skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Dynamical disparity between hydration shell water and RNA in a hydrated RNA system

Abstract

We have performed large-scale molecular dynamics simulations on hammerhead RNA in water and observed disparity in the dynamical properties between water and RNA. The simulations are carried out above the dynamical transition temperature of RNA and is varied from below freezing to ambient temperature. Using this model, we observed different types of relaxation dynamics for water and RNA. While RNA shows a single stretched exponential decay, the water molecules show a double-exponential decay. Both water and RNA dynamics show temperature and spatial dependence on relaxation times. The RNA relaxations are many orders of magnitude slower compared to water for all temperature and spatial length scales. RNA relaxations show predominantly heterogeneous dynamics. Water dynamics in the hydration shell show a combination of interfacial water and bulk-like water properties and the water dynamics are decoupled from the RNA dynamics. Furthermore, these results explain the dynamics of water in the hydration shell and that of RNA.

Authors:
ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]; ORCiD logo [1]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
Oak Ridge National Laboratory, Oak Ridge Leadership Computing Facility (OLCF); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1496008
DOE Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article
Journal Name:
Physical Review E
Additional Journal Information:
Journal Volume: 98; Journal Issue: 6; Journal ID: ISSN 2470-0045
Publisher:
American Physical Society (APS)
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby G., and Goswami, Monojoy. Dynamical disparity between hydration shell water and RNA in a hydrated RNA system. United States: N. p., 2018. Web. doi:10.1103/PhysRevE.98.062407.
Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby G., & Goswami, Monojoy. Dynamical disparity between hydration shell water and RNA in a hydrated RNA system. United States. doi:10.1103/PhysRevE.98.062407.
Bhowmik, Debsindhu, Ganesh, Panchapakesan, Sumpter, Bobby G., and Goswami, Monojoy. Fri . "Dynamical disparity between hydration shell water and RNA in a hydrated RNA system". United States. doi:10.1103/PhysRevE.98.062407.
@article{osti_1496008,
title = {Dynamical disparity between hydration shell water and RNA in a hydrated RNA system},
author = {Bhowmik, Debsindhu and Ganesh, Panchapakesan and Sumpter, Bobby G. and Goswami, Monojoy},
abstractNote = {We have performed large-scale molecular dynamics simulations on hammerhead RNA in water and observed disparity in the dynamical properties between water and RNA. The simulations are carried out above the dynamical transition temperature of RNA and is varied from below freezing to ambient temperature. Using this model, we observed different types of relaxation dynamics for water and RNA. While RNA shows a single stretched exponential decay, the water molecules show a double-exponential decay. Both water and RNA dynamics show temperature and spatial dependence on relaxation times. The RNA relaxations are many orders of magnitude slower compared to water for all temperature and spatial length scales. RNA relaxations show predominantly heterogeneous dynamics. Water dynamics in the hydration shell show a combination of interfacial water and bulk-like water properties and the water dynamics are decoupled from the RNA dynamics. Furthermore, these results explain the dynamics of water in the hydration shell and that of RNA.},
doi = {10.1103/PhysRevE.98.062407},
journal = {Physical Review E},
issn = {2470-0045},
number = 6,
volume = 98,
place = {United States},
year = {2018},
month = {12}
}

Works referenced in this record:

Scalable molecular dynamics with NAMD
journal, January 2005

  • Phillips, James C.; Braun, Rosemary; Wang, Wei
  • Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
  • DOI: 10.1002/jcc.20289