Dynamic Properties of the Photosensory Domain of Deinococcus radiodurans Bacteriophytochrome
| Autor: | Ronald González, Aditya G. Rao, Igor Schapiro, Giovanni Battocchio, Maria Andrea Mroginski |
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| Rok vydání: | 2020 |
| Předmět: |
010304 chemical physics
biology Chemistry Dimer Deinococcus radiodurans Chromophore 010402 general chemistry biology.organism_classification 01 natural sciences 0104 chemical sciences Surfaces Coatings and Films chemistry.chemical_compound Molecular dynamics Monomer Protein structure Chemical physics 0103 physical sciences Materials Chemistry Molecule Deinococcus Physical and Theoretical Chemistry |
| Zdroj: | The Journal of Physical Chemistry B. |
| ISSN: | 1520-5207 1520-6106 |
| DOI: | 10.1021/acs.jpcb.0c00612 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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