/10.1021/nl904192m
    11. Thomas-Otavio Peulen. Exploring Time-Resolved Fluorescence Data: A Software Solution for Model Generation and Analysis. Spectroscopy Journal 2025, 3 (2) , 16. https://doi.org/10.3390/spectroscj3020016
    12. Daniel Gonzalo, Lorenzo Cupellini, Carles Curutchet. On the breakdown of Förster energy transfer theory due to solvent effects: atomistic simulations unveil distance-dependent dielectric screening in calmodulin. Chemical Science 2025, 16 (8) , 3693-3704. https://doi.org/10.1039/D4SC07679F
    13. Sara M. A. Waly, Andrew C. Benniston, Anthony Harriman. Deducing the conformational space for an octa-proline helix. Chemical Science 2024, 15 (5) , 1657-1671. https://doi.org/10.1039/D3SC05287G
    14. Kazuhiro J. Fujimoto, Tomoya Miyashita, Takehisa Dewa, Takeshi Yanai. Determination of FRET orientation factor between artificial fluorophore and photosynthetic light-harvesting 2 complex (LH2). Scientific Reports 2022, 12 (1) https://doi.org/10.1038/s41598-022-19375-2
    15. Annamaria Panniello, Mariachiara Trapani, Massimiliano Cordaro, Carlo Nazareno Dibenedetto, Raffaele Tommasi, Chiara Ingrosso, Elisabetta Fanizza, Roberto Grisorio, Elisabetta Collini, Angela Agostiano, Maria Lucia Curri, Maria Angela Castriciano, Marinella Striccoli. High‐Efficiency FRET Processes in BODIPY‐Functionalized Quantum Dot Architectures. Chemistry – A European Journal 2021, 27 (7) , 2371-2380. https://doi.org/10.1002/chem.202003574
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    17. Alexander Kyrychenko, Mykola V. Rodnin, Chiranjib Ghatak, Alexey S. Ladokhin. Joint refinement of FRET measurements using spectroscopic and computational tools. Analytical Biochemistry 2017, 522 , 1-9. https://doi.org/10.1016/j.ab.2017.01.011
    18. Vladimir Kubyshkin, Nediljko Budisa. Construction of a polyproline structure with hydrophobic exterior using octahydroindole-2-carboxylic acid. Organic & Biomolecular Chemistry 2017, 15 (3) , 619-627. https://doi.org/10.1039/C6OB02306A
    19. Frank R. Beierlein, Miguel Paradas Palomo, Dmitry I. Sharapa, Oleksii Zozulia, Andriy Mokhir, Timothy Clark, . DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes. PLOS ONE 2016, 11 (7) , e0160229. https://doi.org/10.1371/journal.pone.0160229
    20. Luca Garbuio, Bartosz Lewandowski, Patrick Wilhelm, Ludmila Ziegler, Maxim Yulikov, Helma Wennemers, Gunnar Jeschke. Shape Persistence of Polyproline II Helical Oligoprolines. Chemistry – A European Journal 2015, 21 (30) , 10747-10753. https://doi.org/10.1002/chem.201501190
    21. Nadav Amdursky. Electron Transfer across Helical Peptides. ChemPlusChem 2015, 80 (7) , 1075-1095. https://doi.org/10.1002/cplu.201500121
    22. Robert B. Best, Hagen Hofmann, Daniel Nettels, Benjamin Schuler. Quantitative Interpretation of FRET Experiments via Molecular Simulation: Force Field and Validation. Biophysical Journal 2015, 108 (11) , 2721-2731. https://doi.org/10.1016/j.bpj.2015.04.038
    23. Ali Ghavami, Erik Van der Giessen, Patrick R. Onck. Towards a Coarse-Grained Model for Unfolded Proteins. 2013, 3-10. https://doi.org/10.1007/978-94-007-5464-5_1
    24. Delphine Hablot, Raymond Ziessel, Mohammed A. H. Alamiry, Effat Bahraidah, Anthony Harriman. Nanomechanical properties of molecular-scale bridges as visualised by intramolecular electronic energy transfer. Chem. Sci. 2013, 4 (1) , 444-453. https://doi.org/10.1039/C2SC21505E
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    27. Søren Preus, L. Marcus Wilhelmsson. Advances in Quantitative FRET‐Based Methods for Studying Nucleic Acids. ChemBioChem 2012, 13 (14) , 1990-2001. https://doi.org/10.1002/cbic.201200400
    28. Mohammed A. H. Alamiry, Jerry P. Hagon, Anthony Harriman, Thomas Bura, Raymond Ziessel. Resolving the contribution due to Förster-type intramolecular electronic energy transfer in closely coupled molecular dyads. Chem. Sci. 2012, 3 (4) , 1041-1048. https://doi.org/10.1039/C2SC00948J
    29. Daniel Badali, Claudiu C. Gradinaru. The effect of Brownian motion of fluorescent probes on measuring nanoscale distances by Förster resonance energy transfer. The Journal of Chemical Physics 2011, 134 (22) https://doi.org/10.1063/1.3598109
    30. Martin Hoefling, Nicola Lima, Dominik Haenni, Claus A. M. Seidel, Benjamin Schuler, Helmut Grubmüller, . Structural Heterogeneity and Quantitative FRET Efficiency Distributions of Polyprolines through a Hybrid Atomistic Simulation and Monte Carlo Approach. PLoS ONE 2011, 6 (5) , e19791. https://doi.org/10.1371/journal.pone.0019791
    31. Evelyne Deplazes, Dylan Jayatilaka, Ben Corry. Testing the use of molecular dynamics to simulate fluorophore motions and FRET. Physical Chemistry Chemical Physics 2011, 13 (23) , 11045. https://doi.org/10.1039/c1cp20447e
    32. Zhinan Jin, Kenneth A. Johnson. Role of a GAG Hinge in the Nucleotide-induced Conformational Change Governing Nucleotide Specificity by T7 DNA Polymerase. Journal of Biological Chemistry 2011, 286 (2) , 1312-1322. https://doi.org/10.1074/jbc.M110.156737
    33. Alexandra Olaya-Castro, Gregory D. Scholes. Energy transfer from Förster–Dexter theory to quantum coherent light-harvesting. International Reviews in Physical Chemistry 2011, 30 (1) , 49-77. https://doi.org/10.1080/0144235X.2010.537060
    34. Mahmoud Moradi, Jung‐Goo Lee, Volodymyr Babin, Christopher Roland, Celeste Sagui. Free energy and structure of polyproline peptides: An ab initio and classical molecular dynamics investigation. International Journal of Quantum Chemistry 2010, 110 (15) , 2865-2879. https://doi.org/10.1002/qua.22875
    35. Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Celeste Sagui. A classical molecular dynamics investigation of the free energy and structure of short polyproline conformers. The Journal of Chemical Physics 2010, 133 (12) https://doi.org/10.1063/1.3481087
    36. D. Hofmann, T. Körzdörfer, S. Kümmel. Energy transfer and Förster’s dipole coupling approximation investigated in a real-time Kohn-Sham scheme. Physical Review A 2010, 82 (1) https://doi.org/10.1103/PhysRevA.82.012509
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    The Journal of Physical Chemistry A

    Cite this: J. Phys. Chem. A 2009, 113, 16, 4639–4646
    Click to copy citationCitation copied!
    https://doi.org/10.1021/jp811395r
    Published March 5, 2009
    Copyright © 2009 American Chemical Society
    Request reuse permissions

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