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Yamamoto, Naoki*; Nakanishi, Masahiro*; Rajan, R.*; Nakagawa, Hiroshi
Biophysics and Physicobiology (Internet), 18, p.284 - 288, 2021/12
Water is an indispensable solvent for living things. 
60% of our body is composed of water, the lack of which causes lots of fatal problems. It has also been known that protein function is performed only when it accompanies water molecules around the surface, i.e. hydration water molecules. Therefore, it is essential to understand how water and biological component interact with each other in the view point of structure and dynamics. Freezing is a fundamental and simple phenomenon of water, and thus can be used as a probe for the purpose. Furthermore, preservation of cells and proteins under low temperature is crucial for numerous applications, which in turn triggers a myriad of undesirable consequences because of the freezing.
Nakagawa, Hiroshi; Kataoka, Mikio*
Biophysics and Physicobiology (Internet), 16, p.213 - 219, 2019/00
Incoherent neutron scattering (INS) is one of the useful experimental methods for studying protein dynamics at the pico-nanosecond timescale. At this timescale, protein dynamics is highly coupled with hydration, which is observed as protein dynamical transition (PDT). INS is very sensitive to hydrogen atomic dynamics because of the large incoherent scattering cross section of hydrogen atom, and thus, the INS of a hydrated protein provides overall dynamic information about the protein, including hydration water. Separation of hydration water dynamics is essential for understanding hydration-related protein dynamics. H
O/DO exchange is an effective method in the context of INS experiments for observing the dynamics of protein and hydration water separately. Neutron scattering is directly related to the van Hove space-time correlation function, which can be calculated quantitatively by performing molecular dynamics (MD) simulations. Diffusion and hydrogen bond dynamics of hydration water can be analyzed by performing MD simulation. MD simulation is useful for analyzing the dynamic coupling mechanism in hydration-related protein dynamics from the viewpoint of interpreting INS data because PDT is induced by hydration. In the present work, we demonstrate the methodological advantages of the HO/DO exchange technique in INS and the compatibility of INS and MD simulation as tools for studying protein dynamics and hydration water.
Matsuo, Tatsuhito; Takeda, Soichi*; Oda, Toshiro*; Fujiwara, Satoru
Biophysics and Physicobiology (Internet), 12, p.145 - 158, 2015/12
