Proceedings of the National Academy of Sciences of the United States of America

About the PNAS Member Editor
Name McCammon, J. Andrew
Location University of California, San Diego
Primary Field Biophysics and Computational Biology
Secondary Field Chemistry
 Research Interests
Molecular movement underlies all cellular processes. Substrates and hormones diffuse to enzymes and receptors, respectively, to initiate catalytic and signaling events. The binding of such molecules to one another generally requires internal motions, analogous to the fitting of a hand into a glove. The interactions of these molecules are highly selective to maintain order in the heavy molecular traffic in and around cells. Our group studies biomolecular and cellular activity by computer simulation of molecular motion. In molecular dynamics simulations, the atoms of a biological molecule-and often those in its solvent surroundings--are represented explicitly in a computer model, and Newton's equations of motion are applied to generate representative trajectories of the atoms. We have adapted such simulations to show how ligands bind to proteins, and how strongly. These methods have proved useful in drug-discovery applications, e.g., in the development of compounds that are now used for the treatment of HIV infections. We have also developed implicit treatments of solvent with corresponding descriptions of solute motion (Brownian dynamics), and shown how electrostatic interactions speed the diffusional encounter of certain enzymes and their substrates. At the largest scales, we are drawing on the increasing knowledge of the structure of cellular structures and of the physicochemical properties of their molecular components, to initiate simulation studies at the cellular level.

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