Title:	Molecular Dynamics simulation of phytochrome for analysis of NMR data
DNr:	SNIC 2020/13-115
Project Type:	SNIC Small Compute
Principal Investigator:	Sebastian Westenhoff <sebastian.westenhoff@kemi.uu.se>
Affiliation:	Göteborgs universitet
Duration:	2020-12-21 – 2022-01-01
Classification:	10203
Keywords:

Abstract

Phytochrome proteins detect light controlling the growth development and motion of plants and bacteria. Here, we request 5000h for running molecular dynamics simulations (Gromacs) for phytochrome photosensors. The simulations will yield a library of conformations, from which we will select the best fits against our NMR (RDC) data. We have used this approach before (Issakson et al, Structure, 2020) and now we want to extend the study by covering a significantly larger conformational space in the simulations and with more specific NMR data. The goal is to refine the structural changes that occur when phytochrome proteins are activated by light. We have working run files for the MD simulations.