QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester A + D Associative Mechanism with an O2' H Internal Proton Transfer.
The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and i...
| Publicado en: | Journal of the American Chemical Society Vol. 136; no. 3; pp. 927 - 937 |
|---|---|
| Autores principales: | , , |
| Formato: | Artículo |
| Publicado: |
American Chemical Society
1/22/2014
|
| Materias: | |
| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=hlh&AN=95065888&site=ehost-live header: @attributes: shortDbName: hlh uiTerm: 95065888 longDbName: Humanities International Complete uiTag: AN controlInfo: bkinfo: jinfo: jid: 00027863 ACS jtl: Journal of the American Chemical Society issn: 00027863 maglogo: N pubinfo: dt: 1/22/2014 vid: 136 iid: 3 pid: 997 pub: American Chemical Society artinfo: ui: 95065888 10.1021/ja406122c ppf: 927 ppct: 10 formats: tig: atl: QM/MM Simulation (B3LYP) of the RNase A Cleavage-Transesterification Reaction Supports a Triester A + D Associative Mechanism with an O2' H Internal Proton Transfer. aug: au: Elsässer, Brigitta Fels, Gregor Weare, John H. affil: Department of Chemistry, University of Paderborn, Warburgerstr. 100, D-33098 Paderborn, Germany Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Dr. 92093 La Jolla, California, United States su: Ribonuclease A Scission (Chemistry) Transesterification kinetics Proton transfer reaction kinetics Free energy (Thermodynamics) Quantum chemistry Nucleophilic catalysis sug: subj: Ribonuclease A Scission (Chemistry) Transesterification kinetics Proton transfer reaction kinetics Free energy (Thermodynamics) Quantum chemistry Nucleophilic catalysis ab: The mechanism of the backbone cleavage-transesterification step of the RNase A enzyme remains controversial even after 60 years of study. We report quantum mechanics/molecule mechanics (QM/MM) free energy calculations for two optimized reaction paths based on an analysis of all structural data and identified by a search for reaction coordinates using a reliable quantum chemistry method (B3LYP), equilibrated structural optimizations, and free energy estimations. Both paths are initiated by nucleophilic attack of the ribose O2' oxygen on the neighboring diester phosphate bond, and both reach the same product state (PS) (a O3'-O2' cyclic phosphate and a O5' hydroxyl terminated fragment). Path 1, resembles the widely accepted dianionic transition-state (TS) general acid (His 1 19)/base (His12) classical mechanism. However, this path has a barrier (25 kcal/ mol) higher than that of the rate-limiting hydrolysis step and a very loose TS. In Path 2, the proton initially coordinating the O2' migrates to the nonbridging O1P in the initial reaction path rather than directly to the general base resulting in a triester (substrate as base) A + D mechanism with a monoanionic wealdy stable intermediate. The structures in the transition region are associative with low barriers (TS1 10, TS2 7.5 kcal/mol). The Path 2 mechanism is consistent with the many results from enzyme and buffer catalyzed and uncatalyzed analog reactions and leads to a PS consistent with the reactive state for the following hydrolysis step. The differences between the consistently estimated barriers in Path 1 and 2 lead to a 10 difference in rate strongly supporting the less accepted triester mechanism. pubtype: Academic Journal doctype: Article src: R language: English refInfo: copyright: @attributes: flag: Y dt: @attributes: year: 2014 holdings: @attributes: islocal: N |
|---|