Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physicochemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with the main focus on the photoconversion mechanism involving a tetrapyrrole chromophore. In this computational work, we concentrate on the long-scale dynamic motion of the photosensory domain of Deinococcus radiodurans by means of classical all-atom molecular dynamics (MD) simulations. Conventional and accelerated MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB, are tested in long atomistic simulations to confront the dynamics of monomer and dimer forms. These calculations highlight dissimilar equilibrium conformations in aqueous solutions and, in turn, different large-scale dynamic behaviors of the monomer form vs the dimer form. While the phytochrome in a monomer form tends to close the cavity entailed between the GAF and PHY domains, the opposite trend is predicted for the phytochrome dimer, which opens up as a consequence of the formation of strong salt bridges between the PHY domains of two molecules in water.
Bibliographical noteFunding Information:
The authors acknowledge financial support by the DFG via the SFB 1078. I.S. thanks the SFB 1078 for support within the Mercator program. I.S. gratefully acknowledges funding by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 678169, “PhotoMutant”). The authors thank Dr. T. Utesch for reading the manuscript and providing valuable suggestions.
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