Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.

• MeSH
• biofyzika metody   MeSH
• fosfáty chemie   MeSH
• fosforylace MeSH
• hořčík chemie   MeSH
• katalýza MeSH
• konformace nukleové kyseliny MeSH
• kvantová teorie MeSH
• lidé MeSH
• molekulární modely MeSH
• počítačová simulace MeSH
• ribozomy chemie   MeSH
• RNA katalytická chemie   MeSH
• RNA virová chemie   MeSH
• RNA chemie   MeSH
• software MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• fosfáty MeSH
• hammerhead ribozyme MeSH Prohlížeč
• hořčík MeSH
• RNA katalytická MeSH
• RNA virová MeSH
• RNA MeSH