Trapped water molecules are essential to structural dynamics and function of a ribozyme.

ABSTRACT: Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular dynamics simulation and single molecule fluorescence spectroscopy approaches, we find that a ribozyme from a subviral plant pathogen exhibits a coupled hydrogen bonding network that communicates dynamic structural rearrangements throughout the catalytic core in response to site-specific chemical modification. Trapped long-residency water molecules are critical for this network and only occasionally exchange with bulk solvent as they pass through a breathing interdomain base stack. These highly structured water molecules line up in a string that may potentially also be involved in specific base

SUBMITTER: Rhodes MM 

PROVIDER: S-EPMC1569172 | biostudies-literature | 2006 Sep

REPOSITORIES: biostudies-literature