Literature DB >> 30566356

Structural Relaxation Processes and Collective Dynamics of Water in Biomolecular Environments.

Sara Capponi, Stephen H White, Douglas J Tobias, Matthias Heyden1.   

Abstract

In this simulation study, we investigate the influence of biomolecular confinement on dynamical processes in water. We compare water confined in a membrane protein nanopore at room temperature to pure liquid water at low temperatures with respect to structural relaxations, intermolecular vibrations, and the propagation of collective modes. We observe distinct potential energy landscapes experienced by water molecules in the two environments, which nevertheless result in comparable hydrogen bond lifetimes and sound propagation velocities. Hence, we show that a viscoelastic argument that links slow rearrangements of the water-hydrogen bond network to ice-like collective properties applies to both, the pure liquid and biologically confined water, irrespective of differences in the microscopic structure.

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Year:  2019        PMID: 30566356      PMCID: PMC6476566          DOI: 10.1021/acs.jpcb.8b12052

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  44 in total

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Journal:  Phys Rev Lett       Date:  1996-02-05       Impact factor: 9.161

2.  High-resolution neutron scattering measurement of the dynamic structure factor of heavy water

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Journal:  Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics       Date:  2000-09

3.  Biological water at the protein surface: dynamical solvation probed directly with femtosecond resolution.

Authors:  Samir Kumar Pal; Jorge Peon; Ahmed H Zewail
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-12       Impact factor: 11.205

4.  Temperature-dependent hydrogen-bond geometry in liquid water.

Authors:  Kristofer Modig; Bernd G Pfrommer; Bertil Halle
Journal:  Phys Rev Lett       Date:  2003-02-19       Impact factor: 9.161

5.  Single-particle and collective dynamics of protein hydration water: a molecular dynamics study.

Authors:  M Tarek; D J Tobias
Journal:  Phys Rev Lett       Date:  2002-12-17       Impact factor: 9.161

6.  Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations.

Authors:  Alexander D Mackerell; Michael Feig; Charles L Brooks
Journal:  J Comput Chem       Date:  2004-08       Impact factor: 3.376

7.  Brillouin neutron scattering in heavy water: evidence for two-mode collective dynamics.

Authors:  F Sacchetti; J-B Suck; C Petrillo; B Dorner
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-06-04

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Journal:  Phys Rev Lett       Date:  1985-06-24       Impact factor: 9.161

9.  The melting temperature of the most common models of water.

Authors:  C Vega; E Sanz; J L F Abascal
Journal:  J Chem Phys       Date:  2005-03-15       Impact factor: 3.488

Review 10.  Water dynamics in the hydration layer around proteins and micelles.

Authors:  Biman Bagchi
Journal:  Chem Rev       Date:  2005-09       Impact factor: 60.622

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  3 in total

Review 1.  Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.

Authors:  Charlotte I Lynch; Shanlin Rao; Mark S P Sansom
Journal:  Chem Rev       Date:  2020-08-25       Impact factor: 60.622

2.  Letter to the Editor: Distanced Inspiration from the Career of Stephen H. White.

Authors:  Charles R Sanders
Journal:  J Membr Biol       Date:  2020-10-24       Impact factor: 1.843

3.  Structural determinants of a permeation barrier of the SecYEG translocon in the active state.

Authors:  Ekaterina Sobakinskaya; Heinrich Krobath; Thomas Renger; Frank Müh
Journal:  Phys Chem Chem Phys       Date:  2021-11-24       Impact factor: 3.676

  3 in total

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