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The Structural Changes in the Signaling Mechanism of Bacteriophytochromes in Solution Revealed by a Multiscale Computational Investigation

preprint
submitted on 15.01.2021, 10:52 and posted on 18.01.2021, 09:22 by Veronica Macaluso, Giacomo Salvadori, Lorenzo Cupellini, Benedetta Mennucci
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 chomophore 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. 

Funding

Light-Induced Function: from Excitation to Signal through Time and Space. European Research Council

History

Email Address of Submitting Author

veronica.macaluso@dcci.unipi.it

Institution

Department of Chemistry and Industrial Chemistry, University of Pisa

Country

Italy

ORCID For Submitting Author

https://orcid.org/0000-0001-6115-0529

Declaration of Conflict of Interest

There are no conflicts to declare.