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Dynamic Properties of the Photosensory Domain of Deinococcus Radiodurans Bacteriophytochrome.

Phytochromes are biological photoreceptors found in all kingdoms of life. Numerous physico-chemical and spectroscopic studies of phytochromes have been carried out for many decades, both experimentally and computationally, with main focus on the photoconversion mechanism involving the tetrapyrrole chromophore. In this computational work we concentrate on long scale dynamic motion of the photosensory domain of Deinococcus Radiodurans by means of classical all-atoms molecular dynamics (MD) simulations. Conventional- and accelerated- MD methods in combination with two different force fields, CHARMM27 and AMBER ff14SB were 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 behaviour of monomer form vs dimer. While the phytochrome in a monomer form tends to close the cavity entailed between GAF- and PHY- domains, the opposite trend is predicted for the phytochrome dimer which opens up as consequence of the formation of strong salt bridges between PHY-domains of two molecules in water.