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The structural changes in the signaling mechanism of bacteriophytochromes in solution revealed by a multiscale computational investigation

Authors :
Macaluso, Veronica
Salvadori, Giacomo
Cupellini, Lorenzo
Mennucci, Benedetta
Source :
Chemical Science
Publication Year :
2021

Abstract

Phytochromes are red-light sensing proteins, with important light-regulatory roles in different organisms, which are capturing an increasing interest in bioimaging and optogenetics. Upon absorption of light by the embedded bilin chromophore, they undergo structural changes that extend from the chromophore to the protein and finally drive the biological function. Up to now, the underlying mechanism still has to be characterized fully. Here we investigate the Pfr activated form of a bacterial phytochrome, by combining extensive molecular dynamics simulations with a polarizable QM/MM description of the spectroscopic properties, revealing a large structure relaxation in solution, compared to the crystal structure, both in the chromophore-binding pocket and in the overall structure of the phytochrome. Our results indicate that the final opening of the dimeric structure is preceded by an important internal reorganization of the phytochrome specific (PHY) domain involving a bend of the helical spine connecting the PHY domain with the chromophore-binding domain, opening the way to a new understanding of the activation pathway.<br />A combination of MD simulations and a polarizable QM/MM description of a bacteriophytochrome in solution reveals the changes in the chromophore-binding pocket and in the overall structure of the phytochrome involved in the signaling mechanism.

Details

ISSN :
20416520
Database :
OpenAIRE
Journal :
Chemical Science
Accession number :
edsair.doi.dedup.....49c5b952a444e43d7c0e4adef3bd6507
Full Text :
https://doi.org/10.1039/d1sc00186h