Mechanism of Deep-Sea Fish α-Actin Pressure Tolerance Investigated by Molecular Dynamics Simulations |
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| Authors: | Nobuhiko Wakai Kazuhiro Takemura Takami Morita Akio Kitao |
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| Institution: | 1. Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.; 2. Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.; 3. Research Center for Fisheries Oceanography and Marine Ecosystem, National Research Institute of Fisheries Sciences, Fisheries Research Agency, Kanagawa, Japan.; Jacobs University Bremen, Germany, |
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| Abstract: | The pressure tolerance of monomeric α-actin proteins from the deep-sea fish Coryphaenoides armatus and C. yaquinae was compared to that of non-deep-sea fish C. acrolepis, carp, and rabbit/human/chicken actins using molecular dynamics simulations at 0.1 and 60 MPa. The amino acid sequences of actins are highly conserved across a variety of species. The actins from C. armatus and C. yaquinae have the specific substitutions Q137K/V54A and Q137K/L67P, respectively, relative to C. acrolepis, and are pressure tolerant to depths of at least 6000 m. At high pressure, we observed significant changes in the salt bridge patterns in deep-sea fish actins, and these changes are expected to stabilize ATP binding and subdomain arrangement. Salt bridges between ATP and K137, formed in deep-sea fish actins, are expected to stabilize ATP binding even at high pressure. At high pressure, deep-sea fish actins also formed a greater total number of salt bridges than non-deep-sea fish actins owing to the formation of inter-helix/strand and inter-subdomain salt bridges. Free energy analysis suggests that deep-sea fish actins are stabilized to a greater degree by the conformational energy decrease associated with pressure effect. |
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