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Computational study of the absorption spectra of green fluorescent protein mutants
Author(s) -
Patnaik Soumya S.,
Trohalaki Steven,
Naik Rajesh R.,
Stone Morley O.,
Pachter Ruth
Publication year - 2007
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20642
Subject(s) - chemistry , chromophore , molecular dynamics , preprint , hydrogen bond , fluorescence , absorption spectroscopy , spectral line , absorption (acoustics) , green fluorescent protein , density functional theory , chemical physics , computational chemistry , molecule , quantum mechanics , physics , photochemistry , optics , organic chemistry , biochemistry , gene
In this work, we present a theoretical study of the relationship between molecular structure and the red‐shift in absorption spectra of S65G and S65T green fluorescent protein (GFP) mutants. To identify the effects of the protein environment, we combined results from molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics calculations to obtain structural properties, and applied time‐dependent density functional theory to calculate the excitation energies. By using results from the MD simulations, we were able to provide a systematic analysis of the structural details that may effect the red‐shift in the absorption spectra when taking into account temperature effects. Furthermore, a detailed study of hydrogen bonding during the MD simulations demonstrated differences between S65G and S65T, for example, regarding hydrogen bonding with Glu222. An analysis of the absorption spectra for different forms of the chromophore emphasized the dominance of the anionic forms in solution for the S65G and S65T GFP mutants. © 2007 Wiley Periodicals, Inc. Biopolymers 85: 253–263, 2007. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com