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 structural basis of photoconversions and to characterize redox properties of these systems.


Related Publications

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., submitted (2017) Abstract 

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  PDF 

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  PDF 

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  PDF 

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  PDF 

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  PDF 

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  PDF 

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