Paper Citing NAMD - Abstract
Lee, Tai-Sung; York, Darrin M.
Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 130:7168-+, JUN 11 2008
A series of ten 60 ns molecular dynamics (MD) simulations of the native and mutated full length hammerhead ribozymes in the reactant state and in an activated precursor state (G8:2'OH deprotonated) are reported. Mutant simulations include the C3U, G8A, and G81 single mutants and a C3U/G8A double mutant 0 that exhibits an experimental rescue effect. The results provide critical details into the origin of the observed mutation effects and support a mechanism where the 2'OH of G8 acts as a general acid catalyst that is held in position through Watson-Crick hydrogen bonding between G8 and C3.
