Martin Karplus

The research of Professor Martin Karplus and his group is directed toward understanding the electronic structure, geometry, and dynamics of molecules of chemical and biological interest. In each study a problem that needs to be solved is isolated and the methods required are developed and applied. In recent years, techniques of ab initio and semi-empirical quantum mechanics, theoretical and computational statistical mechanics, classical and quantum dynamics as well as other approaches, including experimental NMR, have been used.

Solution Dynamics and Thermodynamics. The availability of a deeper understanding of the statistical mechanics of liquids and the development of molecular dynamics and Monte Carlo simulation techniques make it possible to attempt a microscopic (first principles) approach to a variety of problems in the chemistry of solutions. Under study are the conformational equilibria of biopolymers, cage effects in reaction dynamics, and the spectra of molecules in solution.

Protein and Nucleic Acids. These biopolymers play an essential role in living systems. The applications of molecular and harmonic dynamics techniques have delineated the time scales and magnitudes of the fluctuations that occur and have indicated their functional importance. Free energy simulations make it possible to determine the effects of mutations on function and stability. Methods are now being used to study enzyme reactions at the same level of detail as is available from the theory of gas phase reactions. A recent field of research is concerned with the study of biomolecular motors, such as myosin.

Selected Publications

1. Aspects of Protein Reaction Dynamics: Deviations from Simple Behavior, J. Phys. Chem. B 104, 11-27 (2000), by M. Karplus.

2. Understanding Protein Folding via Free-Energy Surfaces from Theory and Experiment, TiBS 25, 331-339 (2000), by A. R. Dinner, A. Sali, L. J. Smith, C. M. Dobson, and M. Karplus.

3. A Dynamic Model for the Allosteric Mechanism of GroEL, J. Mol. Biol. 302, 303-313 (2000), by J. Ma, P. B. Sigler, Z. Xu and M. Karplus.

4. Triosephosphate Isomerase: A Theoretical Comparison of Alternative Pathways, J. Am. Chem. Soc. 123, 2284-2290 (2001), by Q. Cui and M. Karplus.

5. Uracil-DNA Glycosylase Acts by Substrate Autocatalysis, Nature 413, 752-755 (2001), by A. R. Dinner, G. M. Blackburn, and M. Karplus.

6. Molecular Dynamics and Protein Function, Proc. Natl. Acad. Sci. USA 102, 6679-6685 (2005), by M. Karplus and J. Kuriyan.

7. A Structure-Based Model for the Synthesis and Hydrolysis of ATP by F1 ATPase, Cell 123, 195-205 (2005), by Y. Q. Gao, W. Yang, and M. Karplus.

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