Unraveling the mechanisms of ribozyme catalysis with multiscale simulations

Tai Sung Lee; George M. Giambaşu; Adam Moser; Kwangho Nam; Carlos Silva-Lopez; Francesca Guerra; Olalla Nieto-Faza; Timothy J. Giese; Jiali Gao; Darrin M. York

doi:10.1007/978-1-4020-9956-4_14

Unraveling the mechanisms of ribozyme catalysis with multiscale simulations

Tai Sung Lee, George M. Giambaşu, Adam Moser, Kwangho Nam, Carlos Silva-Lopez, Francesca Guerra, Olalla Nieto-Faza, Timothy J. Giese, Jiali Gao, Darrin M. York

Chemistry (Twin Cities)

Research output: Chapter in Book/Report/Conference proceeding › Chapter

2 Scopus citations

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.

Original language	English (US)
Title of host publication	Challenges and Advances in Computational Chemistry and Physics
Publisher	Springer
Pages	377-408
Number of pages	32
DOIs	https://doi.org/10.1007/978-1-4020-9956-4_14
State	Published - 2009

Publication series

Name	Challenges and Advances in Computational Chemistry and Physics
Volume	7
ISSN (Print)	2542-4491
ISSN (Electronic)	2542-4483

Bibliographical note

Publisher Copyright:
© Springer Science+Business Media B.V. 2009.

Keywords

DFT functional
QM/MM
Ribozyme catalysis
linear-scaling method
multiscale simulation

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10.1007/978-1-4020-9956-4_14

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Lee, T. S., Giambaşu, G. M., Moser, A., Nam, K., Silva-Lopez, C., Guerra, F., Nieto-Faza, O., Giese, T. J., Gao, J., & York, D. M. (2009). Unraveling the mechanisms of ribozyme catalysis with multiscale simulations. In Challenges and Advances in Computational Chemistry and Physics (pp. 377-408). (Challenges and Advances in Computational Chemistry and Physics; Vol. 7). Springer. https://doi.org/10.1007/978-1-4020-9956-4_14

Unraveling the mechanisms of ribozyme catalysis with multiscale simulations. / Lee, Tai Sung; Giambaşu, George M.; Moser, Adam et al.
Challenges and Advances in Computational Chemistry and Physics. Springer, 2009. p. 377-408 (Challenges and Advances in Computational Chemistry and Physics; Vol. 7).

Research output: Chapter in Book/Report/Conference proceeding › Chapter

Lee, TS, Giambaşu, GM, Moser, A, Nam, K, Silva-Lopez, C, Guerra, F, Nieto-Faza, O, Giese, TJ, Gao, J & York, DM 2009, Unraveling the mechanisms of ribozyme catalysis with multiscale simulations. in Challenges and Advances in Computational Chemistry and Physics. Challenges and Advances in Computational Chemistry and Physics, vol. 7, Springer, pp. 377-408. https://doi.org/10.1007/978-1-4020-9956-4_14

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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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AU - Guerra, Francesca

AU - Nieto-Faza, Olalla

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AB - 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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Unraveling the mechanisms of ribozyme catalysis with multiscale simulations

Abstract

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Keywords

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