Dynamics of tRNA at different levels of hydration

J. H. Roh, R. M. Briber, A. Damjanovic, D. Thirumalai, S. A. Woodson, A. P. Sokolov

Research output: Contribution to journalArticle

Abstract

The influence of hydration on the nanosecond timescale dynamics of tRNA is investigated using neutron scattering spectroscopy. Unlike protein dynamics, the dynamics of tRNA is not affected by methyl group rotation. This allows for a simpler analysis of the influence of hydration on the conformational motions in RNA. We find that hydration affects the dynamics of tRNA significantly more than that of lysozyme. Both the characteristic length scale and the timescale of the conformational motions in tRNA depend strongly on hydration. Even the characteristic temperature of the so-called "dynamical transition" appears to be hydration-dependent in tRNA. The amplitude of the conformational motions in fully hydrated tRNA is almost twice as large as in hydrated lysozyme. We ascribe these differences to a more open and flexible structure of hydrated RNA, and to a larger fraction and different nature of hydrophilic sites. The latter leads to a higher density of water that makes the biomolecule more flexible. All-atom molecular-dynamics simulations are used to show that the extent of hydration is greater in tRNA than in lysozyme. We propose that water acts as a "lubricant" in facilitating enhanced motion in solvated RNA molecules.

Original languageEnglish (US)
Pages (from-to)2755-2762
Number of pages8
JournalBiophysical Journal
Volume96
Issue number7
DOIs
StatePublished - 2009

Fingerprint

Transfer RNA
Muramidase
RNA
Lubricants
Water
Neutrons
Molecular Dynamics Simulation
Spectrum Analysis
Temperature
Proteins

ASJC Scopus subject areas

  • Biophysics

Cite this

Roh, J. H., Briber, R. M., Damjanovic, A., Thirumalai, D., Woodson, S. A., & Sokolov, A. P. (2009). Dynamics of tRNA at different levels of hydration. Biophysical Journal, 96(7), 2755-2762. https://doi.org/10.1016/j.bpj.2008.12.3895

Dynamics of tRNA at different levels of hydration. / Roh, J. H.; Briber, R. M.; Damjanovic, A.; Thirumalai, D.; Woodson, S. A.; Sokolov, A. P.

In: Biophysical Journal, Vol. 96, No. 7, 2009, p. 2755-2762.

Research output: Contribution to journalArticle

Roh, JH, Briber, RM, Damjanovic, A, Thirumalai, D, Woodson, SA & Sokolov, AP 2009, 'Dynamics of tRNA at different levels of hydration', Biophysical Journal, vol. 96, no. 7, pp. 2755-2762. https://doi.org/10.1016/j.bpj.2008.12.3895
Roh JH, Briber RM, Damjanovic A, Thirumalai D, Woodson SA, Sokolov AP. Dynamics of tRNA at different levels of hydration. Biophysical Journal. 2009;96(7):2755-2762. https://doi.org/10.1016/j.bpj.2008.12.3895
Roh, J. H. ; Briber, R. M. ; Damjanovic, A. ; Thirumalai, D. ; Woodson, S. A. ; Sokolov, A. P. / Dynamics of tRNA at different levels of hydration. In: Biophysical Journal. 2009 ; Vol. 96, No. 7. pp. 2755-2762.
@article{dda7d89372d04f20b37363a9af6b42f0,
title = "Dynamics of tRNA at different levels of hydration",
abstract = "The influence of hydration on the nanosecond timescale dynamics of tRNA is investigated using neutron scattering spectroscopy. Unlike protein dynamics, the dynamics of tRNA is not affected by methyl group rotation. This allows for a simpler analysis of the influence of hydration on the conformational motions in RNA. We find that hydration affects the dynamics of tRNA significantly more than that of lysozyme. Both the characteristic length scale and the timescale of the conformational motions in tRNA depend strongly on hydration. Even the characteristic temperature of the so-called {"}dynamical transition{"} appears to be hydration-dependent in tRNA. The amplitude of the conformational motions in fully hydrated tRNA is almost twice as large as in hydrated lysozyme. We ascribe these differences to a more open and flexible structure of hydrated RNA, and to a larger fraction and different nature of hydrophilic sites. The latter leads to a higher density of water that makes the biomolecule more flexible. All-atom molecular-dynamics simulations are used to show that the extent of hydration is greater in tRNA than in lysozyme. We propose that water acts as a {"}lubricant{"} in facilitating enhanced motion in solvated RNA molecules.",
author = "Roh, {J. H.} and Briber, {R. M.} and A. Damjanovic and D. Thirumalai and Woodson, {S. A.} and Sokolov, {A. P.}",
year = "2009",
doi = "10.1016/j.bpj.2008.12.3895",
language = "English (US)",
volume = "96",
pages = "2755--2762",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "7",

}

TY - JOUR

T1 - Dynamics of tRNA at different levels of hydration

AU - Roh, J. H.

AU - Briber, R. M.

AU - Damjanovic, A.

AU - Thirumalai, D.

AU - Woodson, S. A.

AU - Sokolov, A. P.

PY - 2009

Y1 - 2009

N2 - The influence of hydration on the nanosecond timescale dynamics of tRNA is investigated using neutron scattering spectroscopy. Unlike protein dynamics, the dynamics of tRNA is not affected by methyl group rotation. This allows for a simpler analysis of the influence of hydration on the conformational motions in RNA. We find that hydration affects the dynamics of tRNA significantly more than that of lysozyme. Both the characteristic length scale and the timescale of the conformational motions in tRNA depend strongly on hydration. Even the characteristic temperature of the so-called "dynamical transition" appears to be hydration-dependent in tRNA. The amplitude of the conformational motions in fully hydrated tRNA is almost twice as large as in hydrated lysozyme. We ascribe these differences to a more open and flexible structure of hydrated RNA, and to a larger fraction and different nature of hydrophilic sites. The latter leads to a higher density of water that makes the biomolecule more flexible. All-atom molecular-dynamics simulations are used to show that the extent of hydration is greater in tRNA than in lysozyme. We propose that water acts as a "lubricant" in facilitating enhanced motion in solvated RNA molecules.

AB - The influence of hydration on the nanosecond timescale dynamics of tRNA is investigated using neutron scattering spectroscopy. Unlike protein dynamics, the dynamics of tRNA is not affected by methyl group rotation. This allows for a simpler analysis of the influence of hydration on the conformational motions in RNA. We find that hydration affects the dynamics of tRNA significantly more than that of lysozyme. Both the characteristic length scale and the timescale of the conformational motions in tRNA depend strongly on hydration. Even the characteristic temperature of the so-called "dynamical transition" appears to be hydration-dependent in tRNA. The amplitude of the conformational motions in fully hydrated tRNA is almost twice as large as in hydrated lysozyme. We ascribe these differences to a more open and flexible structure of hydrated RNA, and to a larger fraction and different nature of hydrophilic sites. The latter leads to a higher density of water that makes the biomolecule more flexible. All-atom molecular-dynamics simulations are used to show that the extent of hydration is greater in tRNA than in lysozyme. We propose that water acts as a "lubricant" in facilitating enhanced motion in solvated RNA molecules.

UR - http://www.scopus.com/inward/record.url?scp=67549115957&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67549115957&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2008.12.3895

DO - 10.1016/j.bpj.2008.12.3895

M3 - Article

C2 - 19348758

AN - SCOPUS:67549115957

VL - 96

SP - 2755

EP - 2762

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 7

ER -