Triple-decker motif for red-shifted fluorescent protein mutants

Journal of Physical Chemistry Letters

Volumn 4, Issue 10, 2013, Pages 1743-1747

  Grigorenko, Bella L ^a   Nemukhin, Alexander V ^a,b   Polyakov, Igor V ^a   Krylov, Anna I ^c  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b EMANUEL INSTITUTE OF BIOCHEMICAL PHYSICS   (Russian Federation)

^c UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

stacking; computational design; fluorescent proteins; optical spectra; structure

Indexed keywords

ABSORPTION AND EMISSIONS; COMPUTATIONAL DESIGN; ELECTRONIC STRUCTURE CALCULATIONS; EXTENDED CONJUGATION; FLUORESCENT PROTEIN; FLUORESCENT PROTEINS (FPS); OPTICAL SPECTRA; STACKING INTERACTION;

AMINO ACIDS; DOPPLER EFFECT; ELECTRONIC STRUCTURE; FLUORESCENCE; PHOTOBLEACHING; PROTEINS; STRUCTURE (COMPOSITION);

CHROMOPHORES;

EID: 84878081496     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz4006288     Document Type: Article

References (34)

1. Tsien, R. Y. The Green Fluorescent Protein Annu. Rev. Biochem. 1998, 67, 509-544 (Pubitemid 28411137)
2. Zimmer, M. Green Fluorescent Protein (GFP): Applications, Structure, and Related Photophysical Behavior Chem. Rev. 2002, 102, 759-781 (Pubitemid 35377613)
3. Remington, S. J. Fluorescent Proteins: Maturation, Photochemistry and Photophysics Curr. Opin. Struct. Biol. 2006, 16, 714-721 (Pubitemid 44827725)
4. Craggs, T. D. Green Fluorescent Protein: Structure, Folding and Chromophore Maturation Chem. Soc. Rev. 2009, 38, 2865-2875
5. van Thor, J. J. Photoreactions and Dynamics of the Green Fluorescent Protein Chem. Soc. Rev. 2009, 38, 2935-2950
6. Tonge, P. J.; Meech, S. R. Excited State Dynamics in the Green Fluorescent Protein J. Photochem. Photobiol., A 2009, 205, 1-11
7. Remington, S. J. Green Fluorescent Protein: A Perspective Protein Sci. 2011, 20, 1509-1519
8. Subach, F. M.; Verkhusha, V. V. Chromophore Transformations in Red Fluorescent Proteins Chem. Rev. 2012, 112, 4308-4327
9. Shcherbakova, D. M.; Subach, O. M.; Verkhusha, V. V. Red Fluorescent Proteins: Advanced Imaging Applications and Future Design Angew. Chem., Int. Ed. 2012, 51, 10724-1073
10. Subach, F. M.; Piatkevich, K. D.; Verkhusha, V. V. Directed Molecular Evolution to Design Advanced Red Fluorescent Proteins Nat. Methods 2011, 8, 1019-1026
11. Baird, G. S.; Zacharias, D. A.; Tsien, R. Y. Biochemistry, Mutagenesis, and Oligomerization of DsRed, a Red Fluorescent Protein from Coral Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 11984-11989
12. Shu, X.; Shaner, N. C.; Yarbrough, C. A.; Tsien, R. Y.; Remington, S. J. Novel Chromophores and Buried Charges Control Color in mFruits Biochemistry 2006, 45, 9639-9647 (Pubitemid 44257411)
13. Laurent, A. D.; Mironov, V. A.; Chapagain, P. P.; Nemukhin, A. V.; Krylov, A. I. Exploring Structural and Optical Properties of Fluorescent Proteins by Squeezing: Modeling High-Pressure Effects on the mStrawberry and mCherry Red Fluorescent Proteins J. Phys. Chem. B 2012, 116, 12426-12440
14. Chapagain, P. P.; Regmi, C.; Castillo, W. Fluorescent Protein Barrel Fluctuations and Oxygen Diffusion Pathways in mCherry J. Chem. Phys. 2011, 135, 235101/1-235101/6
15. Wachter, R. M.; Elsliger, M. A.; Kallio, K.; Hanson, G. T.; Remington, S. J. Structural Basis of Spectral Shifts in the Yellow-Emission Variants of Green Fluorescent Protein Structure 1998, 6, 1267-1277 (Pubitemid 28485959)
16. Griesbeck, O.; Baird, G. S.; Campbell, R. E.; Zacharias, D. A.; Tsien, R. Y. Reducing the Environmental Sensitivity of Yellow Fluorescent Protein. Mechanism and Applications J. Biol. Chem. 2001, 276, 29188-29194
17. Chica, R. A.; Moore, M. M.; Allen, B. D.; Mayo, S. L. Generation of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 20257-20262
18. Morozova, K. S.; Piatkevich, K. D.; Gould, T. J.; Zhang, J.; Bewersdorf, J.; Verkhusha, V. V. Far-Red Fluorescent Protein Excitable with Red Lasers for Flow Cytometry and Superresolution STED Nanoscopy Biophys. J. 2010, 99, L13-L15
19. Grigorenko, B. L.; Nemukhin, A. V.; Topol, I. A.; Burt, S. K. Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique: Proposal of Flexible Fragments J. Phys. Chem. A 2002, 106, 10663-10672 (Pubitemid 35361217)
20. Nemukhin, A. V.; Grigorenko, B. L.; Topol, I. A.; Burt, S. K. Flexible Effective Fragment QM/MM Method: Validation through the Challenging Tests J. Comput. Chem. 2003, 24, 1410-1420
21. Warshel, A.; Levitt, M. Theoretical Studies of Enzymatic Reactions: Dielectric Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme J. Mol. Biol. 1976, 103, 227-249
22. Granovsky, A. A. Extended Multi-Configuration Quasi-Degenerate Perturbation Theory: The New Approach to Multi-State Multi-Reference Perturbation Theory J. Chem. Phys. 2011, 134, 214113/1-214113/14
23. Gozem, S.; Huntress, M.; Schapiro, I.; Lindh, R.; Granovsky, A.; Angeli, C.; Olivucci, M. Dynamic Electron Correlation Effects on the Excited State Potential Energy of a Retinal Chromophore Model J. Chem. Theory Comput. 2012, 8, 4069-4080
24. Rhee, Y. M.; Head-Gordon, M. Scaled Second-Order Perturbation Corrections to Configuration Interaction Singles: Efficient and Reliable Excitation Energy Methods J. Phys. Chem. A 2007, 111, 5314-5326 (Pubitemid 47152464)
25. Ormö, M.; Cubitt, A. B.; Kallio, K.; Gross, L. A.; Tsien, R. Y.; Remington, S. J. Crystal Structure of the Aequorea Victoria Green Fluorescent Protein Science 1996, 273, 1392-1395 (Pubitemid 26296528)
26. Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Ultra-Fast Excited State Dynamics in Green Fluorescent Protein: Multiple States and Proton Transfer Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8362-8367 (Pubitemid 26269563)
27. Brejc, K.; Sixma, T. K.; Kitts, P. A.; Kain, S. R.; Tsien, R. Y.; Ormo, M.; Remington, S. J. Structural Basis for Dual Excitation and Photoisomerization of the Aequorea Victoria Green Fluorescent Protein Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 2306-2311 (Pubitemid 27136870)
28. Creemers, T. M. H.; Lock, A. J.; Subramaniam, V.; Jovin, T. M.; Völker, S. Three Photoconvertible Forms of Green Fluorescent Protein Identified by Spectral Hole-Burning Nat. Struct. Biol. 1999, 6, 557-560 (Pubitemid 29252836)
29. Bravaya, K. B.; Grigorenko, B. L.; Nemukhin, A. V.; Krylov, A. I. Quantum Chemistry behind Bioimaging: Insights from Ab Initio Studies of Fluorescent Proteins and their Chromophores Acc. Chem. Res. 2012, 45, 265-275
30. Nemukhin, A. V.; Grigorenko, B. L.; Savitsky, A. P. Computer Modeling of the Structure and Spectra of Fluorescent Proteins Acta Nat. 2009, 1, 33-43
31. Li, X.; Chung, L. W.; Mizuno, H.; Miyawaki, A.; Keiji Morokuma, K. A Theoretical Study on the Nature of On- and Off-States of Reversibly Photoswitching Fluorescent Protein Dronpa: Absorption, Emission, Protonation, and Raman J. Phys. Chem. B 2010, 114, 1114-1126
32. Silva-Junior, M. R.; Schreiber, M.; Sauer, S. P. A.; Thiel, W. Benchmarks of Electronically Excited States: Basis Set Effects on CASPT2 Results J. Chem. Phys. 2010, 133, 174318/1-174318/13
33. Filippi, C.; Buda, F.; Guidoni, L.; Sinicropi, A. Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches J. Chem. Theory Comput. 2012, 8, 112-124
34. Melaccio, F.; Ferré, N.; Olivucci, M. Quantum Chemical Modeling of Rhodopsin Mutants Displaying Switchable Colors Phys. Chem. Chem. Phys. 2012, 14, 12485-12495