PICOSECOND-NANOSECOND DYNAMICS OF HAMMERHEAD RNA VERSUS PROTEIN RNASE A: MD SIMULATION STUDY
Sheila Khodadadi, a) Steven L. Fiedler,b) and Joseph E. Curtisa)
a)National Institute of Standards and Technology, Gaithersburg, Maryland 20899 USA
b) Department of Chemistry and Biochemistry, California State University, Northridge, Northridge, CA 91330-8262
We have performed molecular dynamics simulations of a hydrated polycrystalline powder of the catalytic hammerhead RNA at various temperatures from 50 K to 300 K in order to investigate the ability of current force field parameters to quantitatively reproduce the amplitude and length scale of motions of hydrogen atoms in RNA. We have compared dynamical results of non-exchangeable protons in RNA and protein to pre-existing experimental data obtained by neutron scattering methods using similar systems. We have found that the CHARMM-27 force field adequately reproduces the amplitudes of dynamical motions of RNA at least to the same degree that is achieved in the simulation of hydrated protein powders. We attribute the difference in the amplitudes of motions as a function of temperature between protein and RNA to the presence of more dynamically labile non-exchangeable protons in proteins, which on a pre-proton basis is dominated by methyl hydrogen atoms. In addition, we have found that the structural relaxation that occurs at temperatures around the dynamical transition temperature of RNA at ~200 K is correlated to the relaxation of the nucleic acid / water hydrogen bond network as has been observed for proteins in aqueous and non-aqueous environments.