Literature DB >> 31255295

Universality and Structural Implications of the Boson Peak in Proteins.

Hiroshi Nakagawa1, Yasumasa Joti2, Akio Kitao3, Osamu Yamamuro4, Mikio Kataoka5.   

Abstract

The softness and rigidity of proteins are reflected in the structural dynamics, which are in turn affected by the environment. The characteristic low-frequency vibrational spectrum of a protein, known as boson peak, is an indication of the structural rigidity of the protein at a cryogenic temperature or dehydrated conditions. In this article, the effect of hydration, temperature, and pressure on the boson peak and volumetric properties of a globular protein are evaluated by using inelastic neutron scattering and molecular dynamics simulation. Hydration, pressurization, and cooling shift the boson peak position to higher energy and depress the peak intensity and decreases the protein and cavity volumes. We found the correlation between the boson peak and cavity volume in a protein. A decrease of cavity volume means the increase of rigidity, which is the origin of the boson peak shift. Boson peak is the universal property of a protein, which is rationalized by the correlation.
Copyright © 2019 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Entities:  

Year:  2019        PMID: 31255295      PMCID: PMC6700671          DOI: 10.1016/j.bpj.2019.06.007

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  36 in total

Review 1.  How soft is a protein? A protein dynamics force constant measured by neutron scattering.

Authors:  G Zaccai
Journal:  Science       Date:  2000-06-02       Impact factor: 47.728

2.  Crystalline ribonuclease A loses function below the dynamical transition at 220 K.

Authors:  B F Rasmussen; A M Stock; D Ringe; G A Petsko
Journal:  Nature       Date:  1992-06-04       Impact factor: 49.962

3.  Direct determination of vibrational density of states change on ligand binding to a protein.

Authors:  Erika Balog; Torsten Becker; Martin Oettl; Ruep Lechner; Roy Daniel; John Finney; Jeremy C Smith
Journal:  Phys Rev Lett       Date:  2004-07-09       Impact factor: 9.161

4.  Pressure denaturation of staphylococcal nuclease studied by neutron small-angle scattering and molecular simulation.

Authors:  Amit Paliwal; Dilipkumar Asthagiri; Dobrin P Bossev; Michael E Paulaitis
Journal:  Biophys J       Date:  2004-09-03       Impact factor: 4.033

5.  Protein boson peak originated from hydration-related multiple minima energy landscape.

Authors:  Yasumasa Joti; Akio Kitao; Nobuhiro Go
Journal:  J Am Chem Soc       Date:  2005-06-22       Impact factor: 15.419

6.  Onsets of anharmonicity in protein dynamics.

Authors:  J H Roh; V N Novikov; R B Gregory; J E Curtis; Z Chowdhuri; A P Sokolov
Journal:  Phys Rev Lett       Date:  2005-07-12       Impact factor: 9.161

7.  Translational hydration water dynamics drives the protein glass transition.

Authors:  Alexander L Tournier; Jiancong Xu; Jeremy C Smith
Journal:  Biophys J       Date:  2003-09       Impact factor: 4.033

8.  Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility.

Authors:  T Kamiyama; K Gekko
Journal:  Biochim Biophys Acta       Date:  2000-05-23

9.  High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase.

Authors:  R Kitahara; S Sareth; H Yamada; E Ohmae; K Gekko; K Akasaka
Journal:  Biochemistry       Date:  2000-10-24       Impact factor: 3.162

Review 10.  Protein-water displacement distributions.

Authors:  Wolfgang Doster; Marcus Settles
Journal:  Biochim Biophys Acta       Date:  2005-04-09
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