Journal of the American Chemical Society, volume 135, issue 31, pages 11541-11549

First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route

Grigorenko Bella ^{1, 2}

Nemukhin Alexander ^{1, 2}

Polyakov Igor V. ¹

Morozov Dmitry ¹

Krylov Anna I. ³

Hide authors affiliations Show authors affiliations: 3 affiliations

Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow, 119991, Russian Federation |

N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygina 4, Moscow, 119334, Russian Federation |

Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States |

Publication type: Journal Article

Publication date: 2013-07-25

American Chemical Society (ACS)

Journal: Journal of the American Chemical Society

Quartile SCImago

Quartile WOS

Impact factor: 15

ISSN: 00027863, 15205126

DOI: 10.1021/ja402472y

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General Chemistry

Catalysis

Biochemistry

Colloid and Surface Chemistry

Abstract

Structures and optical spectra of the green fluorescent protein (GFP) forms along the proton transfer route A→I→B are characterized by first-principles calculations. We show that in the ground electronic state the structure representing the wild-type (wt) GFP with the neutral chromophore (A-form) is lowest in energy, whereas the systems with the anionic chromophore (B- and I-forms) are about 1 kcal/mol higher. In the S65T mutant, the structures with the anionic chromophore are significantly lower in energy than the systems with the neutral chromophore. The role of the nearby amino acid residues in the chromophore-containing pocket is re-examined. Calculations reveal that the structural differences between the I- and B-forms (the former has a slightly red-shifted absorption relative to the latter) are based not on the Thr203 orientation, but on the Glu222 position. In the case of wt-GFP, the hydrogen bond between the chromophore and the His148 residue stabilizes the structures with the deprotonated phenolic ring in the I- and B-forms. In the S65T mutant, concerted contributions from the His148 and Thr203 residues are responsible for a considerable energy gap between the lowest energy structure of the B type with the anionic chromophore from other structures.

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Journal of Physical Chemistry B	Journal of Physical Chemistry B, 13, 21.31% Journal of Physical Chemistry B 13 publications, 21.31%
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Journal of Physical Chemistry Letters	Journal of Physical Chemistry Letters, 4, 6.56% Journal of Physical Chemistry Letters 4 publications, 6.56%
Journal of the American Chemical Society	Journal of the American Chemical Society, 2, 3.28% Journal of the American Chemical Society 2 publications, 3.28%
Journal of Computational Chemistry	Journal of Computational Chemistry, 2, 3.28% Journal of Computational Chemistry 2 publications, 3.28%
Russian Journal of Physical Chemistry B	Russian Journal of Physical Chemistry B, 1, 1.64% Russian Journal of Physical Chemistry B 1 publication, 1.64%
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Mendeleev Communications	Mendeleev Communications, 1, 1.64% Mendeleev Communications 1 publication, 1.64%
Chemical Reviews	Chemical Reviews, 1, 1.64% Chemical Reviews 1 publication, 1.64%
Chinese Journal of Chemical Physics	Chinese Journal of Chemical Physics, 1, 1.64% Chinese Journal of Chemical Physics 1 publication, 1.64%
Chemical Physics Reviews	Chemical Physics Reviews, 1, 1.64% Chemical Physics Reviews 1 publication, 1.64%
IUCrJ	IUCrJ, 1, 1.64% IUCrJ 1 publication, 1.64%
Molecules	Molecules, 1, 1.64% Molecules 1 publication, 1.64%
Frontiers in Molecular Biosciences	Frontiers in Molecular Biosciences, 1, 1.64% Frontiers in Molecular Biosciences 1 publication, 1.64%
Scientific Reports	Scientific Reports, 1, 1.64% Scientific Reports 1 publication, 1.64%
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Photochemistry and Photobiology	Photochemistry and Photobiology, 1, 1.64% Photochemistry and Photobiology 1 publication, 1.64%
Angewandte Chemie	Angewandte Chemie, 1, 1.64% Angewandte Chemie 1 publication, 1.64%
Angewandte Chemie - International Edition	Angewandte Chemie - International Edition, 1, 1.64% Angewandte Chemie - International Edition 1 publication, 1.64%
Electrophoresis	Electrophoresis, 1, 1.64% Electrophoresis 1 publication, 1.64%
Journal of Chemical Information and Modeling	Journal of Chemical Information and Modeling, 1, 1.64% Journal of Chemical Information and Modeling 1 publication, 1.64%
Nano Letters	Nano Letters, 1, 1.64% Nano Letters 1 publication, 1.64%
Dalton Transactions	Dalton Transactions, 1, 1.64% Dalton Transactions 1 publication, 1.64%
Chemical Science	Chemical Science, 1, 1.64% Chemical Science 1 publication, 1.64%
Optics Express	Optics Express, 1, 1.64% Optics Express 1 publication, 1.64%
	2 4 6 8 10 12 14

Citations by publishers

	5 10 15 20 25 30
American Chemical Society (ACS)	American Chemical Society (ACS), 27, 44.26% American Chemical Society (ACS) 27 publications, 44.26%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 9, 14.75% Royal Society of Chemistry (RSC) 9 publications, 14.75%
Wiley	Wiley, 7, 11.48% Wiley 7 publications, 11.48%
American Institute of Physics (AIP)	American Institute of Physics (AIP), 3, 4.92% American Institute of Physics (AIP) 3 publications, 4.92%
Springer Nature	Springer Nature, 2, 3.28% Springer Nature 2 publications, 3.28%
Elsevier	Elsevier, 2, 3.28% Elsevier 2 publications, 3.28%
Pleiades Publishing	Pleiades Publishing, 1, 1.64% Pleiades Publishing 1 publication, 1.64%
Autonomous Non-profit Organization Editorial Board of the journal Uspekhi Khimii	Autonomous Non-profit Organization Editorial Board of the journal Uspekhi Khimii, 1, 1.64% Autonomous Non-profit Organization Editorial Board of the journal Uspekhi Khimii 1 publication, 1.64%
Biophysical Society	Biophysical Society, 1, 1.64% Biophysical Society 1 publication, 1.64%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 1, 1.64% International Union of Crystallography (IUCr) 1 publication, 1.64%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 1, 1.64% Multidisciplinary Digital Publishing Institute (MDPI) 1 publication, 1.64%
Frontiers Media S.A.	Frontiers Media S.A., 1, 1.64% Frontiers Media S.A. 1 publication, 1.64%
IOP Publishing	IOP Publishing, 1, 1.64% IOP Publishing 1 publication, 1.64%
Optical Society of America	Optical Society of America, 1, 1.64% Optical Society of America 1 publication, 1.64%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 1, 1.64% Proceedings of the National Academy of Sciences (PNAS) 1 publication, 1.64%
	5 10 15 20 25 30

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Grigorenko B. et al. First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route // Journal of the American Chemical Society. 2013. Vol. 135. No. 31. pp. 11541-11549.

GOST all authors (up to 50) Copy

Grigorenko B., Nemukhin A., Polyakov I. V., Morozov D., Krylov A. I. First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route // Journal of the American Chemical Society. 2013. Vol. 135. No. 31. pp. 11541-11549.

RIS |

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RIS Copy

TY - JOUR

DO - 10.1021/ja402472y

UR - https://doi.org/10.1021%2Fja402472y

TI - First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route

T2 - Journal of the American Chemical Society

AU - Polyakov, Igor V.

AU - Grigorenko, Bella

AU - Nemukhin, Alexander

AU - Morozov, Dmitry

AU - Krylov, Anna I.

PY - 2013

DA - 2013/07/25 00:00:00

PB - American Chemical Society (ACS)

SP - 11541-11549

IS - 31

VL - 135

SN - 0002-7863

SN - 1520-5126

ER -

BibTex |

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@article{2013_Grigorenko,

author = {Igor V. Polyakov and Bella Grigorenko and Alexander Nemukhin and Dmitry Morozov and Anna I. Krylov},

title = {First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route},

journal = {Journal of the American Chemical Society},

year = {2013},

volume = {135},

publisher = {American Chemical Society (ACS)},

month = {jul},

url = {https://doi.org/10.1021%2Fja402472y},

number = {31},

pages = {11541--11549},

doi = {10.1021/ja402472y}

}

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Grigorenko, Bella, et al. “First-principles characterization of the energy landscape and optical spectra of green fluorescent protein along the A→I→B proton transfer route.” Journal of the American Chemical Society, vol. 135, no. 31, Jul. 2013, pp. 11541-11549. https://doi.org/10.1021%2Fja402472y.

Found error?

Publisher

American Chemical Society (ACS)

Journal

Journal of the American Chemical Society

Quartile SCImago

Quartile WOS

Impact factor

ISSN

00027863 (Print)
15205126 (Electronic)

Labs

Laboratory of Quantum Chemistry and Molecular Modeling

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