A Not Obvious Correlation Between the Structure of Green Fluorescent Protein Chromophore Pocket and Hydrogen Bond Dynamics: A Choreography From ab initio Molecular Dynamics

Frontiers in Molecular Biosciences
Federico CoppolaNadia Rega

Abstract

The Green Fluorescent Protein (GFP) is a widely studied chemical system both for its large amount of applications and the complexity of the excited state proton transfer responsible of the change in the protonation state of the chromophore. A detailed investigation on the structure of the chromophore environment and the influence of chromophore form (either neutral or anionic) on it is of crucial importance to understand how these factors could potentially influence the protein function. In this study, we perform a detailed computational investigation based on the analysis of ab-initio molecular dynamics simulations, to disentangle the main structural quantities determining the fine balance in the chromophore environment. We found that specific hydrogen bonds interactions directly involving the chromophore (or not), are correlated to quantities, such as the volume of the cavity in which the chromophore is embedded and that it is importantly affected by the chromophore protonation state. The cross-correlation analysis performed on some of these hydrogen bonds and the cavity volume, demonstrates a direct correlation among them and we also identified the ones specifically involved in this correlation. We also found that specific i...Continue Reading

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Citations

Jun 15, 2021·Frontiers in Molecular Biosciences·Chong FangPeriklis Pantazis
Nov 9, 2021·The Journal of Physical Chemistry. B·Alice R WalkerTodd J Martínez

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Methods Mentioned

BETA
X-ray
neutron
NMR

Software Mentioned

Gaussian
MolProbity
AMBER
ONIOM

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