Faculty

J. ANDREW MCCAMMON

Professor of Pharmacology and Chemistry & Biochemistry

email: jmccammon@ucsd.edu

website: http://mccammon.ucsd.edu

Ph.D., Harvard University

Key Words: Computer-aided Molecular Design; Theory of Molecular Recognition

The students and postdoctoral researchers in our group are developing and applying computer simulation methods to study biomolecular structure, dynamics and function. One method that we use is molecular dynamics. In this method, we use supercomputers to solve the equations of motion of the atoms in enzymes, antibody molecules, lipid membranes, and other systems. The atomic motion is viewed on color graphics devices and is analyzed more quantitatively to determine reaction mechanisms, binding constants, etc. Another simulation method involves calculating the electrostatic fields around biomolecules and analyzing how these fields influence the diffusional encounters of the molecules in solution. This method allows us to predict the effects of mutations on the rates of binding and catalysis in important enzymes.

The methods that we are developing are of practical importance, e.g. in the design of new pharmaceuticals and enzymes, as well as of fundamental importance in providing detailed insights concerning biomolecular activity. Students trained in our group are therefore able to choose among a variety of career paths in industry, government laboratories, medical research institutes, or universities.

Selected Publications:

Gullingsrud, J., C. Kim, S.S. Taylor, J.A. McCammon. Dynamic binding of PKA regulatory subunit RIalpha. Structure 14, 141–149 (2006).

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).

Bui, J., J.A. McCammon. Protein Complex Formation by Acetylcholinesterase and the Neurotoxin Fasciculin-2 Appears to Involve an Induced Fit Mechanism. Proc. Natl. Acad. Sci. USA 103, 15451-15456 (2006).

Hamelberg, D., T. Shen, J.A. McCammon. Insight into the role of hydration on protein dynamics. J. Chem. Phys. 125, article number 094905 (2006).

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).

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. in press (2007).

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. in press (2007).