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Unraveling the Mechanisms of Ribozyme Catalysis with Multiscale Simulations

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Multi-scale Quantum Models for Biocatalysis

Part of the book series: Challenges and Advances in Computational Chemistry and Physics ((COCH,volume 7))

Abstract

Description of a multiscale simulation strategy we have developed to attack problems of RNA catalysis is presented. Ribozyme systems give special challenges not present in typical protein systems, and consequently demand new methods. The main methodological components are herein summarized, including the assembly of the QCRNA database, parameterization of the AM1/d-PhoT Hamiltonian, and development of new semiempirical functional forms for improved charge-dependent response properties, methods for coupling many-body exchange, correlation and dispersion into the QM/MM interaction, and generalized methods for linear-scaling electrostatics, solvation and solvent boundary potentials. Results for a series of case studies ranging from noncatalytic reaction models that compare the effect of new DFT functionals, and on catalytic RNA systems including the hairpin, hammerhead and L1 ligase ribozymes are discussed

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Authors and Affiliations

  1. Biomedical Informatics and Computational Biology, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA

    Tai-Sung Lee, George M. Giambaşu, Timothy J. Giese & Darrin M. York

  2. Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455, USA

    Tai-Sung Lee, George M. Giambaşu, Adam Moser, Carlos Silva-Lopez, Francesca Guerra, Olalla Nieto-Faza, Jiali Gao & Darrin M. York

  3. Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA

    Kwangho Nam

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Lee, TS. et al. (2009). Unraveling the Mechanisms of Ribozyme Catalysis with Multiscale Simulations. In: York, D.M., Lee, TS. (eds) Multi-scale Quantum Models for Biocatalysis. Challenges and Advances in Computational Chemistry and Physics, vol 7. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9956-4_14

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