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J. Andrew McCammon
Statistical mechanics and computational chemistry, with applications to biological systems
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| Contact Information |
| Office: UH 4246 |
| Phone: (858) 534-2905 |
| Fax: (858) 534-4974 |
| Email: jmccammo@ucsd.edu |
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| View group members
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| Education and Appointments |
| 1976 |
Ph.D., Harvard University
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| 1969 |
B.A., Pomona College
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| Awards and Academic Honors |
| 2008 |
American Chemical Society National Award for Computers in Chemical and Pharmaceutical Research |
| 2006 |
Elected Fellow, American Academy of Arts and Sciences |
| 2003 |
UCSD SPPS Associated Students Teaching Award |
| 2002 |
Chancellor's Associates Award for Research |
| 2000 |
Appointed Investigator, Howard Hughes Medical Institute |
| 1999 |
Elected Fellow, Biophysical Society |
| 1997 |
Elected Fellow, American Association for the Advancement of Science |
| 1995- |
Joseph E. Mayer Chair of Theoretical Chemistry, U.C. San Diego |
| 1995 |
Smithsonian Award for Breakthrough Computational Science |
| 1991 |
Centennial Lecture, University of Chicago |
| 1987-1992 |
George Hitchings Award for Innovative Methods in Drug Design, Burroughs Wellcome Fund |
| 1984 |
Elected Fellow, American Physical Society |
| 1982-87 |
Dreyfus Teacher-Scholar Award |
| 1981-1994 |
M.D. Anderson Chair of Chemistry, University of Houston |
| 1980-85 |
N.I.H. Research Career Development Award |
| 1980-84 |
Sloan Research Fellow |
| 1976-1978 |
N.S.F./N.I.H. Postdoctoral Fellow, Harvard University |
| Research Interests |
Most chemical reactions are carried out in solution. The solvent surroundings affect such reactions in a variety of important ways. For example, the rates of reactions between ionized molecules are often limited by the rate at which the reactants diffuse through the solvent and come into contact. Also, specific solvation effects often determine the relative free energies or stabilities of reactant, transition state, and product molecules. In our group, we study such phenomena using methods from statistical mechanics. These methods range from simulation studies, in which the equations of motion of the atoms in a model system are solved on a computer, to formal studies in which we develop and solve differential or other equations.
We also use computer models and formal techniques to examine how protein molecules function. The proteins of interest include enzymes and ligand binding proteins such as antibody molecules. The theoretical studies show, for example, how a substrate may be attracted to the active site of an enzyme by electrostatic interactions, and how the atoms within an enzyme move to participate in the catalytic transformation of a bound substrate. These methods are of practical importance in the design of new enzymes that can be synthesized by genetic engineering techniques, and in the design of new drugs that bind strongly to their receptors.
Our simulation studies benefit from the excellent computing facilities to which we have access. These facilities include parallel supercomputers and sophisticated computer graphics systems that allow for the visualization of the atomic dynamics in solutions or protein molecules by virtual reality methods.
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| Primary Research Area: |
Interdisciplinary Specialties: |
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Physical/Analytical Chemistry
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Biophysics
Computational and Theoretical
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| Selected Publications |
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Gullingsrud, J., C. Kim, S.S. Taylor, J.A. McCammon. Dynamic binding of PKA regulatory subunit RIalpha. Structure 14, 141-149 (2006).
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Dzubiella, J., J.M.J. Swanson, J.A. McCammon. Coupling hydrophobic, dispersion, and electrostatic contributions in continuum solvent models. Phys. Rev. Letters 96, article 087802 (2006).
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Lu, B., X. Cheng, J. Huang, J.A. McCammon. An order N algorithm for computation of electrostatic interactions in biomolecular systems. Proc. Natl. Acad. Sci. USA 103, 19314-19319 (2006).
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Cheng, Y., J.K. Suen, D. Zhang, S.D. Bond, Y. Zhang, Y. Song, N.A. Baker, C.L. Bajaj, M.J. Holst, J.A. McCammon. Finite Element Analysis of the Time-Dependent Smoluchowski Equation for Acetylcholinesterase Reaction Rate Calculations. Biophys. J. 92, 3397-3406 (2007).
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Trylska, J., V. Tozzini, C.E. Chang, J.A. McCammon. HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys. J. 92, 4179-4187 (2007).
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Minh, D.L.D, D. Hamelberg, J.A. McCammon. Accelerated entropy estimates with accelerated dynamics. J. Chem. Phys. 127, article number 154105 (2007).
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Amaro, R.E., R.V. Swift, J.A. McCammon. Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei. PLoS Neglected Tropical Diseases 1, article number e68 (2007).
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Gorfe, A.A., C.E. Chang, I. Ivanov, J.A. McCammon. Dynamics of the acetylcholinesterase tetramer. Biophys. J. in press (2008).
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