Literature DB >> 20371332

Dynamics of biological macromolecules: not a simple slaving by hydration water.

S Khodadadi1, J H Roh, A Kisliuk, E Mamontov, M Tyagi, S A Woodson, R M Briber, A P Sokolov.   

Abstract

We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account. Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 20371332      PMCID: PMC2849066          DOI: 10.1016/j.bpj.2009.12.4284

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


  32 in total

1.  Dielectric relaxation and solvation dynamics of water in complex chemical and biological systems.

Authors:  N Nandi; K Bhattacharyya; B Bagchi
Journal:  Chem Rev       Date:  2000-06-14       Impact factor: 60.622

2.  Slaving: solvent fluctuations dominate protein dynamics and functions.

Authors:  P W Fenimore; H Frauenfelder; B H McMahon; F G Parak
Journal:  Proc Natl Acad Sci U S A       Date:  2002-11-20       Impact factor: 11.205

3.  Hydration, slaving and protein function.

Authors:  Hans Frauenfelder; P W Fenimore; B H McMahon
Journal:  Biophys Chem       Date:  2002-07-10       Impact factor: 2.352

4.  Effect of the environment on the protein dynamical transition: a neutron scattering study.

Authors:  Alessandro Paciaroni; Stefania Cinelli; Giuseppe Onori
Journal:  Biophys J       Date:  2002-08       Impact factor: 4.033

5.  Protein and solvent dynamics: how strongly are they coupled?

Authors:  G Caliskan; D Mechtani; J H Roh; A Kisliuk; A P Sokolov; S Azzam; M T Cicerone; S Lin-Gibson; I Peral
Journal:  J Chem Phys       Date:  2004-07-22       Impact factor: 3.488

6.  Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations.

Authors:  Taner E Dirama; Gustavo A Carri; Alexei P Sokolov
Journal:  J Chem Phys       Date:  2005-06-22       Impact factor: 3.488

7.  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

8.  Dynamic transition in tRNA is solvent induced.

Authors:  Gokhan Caliskan; Robert M Briber; D Thirumalai; Victoria Garcia-Sakai; Sarah A Woodson; Alexei P Sokolov
Journal:  J Am Chem Soc       Date:  2006-01-11       Impact factor: 15.419

9.  Dynamics of tRNA at different levels of hydration.

Authors:  J H Roh; R M Briber; A Damjanovic; D Thirumalai; S A Woodson; A P Sokolov
Journal:  Biophys J       Date:  2009-04-08       Impact factor: 4.033

Review 10.  Protein-water displacement distributions.

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

1.  Solvent effect on librational dynamics of spin-labelled haemoglobin by ED- and CW-EPR.

Authors:  Francesco Scarpelli; Rosa Bartucci; Luigi Sportelli; Rita Guzzi
Journal:  Eur Biophys J       Date:  2010-11-25       Impact factor: 1.733

2.  Role of methyl groups in dynamics and evolution of biomolecules.

Authors:  Jonathan D Nickels; Joseph E Curtis; Hugh O'Neill; Alexei P Sokolov
Journal:  J Biol Phys       Date:  2012-04-14       Impact factor: 1.365

3.  Molecular Dynamics and NMR Shed Light on Motions Underpinning Dynamical Transitions in Biomolecules.

Authors:  Lennart Nilsson
Journal:  Biophys J       Date:  2015-06-16       Impact factor: 4.033

4.  Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP.

Authors:  Jonathan D Nickels; Hugh O'Neill; Liang Hong; Madhusudan Tyagi; Georg Ehlers; Kevin L Weiss; Qiu Zhang; Zheng Yi; Eugene Mamontov; Jeremy C Smith; Alexei P Sokolov
Journal:  Biophys J       Date:  2012-10-02       Impact factor: 4.033

5.  Dynamical coupling of intrinsically disordered proteins and their hydration water: comparison with folded soluble and membrane proteins.

Authors:  F-X Gallat; A Laganowsky; K Wood; F Gabel; L van Eijck; J Wuttke; M Moulin; M Härtlein; D Eisenberg; J-P Colletier; G Zaccai; M Weik
Journal:  Biophys J       Date:  2012-07-03       Impact factor: 4.033

6.  NMR Water Self-Diffusion and Relaxation Studies on Sodium Polyacrylate Solutions and Gels in Physiologic Ionic Solutions.

Authors:  Ruiliang Bai; Peter J Basser; Robert M Briber; Ferenc Horkay
Journal:  J Appl Polym Sci       Date:  2014-03-15       Impact factor: 3.125

7.  On the use of ultracentrifugal devices for routine sample preparation in biomolecular magic-angle-spinning NMR.

Authors:  Abhishek Mandal; Jennifer C Boatz; Travis B Wheeler; Patrick C A van der Wel
Journal:  J Biomol NMR       Date:  2017-02-22       Impact factor: 2.835

8.  Anomalously Rapid Hydration Water Diffusion Dynamics Near DNA Surfaces.

Authors:  John M Franck; Yuan Ding; Katherine Stone; Peter Z Qin; Songi Han
Journal:  J Am Chem Soc       Date:  2015-09-10       Impact factor: 15.419

9.  Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin.

Authors:  Camille J Roche; David Dantsker; Elizabeth R Heller; Joseph E Sabat; Joel M Friedman
Journal:  Chem Phys       Date:  2013-08-30       Impact factor: 2.348

10.  Nonthermal excitation effects mediated by sub-terahertz radiation on hydrogen exchange in ubiquitin.

Authors:  Yuji Tokunaga; Masahito Tanaka; Hitoshi Iida; Moto Kinoshita; Yuya Tojima; Koh Takeuchi; Masahiko Imashimizu
Journal:  Biophys J       Date:  2021-05-01       Impact factor: 3.699

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