QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.
The hairpin ribozyme is a prominent member of small ribozymes since it does not require metal ions to achieve catalysis. Guanine 8 (G8) and adenine 38 (A38) have been identified as key participants in self-cleavage and -ligation. We have carried out hybrid quantum-mechanical/molecular mechanical (QM/MM) calculations to evaluate the energy along several putative reaction pathways. The error of our DFT description of the QM region was tested and shown to be ~1 kcal/mol. We find that self-cleavage of the hairpin ribozyme may follow several competing microscopic reaction mechanisms, all with calculated activation barriers in good agreement with those from experiment (20-21 kcal/mol). The initial nucleophilic attack of the A-1(2'-OH) group on the scissile phosphate is predicted to be rate-limiting in all these mechanisms. An unprotonated G8(-) (together with A38H(+)) yields a feasible activation barrier (20.4 kcal/mol). Proton transfer to a nonbridging phosphate oxygen also leads to feasible reaction pathways. Finally, our calculations consider thio-substitutions of one or both nonbridging oxygens of the scissile phosphate and predict that they have only a negligible effect on the reaction barrier, as observed experimentally.
Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, tr. 17 listopadu 12, 771 46 Olomouc, Czech Republic.
Vojtěch
V
Mlýnský
Pavel
P
Banáš
Nils G
NG
Walter
Jiří
J
Šponer
Michal
M
Otyepka
D002384:Catalysis; D056004:Molecular Dynamics Simulation; D010100:Oxygen / Q000737:chemistry; D011522:Protons; D011789:Quantum Theory; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
D011522:Protons; D016337:RNA, Catalytic; C418481:hairpin ribozyme; D010100:Oxygen