Solvated Molecular Dynamics Simulations for publication: Chemical Mechanism of Allosteric and Asymmetric Dark Reversion in a Bacterial Phytochrome Uncovered by Cryo-EM.

This is a dataset of solvated molecular dynamics simulations of a full-length bacterial phytochrome of Pseudomonas aeruginosa (PaBphP) investigating the dark reversion mechanism (see publication for further information: https://pubs.acs.org/doi/10.1021/jacs.5c17531). Phytochromes are red light photoswitches in plants, bacteria and fungi controlling diverse biological processes. They exits mainly in two states: the red light absorbing Pr state (both monomers in Pr), and the far-red light absorbing Pfr state (both monomers in Pfr). While left in the dark, they revert to the thermodynamically more stable state, in the case of PaBphP the Pfr state. In this study we investigated this dark reversion reaction and encountered a newly identified hybrid state PrPfr (one monomer Pr and the other Pfr), identifiable by an internal asymmetry in the system. This allows us to further elucidate the dark reversion mechanism to provide a structural framework for tuning phytochrome signaling lifetimes. Dry versions of the simulations are available on Zenodo (10.5281/zenodo.15796800). There are each three replicas in the PrPr state as well as in the PrPfr hybrid state. As force-field ff14SB (force field 14 with Side-chain and Backbone modifications)(Maier et al. JCTC, 2015) was used with the TIP3P (Transferable Intermolecular Potential 3P)(Joergensen et al. JCP, 1983) water model (10 Å minimum wall distance), utilizing the AMBER24 (Assisted model building with energy refinement) tool kit, i.e., the tleap implementation. (Case et al., JCIM, 2023) Charges were neutralized with a uniform background charge and the systems were equilibrated with a multistep protocol. Both systems were simulated for approximately 250 ns three times in an NpT ensemble (constant particle number N, pressure p and temperature T)(using pmemd.cuda)(Salomon-Ferrer et al. JCTC, 2013), using a time step of 2 fs, since the SHAKE algorithm was applied. (Miyamoto et al. JCC, 1992) The particle-mesh Ewald (PME) method took care of electrostatic interactions. The Langevin thermostat kept the temperature at 300 K and the Monte Carlo barostat kept pressure at 1 bar.