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1251 Wescoe Hall Drive Malott Hall Room 5090 University of Kansas Lawrence, KS 66045 Phone: (785) 864-5060 Fax: (785) 864-5396 Email: kkuczera@ku.edu |
Computer Simulations of Biomolecular Structure, Dynamics and Thermodynamics
Physical and theoretical chemistry: molecular dynamics simulations, statistical mechanics, quantum chemistry, biological molecules and solutions.
Studies of fundamental properties of complex biological and organic molecules have profound implications for many areas of science, as well as practical applications in curing disease, protecting the environment, improving industrial processes and designing new materials. Although experimental investigations remain the main source of information on large molecular systems, their theoretical and computational studies are gaining importance in recent years. This is due to great increases in computer power and development of efficient computational algorithms, and to the growing understanding that simulations provide unprecedented detail of information which can be fruitfully employed to uncover the microscopic mechanisms of observable, macroscopic properties of molecular systems.
Professor Kuczera's research focuses on the use of methods of modern computational chemistry to study structure, dynamics and thermodynamics of complex molecular systems. The methods used involve mainly molecular dynamics simulations and quantum chemistry. The overall goal is to relate the detailed microscopic information provided by the simulations to observable, macroscopic physical, chemical and biological properties. Besides providing a basic understanding of important classes of molecules, the simulation results provide predictions on how to manipulate the properties for practical purposes. The work involves using existing simulation programs, development of new methods and algorithms for molecular modeling, and collaborations with experimental groups on specific systems.
Recent projects include modeling of properties of the protein calmodulin in its normal and oxidatively damaged states, related to understanding the processes of aging and/or development of neurodegenerative diseases; simulations of the structure and dynamics of the membrane protein phospholamban, aimed at explaining the mechanism by which it regulates transmembrane calcium pumping; normal mode and molecular dynamics studies of domain motions in the enzyme S-Adenosylhomocysteine hydrolase, explaining microscopic details of its activity and guiding design of effective inhibitors; modeling the water-membrane transfer and helix-coil equilibria in model peptides, providing microscopic insights into the detailed effects of temperature and environment on peptide structure; simulations the structure and molecular motions in carbon-dioxide expanded organic liquids, helping explain how the physical properties of these novel environmentally beneficial media can be modulated by adjusting operating pressure.
J. Mahadevan, C. Xu, T. Siahaan and K. Kuczera, Molecular dynamics simulations of conformational behavior of linear RGD peptidomimetics and cyclic prodrugs in aqueous and octane solutions. J. Biomol. Struct. Dyn., 19:775-788 (2002).
G. S. Jas and K. Kuczera, Free energy simulations of the oxidation of {C}-terminal methionines in calmodulin''. Proteins, 48:257-268 (2002).
C. Yang, G. S. Jas and K. Kuczera, Structure, dynamics and interactions with kinase targets: Computer simulations of calmodulin. Biochim. Biophys. Acta, 1697:289-300 (2004).
G. S. Jas and K. Kuczera. Equilibrium structure and folding of a helix-forming peptide: circular dichroism measurements and replica-exchange molecular dynamics simulations. Biophysical J., 87:3786-3798 (2004).
Y. Houndonougbo, G. S. Jas and K. Kuczera. Structure and dynamics of phospholamban in solution and membrane bilayer: Computer simulations. Biochemistry, 44:1780-1792 (2005).
M. Wang, R. L. Schowen, R. T. Borchardt and K. Kuczera. Domain motions and the open-to-closed conformational transition of an enzyme: A normal mode analysis of S-adenosyl-L-homocysteine hydrolase. Biochemistry, 44:7228-7239 (2005).
Q. Cheng, D. R. Benson, M. Rivera-Laos and K. Kuczera. "Influence of point mutations on the flexibility of cytochrome b5: Molecular dynamics simulations of holoproteins'', Biopolymers, 83:297-312 (2006).
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