Understanding photoactive proteins in gas phase and in realistic environments
We are using state-of-the art electronic structure methods to study photophysical properties of photoactive proteins (GFP, PYP, etc).
Our computational studies aim to elucidate mechanistic details of the photocycle and to develop design principles for better
fluorescent probes for bioimaging applications. Among many aspects of their electronic structure,
we are investigating structural basis of photoconversions and characterizing redox properties of these systems.
Related Publications
313. G.Giudetti, A.R. Blinova, B.L. Grigorenkob, and A.I. Krylov
A computational study of possible mechanisms of singlet oxygen generation in miniSOG photoactive protein
Mol. Phys.
, in press
(2024)
Abstract
PDF Supporting info
257. T. Sen, Y. Ma, I. Polyakov, B. L. Grigorenko, A. V. Nemukhin, and A. I. Krylov
Interplay between locally excited and charge transfer states
governs the photoswitching mechanism in fluorescent protein Dreiklang
J. Phys. Chem. B 125, 757 – 770
(2021)
Abstract
PDF Supporting info
256. M.-A. Mroginski, S. Adam, G. S. Amoyal, A. Barnoy, A.-N. Bondar, V. Borin, J. R. Church, T. Domratcheva, B. Ensing, F. Fanelli, N. Ferre, O. Filiba, L. P. Gonzalez, R. Gonzalez, C. E. Gonzalez-Espinoza, R. K. Kar, L. Kemmler, S. S. Kim, J. Kongsted, A.I. Krylov, Y. Lahav, M. Lazaratos, Q. NasserEddin, I. Navizet, A.V. Nemukhin, M. Olivucci, J.M.H. Olsen, A. P. de Alba Ortiz, E. Pieri, A. G. Rao, Y. M. Rhee, N. Ricardi, S. Sen, I. Solov'yov, L. De Vico, T. A. Wesolowski, C. Wiebeler, X. Yang, and I. Schapiro
Frontiers in multiscale modelling of photoreceptor proteins
Photochem. Photobiol.
97, 243 – 269
(2021)
Abstract
PDF
230. T. Sen, A. V. Mamontova, A. V. Titelmayer, A. M. Shakhov, A. A. Astafiev, A. Acharya, K. A. Lukyanov, A. I. Krylov, and A. M. Bogdanov
Influence of the first chromophore-forming residue on photobleaching and oxidative photoconversion of EGFP and EYFP
Int. J. Mol. Sci.
20, 5229
(2019)
Abstract
PDF Supporting info
229. B. L. Grigorenko, I. Polyakov, A. I. Krylov, and A. V. Nemukhin
Computational modeling reveals the mechanism of fluorescent state recovery in the reversibly photoswitchable protein Dreiklang
J. Phys. Chem. B
123, 8901 – 8909
(2019)
Abstract
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221. A. V. Nemukhin, B. L. Grigorenko, M. Khrenova, and A. I. Krylov
Computational challenges in modeling
of representative bioimaging proteins: GFP-Like proteins,
flavoproteins, and phytochromes
J. Phys. Chem. B
123, 6133 – 6149
(2019)
Abstract
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217. B. L. Grigorenko, E. D. Kots, A. I. Krylov, and A. V. Nemukhin
Modeling of the glycine tripeptide cyclization in the Ser65Gly/Tyr66Gly mutant of green fluorescent protein
Mendeleev Comm.
29, 187 – 189
(2019)
Abstract
PDF Supporting info
203. Yu. G. Ermakova, T. Sen, Yu. A. Bogdanova, A. Yu. Smirnov, N. S. Baleeva, A. I. Krylov, and M. S. Baranov
Pyridinium analogues of green fluorescent protein chromophore:
Fluorogenic dyes with large solvent-dependent Stokes shifts
J. Chem. Phys. Lett. 8, 1958 – 1963
(2018)
Abstract
PDF Supporting info
191. M. Khrenova, I. Polyakov, B. L. Grigorenko, A. I. Krylov, and A. V. Nemukhin
Improving the design of the triple-decker motif in red fluorescent proteins
J. Phys. Chem. B. 121, 10602 – 10609
(2017)
Abstract
PDF Supporting info
185. B.L. Grigorenko, A.I. Krylov, and A.V. Nemukhin
Molecular modeling clarifies the mechanism of chromophore maturation
in the green fluorescent protein
J. Am. Chem. Soc. 139, 10239 – 10249
(2017)
Abstract
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176. A. Acharya, A.M. Bogdanov, K.B. Bravaya, B.L. Grigorenko, A.V. Nemukhin, K.A. Lukyanov, and A.I. Krylov
Photoinduced chemistry in fluorescent proteins: Curse or blessing?
Chem. Rev. 117, 758 – 795
(2017)
Abstract
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169. A.M. Bogdanov, A. Acharya, A. Titelmayer, A.V. Mamontova, K.B. Bravaya, A.B. Kolomeisky, K.A. Lukyanov, and A.I. Krylov
Turning on and off photoinduced electron transfer in fluorescent
proteins by pi-stacking, halide binding, and Tyr145 mutations
J. Am. Chem. Soc. 138, 4807 – 4817
(2016)
Abstract
PDF Supporting info
162. S. Faraji and A.I. Krylov
On the nature of an extended Stokes shift in the mPlum fluorescent protein
J. Phys. Chem. B 119, 13052 – 13062
(2015)
Abstract
PDF Supporting info
158. B.L. Grigorenko, A.V. Nemukhin, I.V. Polyakov, M.G. Khrenova, and A.I. Krylov
A light-induced reaction with oxygen leads to chromophore decomposition and
irreversible photobleaching in GFP-type proteins
J. Phys. Chem. B 119, 5444–5452
(2015)
Abstract
PDF Supporting info
156. K. Nanda and A.I. Krylov
Two-photon absorption cross sections within equation-of-motion
coupled-cluster formalism using resolution-of-the-identity and Cholesky decomposition representations:
Theory, implementation, and benchmarks
J. Chem. Phys. 142, 064118
(2015)
Abstract
PDF Supporting info
155. J. Lazzari-Dean, A.I. Krylov, and K.B. Bravaya
The effects of resonance delocalization and the extent of
pi-system on ionization energies of model fluorescent proteins chromophores
Int. J. Quant. Chem. 115, 1258 – 1264
(2015)
Abstract
PDF Supporting info
144. R.B. Vegh, K.B. Bravaya, D.A. Bloch, A.S. Bommarius, L.M. Tolbert, M. Verkhovsky, A.I. Krylov, and K.M. Solntsev
Chromophore photoreduction in red fluorescent proteins is responsible
for bleaching and phototoxicity
J. Phys. Chem. B 118, 4527 – 4534
(2014)
Abstract
PDF Supporting info
136. B.L. Grigorenko, A.V. Nemukhin, I. Polyakov, D. Morozov, and A.I. Krylov
First-principle characterization of the energy landscape and optical spectra of the Green Fluorescent
Protein along A-I-B proton transfer route
J. Am. Chem. Soc. 135, 11541–11549
(2013)
Abstract
PDF Supporting info
134. K.B. Bravaya and A.I. Krylov
On the photodetachment from the Green Fluorescent Protein chromophore
J. Phys. Chem. A 117, 11815 – 11822
(2013)
Abstract
PDF Supporting info
132. B.L. Grigorenko, A.V. Nemukhin, I. Polyakov, and A.I. Krylov
Triple-decker motif for red-shifted fluorescent protein mutants
J. Phys. Chem. Lett. 4, 1743 – 1747
(2013)
Abstract
PDF Supporting info
128. S. Naseem, A.D. Laurent, E.C. Carroll, M. Vengris, M. Kumauchi, W.D. Hoff, A.I. Krylov, and D.S. Larsen
Photo-isomerization upshifts the pKa of the photoactive yellow protein chromophore to contribute to photocycle propagation
J. Photochem. Photobiol. A 270, 43 – 52
(2013)
Abstract
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125. A.D. Laurent, V.A. Mironov, P.P. Chapagain, A.V. Nemukhin, and A.I. Krylov
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 116, 12426 – 12440
(2012)
Abstract
PDF Supporting info
124. D. Ghosh, A. Acharya, S.C. Tiwari, and A.I. Krylov
Towards understanding the redox properties of model chromophores
from the green fluorescent protein family: An interplay between
conjugation, resonance stabilization, and solvent effects
J. Phys. Chem. B 116, 12398 – 12405
(2012)
Abstract
PDF Supporting info
118. B. Grigorenko, A.V. Nemukhin, D.I. Morozov, I. Polyakov, K.B. Bravaya, and A.I. Krylov
Towards molecular-level characterization of photo-induced decarboxylation of the green fluorescent protein: Accessibility of the charge-transfer states
J. Chem. Theor. Chem. 8, 1912 – 1920
(2012)
Abstract
PDF Supporting info
115. K.B. Bravaya, O.M. Subach, N. Korovina, V.V. Verkhusha, and A.I. Krylov
An insight into the common mechanism of the chromophore
formation in the red fluorescent proteins:
The elusive blue intermediate revealed
J. Am. Chem. Soc. 134, 2807 – 2814
(2012)
Abstract
PDF Supporting info
113. 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
Acc. Chem. Res. 45, 265 – 275
(2012)
Abstract
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111. K.M. Solntsev, D. Ghosh, O. Amador, M. Josowics, and A.I. Krylov
Correction to "What Drives the Redox Properties of Model Green Fluorescence Protein Chromophores?"
J. Phys. Chem. Lett. 2, 2695
(2011)
PDF
109. D. Zuev, K.B. Bravaya, M. Makarova, and A.I. Krylov
Effect of microhydration on the electronic structure of the
chromophores of the photoactive yellow and green fluorescent proteins
J. Chem. Phys. 135, 194304
(2011)
Abstract
PDF Supporting info
108. K.M. Solntsev, D. Ghosh, O. Amador, M. Josowics, and A.I. Krylov
What drives the redox properties of model green fluorescence protein chromophores?
J. Phys. Chem. Lett. 2, 2593 – 2597
(2011)
Abstract
PDF
106. K.B. Bravaya, M. Khrenova, B. Grigorenko, A.V. Nemukhin, and A.I. Krylov
The effect of protein environment on
electronically excited and ionized
states of the green fluorescent protein chromophore
J. Phys. Chem. B 8, 8296 – 8303
(2011)
Abstract
PDF Supporting info
105. E. Kamarchik and A.I. Krylov
Non-Condon effects in one- and two-photon absorption spectra of the
green fluorescent protein
J. Chem. Phys. Lett. 2, 488 – 492
(2011)
Abstract
PDF Supporting info
102. D. Zuev, K.B. Bravaya, T.D. Crawford, R. Lindh, and A.I. Krylov
Electronic structure of the two isomers of the anionic form of p-coumaric
acid chromophore
J. Chem. Phys. 134, 034310
(2011)
Abstract
PDF Supporting info
98. I. Polyakov, B. Grigorenko, E. Epifanovsky, A.I. Krylov, and A.V. Nemukhin
Potential energy landscape of the electronic states of the GFP chromophore in different protonation
forms: Electronic transition energies and conical intersections
J. Chem. Theor. Comput. 6, 2377 – 2387
(2010)
Abstract
PDF Supporting info
97. M. Khrenova, A.V. Nemukhin, B. Grigorenko, A.I. Krylov, and T. Domratcheva
Quantum chemistry calculations provide support to the mechanism of the
light-induced structural changes in the flavin-binding photoreceptor protein
J. Chem. Theor. Comput. 6, 2293 – 2302
(2010)
Abstract
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94. E. Epifanovsky, I. Polyakov, B. Grigorenko, A.V. Nemukhin, and A.I. Krylov
The effect of oxidation on the electronic structure of the green
fluorescent protein chromophore
J. Chem. Phys. 132, 115104
(2010)
Abstract
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81. I. Polyakov, E. Epifanovsky, B. Grigorenko, A.I. Krylov, and A.V. Nemukhin
Quantum chemical benchmark studies of the electronic properties of
the green fluorescent protein chromophore: II. Cis-trans isomerization
in water
J. Chem. Theor. Comput. 5, 1907 – 1914
(2009)
Abstract
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80. E. Epifanovsky, I. Polyakov, B. Grigorenko, A.V. Nemukhin, and A.I. Krylov
Quantum chemical benchmark studies of the electronic properties of
the green fluorescent protein chromophore: I. Electronically excited and
ionized states of
the anionic chromophore in the gas phase
J. Chem. Theor. Comput. 5, 1895 – 1906
(2009)
Abstract
PDF Supporting info
