Theoretical analysis of functional mechanisms of biological macromolecules using hybrid quantum mechanics/molecular mechanics molecular dynamics simulation

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In thisstudy, mechanisms of biochemical reactions of crucial biological macromolecularsystems wereanalyzedbyemploying hybrid quantummechanicsQM molecularmechanicsMM molecular dynamicsMDsimulation, whichisastate-of-the-art theoretical methodology. As aconsequence of the analyses, we revealedthe significance of "hybrid ribozyme/protein catalyst" andits reaction mechanism, the functional roles of a novelprotein structural element involving "Nainteraction", modulation mechanismsof electronic structures ofDNA bases by protein-DNA interaction, unidirectional mechanisticvalved mechanisms for ammonia transport in protein, etc.