The broad objective of this research is to establish the foundation for a novel fully quantum mechanical forcefield for simulations of biocatalysis that can be seamlessly integrated with other multi-scale modeling tools and applied to complex biological problems not accessible by other methods. The design of these new computational tools will greatly extend the scope of biocatalysis applications that can be reliably addressed. The impact of this work with be to create a paradigm shift away from conventional mixed quantum mechanical/molecular mechanical (QM/MM) models toward a united fully quantum mechanical approach for molecular simulations of reactive processes in complex environments. The core methods will be based on a new quantum mechanical model for biocatalysis (Biocat-QM) that combines the advantages of existing semiempirical models and extends their capabilities to accurately model reaction barriers, and charge-dependent many-body exchange, polarization and dispersion effects. The Biocat-QM will form the base of a QM/MM model that contains a new form of the QM/MM interaction where non-bonded terms automatically adjust in response to changes in charge state and hybridization. Ultimately, the Biocat-QM will be made into a novel fully quantum mechanical forcefield for simulations of biocatalysis, based on a new linear-scaling quantum method that utilizes a density-overlap repulsion model to circumvent the need for large local basis projections, and that takes advantage of a recently developed adaptive fast-multipole algorithm for efficient calculation of electrostatic interactions for generalized charge distributions. The new tools for simulations of biocatalysis developed in this proposal are designed to surmount the difficulties presented by specific driving applications: the study of the molecular mechanisms of ribozyme catalysis. The methods will be applied to two ribozyme systems that exhibit large-scale conformational changes and divalent metal ion binding coupled with catalysis, and for which very recent structural data has become available through collaborator Prof. William Scott: the full length hammerhead ribozyme and the L1 ligase ribozyme/riboswitch. These systems present unique challenges for which there currently exists no sufficiently reliable biocatalysis simulation model. The computational tools developed in this proposal will be implemented as publicly available modular software, optimized and ported to several high-performance computing platforms, and integrated with the molecular simulation packages AMBER and CHARMM.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM084149-03
Application #
7848164
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Preusch, Peter C
Project Start
2008-04-01
Project End
2010-08-31
Budget Start
2010-04-01
Budget End
2010-08-31
Support Year
3
Fiscal Year
2010
Total Cost
$52,483
Indirect Cost
Name
University of Minnesota Twin Cities
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
555917996
City
Minneapolis
State
MN
Country
United States
Zip Code
55455
Lee, Tai-Sung; Wong, Kin-Yiu; Giambasu, George M et al. (2013) Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis. Prog Mol Biol Transl Sci 120:25-91
Giese, Timothy J; Chen, Haoyuan; Dissanayake, Thakshila et al. (2013) A variational linear-scaling framework to build practical, efficient next-generation orbital-based quantum force fields. J Chem Theory Comput 9:1417-1427
Giamba?u, George M; Lee, Tai-Sung; Scott, William G et al. (2012) Mapping L1 ligase ribozyme conformational switch. J Mol Biol 423:106-22
Kaminski, Steve; Giese, Timothy J; Gaus, Michael et al. (2012) Extended polarization in third-order SCC-DFTB from chemical-potential equalization. J Phys Chem A 116:9131-41
Giese, Timothy J; York, Darrin M (2012) Density-functional expansion methods: Grand challenges. Theor Chem Acc 131:
Wong, Kin-Yiu; York, Darrin M (2012) Exact Relation between Potential of Mean Force and Free-Energy Profile. J Chem Theory Comput 8:3998-4003
Giese, Timothy J; York, Darrin M (2011) Density-functional expansion methods: generalization of the auxiliary basis. J Chem Phys 134:194103
Wong, Kin-Yiu; Lee, Tai-Sung; York, Darrin M (2011) Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme. J Chem Theory Comput 7:1-3
Giambasu, George M; Lee, Tai-Sung; Sosa, Carlos P et al. (2010) Identification of dynamical hinge points of the L1 ligase molecular switch. RNA 16:769-80
Giese, Timothy J; York, Darrin M (2010) Density-functional expansion methods: evaluation of LDA, GGA, and meta-GGA functionals and different integral approximations. J Chem Phys 133:244107

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