Dynamics of tRNA at different levels of hydration.
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.
Roh
J H
JH
Department of Materials Science and Engineering, University of Maryland, College Park, Maryland, USA. rohmio1973@gmail.com
Briber
R M
RM
Damjanovic
A
A
Thirumalai
D
D
Woodson
S A
SA
Sokolov
A P
AP
D004548:Elasticity; D008958:Models, Molecular; D009068:Movement / Q000187:drug effects; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D033363:Neutron Diffraction; D009690:Nucleic Acid Conformation / Q000187:drug effects; D011487:Protein Conformation / Q000187:drug effects; D012343:RNA, Transfer / Q000737:chemistry* / Q000378:metabolism*; D014867:Water / Q000494:pharmacology*
D014867:Water; D012343:RNA, Transfer; D009113:Muramidase