title: Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.
abstract: Herein we summarize our progress toward the understanding of hammerhead ribozyme (HHR) catalysis through a multiscale simulation strategy. Simulation results collectively paint a picture of HHR catalysis: HHR first folds to form an electronegative active site pocket to recruit a threshold occupation of cationic charges, either a Mg(2+) ion or multiple monovalent cations. Catalytically active conformations that have good in-line fitness are supported by specific metal ion coordination patterns that involve either a bridging Mg(2+) ion or multiple Na(+) ions, one of which is also in a bridging coordination pattern. In the case of a single Mg(2+) ion bound in the active site, the Mg(2+) ion undergoes a migration that is coupled with deprotonation of the nucleophile (C17:O2'). As the reaction proceeds, the Mg(2+) ion stabilizes the accumulating charge of the leaving group and significantly increases the general acid ability of G8:O2'. Further computational mutagenesis simulations suggest that the disruptions due to mutations may severely impact HHR catalysis at different stages of the reaction. Catalytic mechanisms supported by the simulation results are consistent with available structural and biochemical experiments, and together they advance our understanding of HHR catalysis.
authors.affiliation: Center for Integrative Proteomics Research and BioMaPS Institute for Quantitative Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA.
authors.forename: Tai-Sung
authors.initials: TS
authors.lastname: Lee
authors.forename: Kin-Yiu
authors.initials: KY
authors.lastname: Wong
authors.forename: George M
authors.initials: GM
authors.lastname: Giambasu
authors.forename: Darrin M
authors.initials: DM
authors.lastname: York
mesh_terms: D055162:Biocatalysis; D016337:RNA, Catalytic / Q000378:metabolism*
chemical_list: D016337:RNA, Catalytic; C427204:hammerhead ribozyme
keywords: RNA; catalysis; combined QM/MM; enzyme; free energy; hammerhead ribozyme; mechanism; simulation