Modeling Structures and Spectra of Fluorescent Proteins in the Coordinate-Locking Cluster Approach: Application to the Photoswitchable Protein AsFP595

I. Topol, J. Collins, A. Nemukhin

Advanced Biomedical Computing Center, Information Systems Program, SAIC-Frederick Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygina, Moscow, Russian Federation.

DOI: 10.4236/cmb.2012.23008                

Abstract

An interest in the fluorescent protein asFP595 is due to unexplained puzzles in its photophysical behavior. We report the results of calculations of structures, absorption, and emission bands in asFP595 by considering model molecular clusters in the coordinate-locking scheme. Both trans and cis conformations of the anionic chromophore are considered. Equilibrium geometry coordinates on the ground potential energy surface were optimized in the density functional theory approaches by considering both large- and reduced-size clusters. The cluster size was reduced to locate positions of the minimum energy points on the excited-state potential surface by using the configuration interaction singles approach. Vertical excitation energies and oscillator strengths were computed by using the ZINDO method. We show that consideration of large clusters mimicking the protein-containing pocket is an essential issue to calculate positions of absorption and emission bands with the accuracy compatible to experiments.

Keywords

Chromophore-Containing Pockets; Coordinate-Locking Scheme; ZINDO; Photoswitchable Fluorescent Proteins; Asfp595

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	L. A. Gross, G. S. Baird, R. C. Hoffman, K. K. Baldridge and R. Y. Tsien, “The Structure of the Chromophore within DsRed, a Red Fluorescent Protein from Coral,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 97, No. 22, 2000, pp. 11990-11995. doi:10.1073/pnas.97.22.11990
[2]	M. Zimmer, “Green Fluorescent Protein (GFP):? Applications, Structure, and Related Photophysical Behavior,” Chemical Reviews, Vol. 102, No. 3, 2002, pp. 759-782. doi:10.1021/cr010142r
[3]	T. Laino, R. Nifosì and V. Tozzini, “Relationship between Structure and Optical Properties in Green Fluorescent Proteins: A Quantum Mechanical Study of the Chromophore Environment,” Chemical Physics, Vol. 298, No. 1-3, 2004, pp. 17-28. doi:10.1016/j.chemphys.2003.10.040
[4]	A. Sinicropi, T. Andruniow, N. Ferre, R. Basosi and M. Olivucci, “Properties of the Emitting State of the Green Fluorescent Protein Resolved at the CASPT2//CASSCF/ CHARMM Level,” Journal of the American Chemical Society, Vol. 127, No. 33, 2005, pp. 11534-11535. doi:10.1021/ja045269n
[5]	P. Amat, G. Granucci, F. Buda, M. Persico and V. Tozzini, “The Chromophore of asFP595:? A Theoretical Study,” The Journal of Physical Chemistry B, Vol. 110, No. 18, 2006, pp. 9348-9353. doi:10.1021/jp057071a
[6]	M. Sun, “Excited State Properties of the Chromophore of the asFP595 Chromoprotein: 2D and 3D Theoretical Analyses,” International Journal of Quantum Chemistry, Vol. 106, No. 4, 2006, pp. 1020-1026. doi:10.1002/qua.20815
[7]	A. V. Nemukhin, I. A. Topol and S. K. Burt, “Electronic Excitations of the Chromophore from the Fluorescent Protein asFP595 in Solutions,” Journal of Chemical Theory and Computation, Vol. 2, No. 2, 2006, pp. 292-299. doi:10.1021/ct050243n
[8]	B. Grigorenko, A. Savitsky, I. Topol, S. Burt and A. Nemukhin, “Ground-State Structures and Vertical Excitations for the Kindling Fluorescent Protein asFP595,” The Journal of Physical Chemistry B, Vol. 110, No. 37, 2006, pp. 18635-18640. doi:10.1021/jp060124j
[9]	B. Grigorenko, A. Savitsky, I. Topol, S. Burt and A. Nemukhin, “Trans and Cis Chromophore Structures in the Kindling Fluorescent Protein asFP595,” Chemical Physics Letters, Vol. 424, No.1-3, 2006, pp.184-188.
[10]	J.-Y. Hasegawa, K. Fujimoto, B. Swerts, T. Miyahara and H. Nakatsuji, “Excited States of GFP Chromophore and Active Site Studied by the SAC-CI Method: Effect of Protein—Environment and Mutations,” Journal of Com- putational Chemistry, Vol. 28, No. 15, 2007, pp. 2443-2452. doi:10.1002/jcc.20667
[11]	L. V. Sch?fer, G. Groenhof, A. R. Klingen, G. M. Ullmann, M. Boggio-Pasqua, M. A. Robb and H. Grubmüller, “Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra,” Angewandte Chemie, Vol.119, No. 4, 2007, pp. 536-542.
[12]	L. V. Sch?fer, G. Groenhof, M. Boggio-Pasqua, M. A. Robb and H. Grubmüller, “Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595,” PLOS Computational Biology Vol. 4, No. 3, 2008, p. e1000034. doi:10.1371/journal.pcbi.1000034
[13]	S. Olsen and S. C. Smith, “Bond Selection in the Photoisomerization Reaction of Anionic Green Fluorescent Protein and Kindling Fluorescent Protein Chromophore Models,” Journal of the American Chemical Society, Vol. 130, No. 27, 2008, pp. 8677-8689. doi:10.1021/ja078193e
[14]	K. B. Bravaya, A. V. Bochenkova, A. A. Granovsky, A. P. Savitsky and A. V. Nemukhin, “Modeling Photoabsorption of the asFP595 Chromophore,” The Journal of Physical Chemistry A, Vol. 112, No. 37, 2008, pp. 8804-8810. doi:10.1021/jp804183w
[15]	A. V. Nemukhin, I. A. Topol, B. L. Grigorenko, A. P. Savitsky and J. R. Collins, “Conformation Dependence of pKa’s of the Chromophores from the Purple asFP595 and Yellow zFP538 Fluorescent Proteins,” Journal of Molecular Structure: THEOCHEM, Vol. 863, No. 1-3, 2008, pp. 39-43. doi:10.1016/j.theochem.2008.05.014
[16]	P. J. Tonge and S. R. Meech, “Excited state dynamics in the green fluorescent protein,” Journal of Photochemistry and Photobiology A Chemistry, Vol. 205, No. 1, 2009, pp. 1-11.
[17]	A. M. Virshup, C. Punwong, T. V. Pogorelov, B. A. Lindquist, C. Ko and T. J. Martinez, “Photodynamics in Complex Environments: Ab Initio Multiple Spawning Quantum Mechanical/Molecular Mechanical Dynamics,” The Journal of Physical Chemistry B, Vol. 113, No. 11, 2009, pp. 3280-3291. doi:10.1021/jp8073464
[18]	A. V. Nemukhin, B. L. Grigorenko and A. P. Savitsky, “Computer Modeling of the Structure and Spectra of Fluorescent Proteins,” Acta Naturae, Vol. 1, No. 2, 2009, pp. 33-43.
[19]	I. A. Topol, J. Collins, I. Polyakov, B. L. Grigorenko and A. V. Nemukhin, “On Photoabsorption of the Neutral Form of the Green Fluorescent Protein Chromophore,” Biophysical Chemistry, Vol. 145, No. 1, 2009, pp. 1-6. doi:10.1016/j.bpc.2009.08.002
[20]	C. Filippi, M. Zaccheddu and F. Buda, “Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for Ab Initio Methods?” Journal of Chemical Theory and Computation, Vol. 5, No. 8, 2009, pp. 2074-2087. doi:10.1021/ct900227j
[21]	I. Topol, J. Collins and A. Nemukhin, “Modeling Spectral Tuning in Monomeric Teal Fluorescent Protein mTFP1,” Biophysical Chemistry, Vol. 149, No. 3, 2010, pp. 78-82. doi:10.1016/j.bpc.2010.04.002
[22]	S. Olsen, K. Lamothe and T. J. Martinez, “Protonic Gating of Excited-State Twisting and Charge Localization in GFP Chromophores: A Mechanistic Hypothesis for Reversible Photoswitching,” Journal of the American Chemical Society, Vol. 132, No. 4, 2010, pp. 1192-1193. doi:10.1021/ja907447k
[23]	Y.-W. Hsiao, E. Sanchez-Garcia, M. Doerr and W. Thiel, “Quantum Refinement of Protein Structures: Implementation and Application to the Red Fluorescent Protein DsRed.M1,” The Journal of Physical Chemistry B, Vol. 114, No. 46, 2010, pp. 15413-15423. doi:10.1021/jp108095n
[24]	I. Topol, J. Collins, A. Savitsky and A. Nemukhin, “Computational Strategy for Tuning Spectral Properties of Red Fluorescent Proteins,” Biophysical Chemistry, Vol. 158, No. 2-3, 2011, pp. 91-95. doi:10.1016/j.bpc.2011.05.016
[25]	A. L. Rusanov, V. A. Mironov, A. S. Goryashenko, B. L. Grigorenko, A. V. Nemukhin and A. P. Savitsky, “Conformational Partitioning in pH-Induced Fluorescence of the Kindling Fluorescent Protein (KFP) ,” The Journal of Physical Chemistry B, Vol. 115, No. 29, 2011, pp. 9195-9201. doi:10.1021/jp1094245
[26]	I. Shelaev, V. Mironov, A. Rusanov, F. Gostev, A. Bochenkova, O. Sarkisov, A. Nemukhin and A. Savitsky, “The Origin of Radiationless Conversion of the Excited State in the Kindling Fluorescent Protein (KFP): Femtosecond Studies and Quantum Modeling,” Laser Physics Letters, Vol. 8, No. 6, 2011, pp. 469-474. doi:10.1002/lapl.201010145
[27]	C. Filippi, F. Buda, L. Guidoni and A. Sinicropi, “Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches,” Journal of Chemical Theory and Computation, Vol. 8, No. 1, 2011, pp. 112-124. doi:10.1021/ct200704k
[28]	G. Cui, Z. Lan and W. Thiel, “Intramolecular Hydrogen Bonding Plays a Crucial Role in the Photophysics and Photochemistry of the GFP Chromophore,” Journal of the American Chemical Society, Vol. 134, No. 3, 2012, pp. 1662-1672. doi:10.1021/ja208496s
[29]	M. Wanko, P. García-Risue?o and A. Rubio, “Excited States of the Green Fluorescent Protein Chromophore: Performance of Ab Initio and Semi-Empirical Methods,” Physica Status Solidi (b), Vol. 249, 2012, pp. 392-400. doi:10.1002/pssb.201100536
[30]	K. B. Bravaya, B. L. Grigorenko, A. V. Nemukhin and A. I. Krylov, “Quantum Chemistry behind Bioimaging: Insights from Ab Initio Studies of Fluorescent Proteins and Their Chromophores,” Accounts of Chemical Research, Vol. 45, No. 2, 2012, pp. 265-275. doi:10.1021/ar2001556
[31]	A. K. Das, J.-Y. Hasegawa, T. Miyahara, M. Ehara and H. Nakatsuji, “Electronic Excitations of the Green Fluorescent Protein Chromophore in Its Protonation States: SAC/ SAC-CI Study,” Journal of Computational Chemistry, Vol. 24, No. 12, 2003, pp. 1421-1431.
[32]	K. B. Bravaya, A. V. Bochenkova, A. A. Granovsky and A. V. Nemukhin, “Modeling of the structure and electronic spectra of green fluorescent protein chromophore,” Russian Journal of Physical Chemistry B, Focus on Physics, Vol. 2, No. 5, 2008, pp. 671-675. doi:10.1134/S1990793108050023
[33]	M. A. L. Marques and E. K. U. Gross, “Time-Dependent Density Functional Theory,” Annual Review of Physical Chemistry, Vol. 55, 2004, pp. 427-455.
[34]	M. C. Zerner, K. B. Lipkowitz, and D. B. Boyd, “Semi Empirical Molecular Orbital Methods,” Reviews in Computational Chemistry, Vol. 2, 1991, pp. 313-366. doi:10.1002/9780470125793.ch8
[35]	P. E. M. Siegbahn and F. Himo,“The Quantum Chemical Cluster Approach for Modeling Enzyme Reactions,” Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, No. 3, 2011, pp. 323-336. doi:10.1002/wcms.13
[36]	K. A. Lukyanov, A. F. Fradkov, N. G. Gurskaya, M. V. Matz, Y. A. Labas, A. P. Savitsky, M. L. Markelov, A. G. Zaraisky, X. Zhao, Y. Fang, W. Tan and S. A. Lukyanov, “Natural Animal Coloration Can Be Determined by a Nonfluorescent Green Fluorescent Protein Homolog,” The Journal of Biological Chemistry, Vol. 275, No. 34, 2000, pp. 25879-25882. doi:10.1074/jbc.C000338200
[37]	D. M. Chudakov, V. V. Belousov, A. G. Zaraisky, V. L. Novoselov, D. B. Staroverov, D. B. Zorov, S. A. Lukyanov and K. A. Lukyanov, “Kindling fluorescent proteins for precise in vivo photolabeling,” Nature Biotechnology, Vol. 21, No. 2, 2003, pp. 191-194. doi:10.1038/nbt778
[38]	D. M. Chudakov, A. V. Feofanov, N. N. Mudrik, S. Lukyanov and K. A. Lukyanov, “Chromophore Environment Provides Clue to Kindling Fluorescent Protein Riddle,” The Journal of Biological Chemistry, Vol. 278, No. 9, 2003, pp. 7215-7219. doi:10.1074/jbc.M211988200
[39]	M. L. Quillin, D. M. Anstrom, X. Shu, S. O’Leary, K. Kallio, D. M. Chudakov and S. Remington, “Kindling Fluorescent Protein from Anemonia sulcata: Dark-State Structure at 1.38 ? Resolution,” Biochemistry, Vol. 44, No. 15, 2005, pp. 5774-5787. doi:10.1021/bi047644u
[40]	M. Andresen, M. C. Wahl, A. C. Stiel, F. Gr?ter, L. V. Sch?fer, S. Trowitzsch, G. Weber, C. Eggeling, H. Grubmüller, S. W. Hell and S. Jakobs, “Structure and Mechanism of the Reversible Photoswitch of a Fluorescent Protein,” Proceedings of the National Academy of Sciences of the United States of America, Vol. 102, No. 37, 2005, pp. 13070-13074. doi:10.1073/pnas.0502772102
[41]	P. G. Wilmann, J. Petersen, R. J. Devenish, M. Prescott and J. Rossjohn, “Variations on the GFP Chromophore: A Polypeptide Fragmentation within the Chromophore Revealed in the 2.1-? Crystal Structure of a Nonfluorescent Chromoprotein from Anemonia sulcata,” The Journal of Biological Chemistry, Vol. 280, No. 4, 2005, pp. 2401-2404. doi:10.1074/jbc.C400484200
[42]	T. A. Schüttrigkeit, T. von Feilitzsch, C. K. Kompa, K. A. Lukyanov, A. P. Savitsky, A. A. Voityuk and M. E. Michel-Beyerle, “Femtosecond Study of Superlinear Light Induced Fluorescence Increase of the Coral Protein asFP595,” Chemical Physics, Vol. 323, No. 2-3, 2006, pp. 149-160. doi:10.1016/j.chemphys.2005.09.039
[43]	J. Nathan Henderson and S. J. Remington, “The Kindling Fluorescent Protein: A Transient Photoswitchable Marker,” Physiology, Vol. 21, No. 3, 2006, pp. 162-170.
[44]	Y. A. Tretyakova, A. A. Pakhomov and V. I. Martynov, “Chromophore Structure of the kindling Fluorescent Pro tein asFP595 from Anemonia sulcata,” Journal of the American Chemical Society, Vol. 129, No. 25, 2007, pp. 7748-7749. doi:10.1021/ja071992c
[45]	A. L. Rusanov, T. V. Ivashina, L. M. Vinokurov, I. I. Fiks, A. G. Orlova , I. V. Turchin, I. G. Meerovich and V. V. Zherdeva, A. P. Savitsky, “Lifetime Imaging of FRET between Red Fluorescent Proteins,” Journal of Biophotonics, Vol. 3, No. 12, 2010, pp. 774-783. doi:10.1002/jbio.201000065
[46]	A. P. Savitsky, A. L. Rusanov, V. V. Zherdeva, T. V. Gorodnicheva, M. G. Khrenova and A. V. Nemukhin, “FLIM-FRET Imaging of Caspase-3 Activity in Live Cells Using Pair of Red Fluorescent Proteins,” Theranostics, Vol. 2, No. 2, 2012, pp. 215-226. doi:10.7150/thno.3885
[47]	B. L. Grigorenko, A. V. Nemukhin, I. A. Topol and S. K. Burt, “Modeling of Biomolecular Systems with the Quantum Mechanical and Molecular Mechanical Method Based on the Effective Fragment Potential Technique:? Proposal of Flexible Fragments,” The Journal of Physical Chemistry A, Vol. 106, No. 44, 2002, pp. 10663-10672. doi:10.1021/jp026464w
[48]	A. V. Nemukhin, B. L. Grigorenko, I. A. Topol and S. K. Burt, “Flexible Effective Fragment QM/MM Method: Validation through the Challenging Tests,” Journal of Computational Chemistry, Vol. 24, No. 12, 2003, pp. 1410-1420. doi:10.1002/jcc.10309
[49]	M. W. Schmidt, K. K. Baldridge, J. A. Boatz, S. T. Elbert, M. S. Gordon, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. Su, T. L. Windus, M. Dupuis and J. A. Montgomery Jr, “General Atomic and Molecular Electronic Structure System,” Journal of Computational Che- mistry, Vol. 14, No. 11, 1993, pp. 1347-1363. doi:10.1002/jcc.540141112
[50]	M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O.
[51]	Q. Wang, L. J. Byrnes, B. Shui, U. F. R?hrig, A. Singh, D. M. Chudakov, S. Lukyanov, W. R. Zipfel, M. I. Kotlikoff and H. Sondermann, “Molecular Mechanism of a Green-Shifted, pH-Dependent Red Fluorescent Protein mKate Variant,” PLoS ONE, Vol. 6, No. 8, 2011, p. e23513. doi:10.1371/journal.pone.0023513
[52]	I. Topol, J. Collins, A. Savitsky and A. Nemukhin, “Modeling Absorption of the Kindling Fluorescent Protein with the Neutral Form of the Chromophore,” Inter- national Journal of Quantum Chemistry, Vol. 112, No. 17, 2012, pp. 2947-2951. doi:10.1002/qua.24134