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How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?

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 hydrog...

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Detalles Bibliográficos
Autores principales: Nakagawa, Hiroshi, Kataoka, Mikio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The Biophysical Society of Japan (BSJ) 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6975894/
https://www.ncbi.nlm.nih.gov/pubmed/31984174
http://dx.doi.org/10.2142/biophysico.16.0_213
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author Nakagawa, Hiroshi
Kataoka, Mikio
author_facet Nakagawa, Hiroshi
Kataoka, Mikio
author_sort Nakagawa, Hiroshi
collection PubMed
description 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(2)O/D(2)O 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 H(2)O/D(2)O exchange technique in INS and the compatibility of INS and MD simulation as tools for studying protein dynamics and hydration water.
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spelling pubmed-69758942020-01-24 How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation? Nakagawa, Hiroshi Kataoka, Mikio Biophys Physicobiol Regular Article 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(2)O/D(2)O 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 H(2)O/D(2)O exchange technique in INS and the compatibility of INS and MD simulation as tools for studying protein dynamics and hydration water. The Biophysical Society of Japan (BSJ) 2019-11-29 /pmc/articles/PMC6975894/ /pubmed/31984174 http://dx.doi.org/10.2142/biophysico.16.0_213 Text en 2019 © The Biophysical Society of Japan This article is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/.
spellingShingle Regular Article
Nakagawa, Hiroshi
Kataoka, Mikio
How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
title How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
title_full How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
title_fullStr How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
title_full_unstemmed How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
title_short How can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
title_sort how can we derive hydration water dynamics with incoherent neutron scattering and molecular dynamics simulation?
topic Regular Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6975894/
https://www.ncbi.nlm.nih.gov/pubmed/31984174
http://dx.doi.org/10.2142/biophysico.16.0_213
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