Issue 15, 2021

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

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.

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

Supplementary files

Article information

Article type
Edge Article
Submitted
11 jan 2021
Accepted
08 mrt 2021
First published
09 mrt 2021
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY-NC license

Chem. Sci., 2021,12, 5555-5565

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

V. Macaluso, G. Salvadori, L. Cupellini and B. Mennucci, Chem. Sci., 2021, 12, 5555 DOI: 10.1039/D1SC00186H

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