Gated Diffusion-controlled Reactions
Center for Theoretical Biological Physics, Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, Department of Pharmacology, University of California at San Diego, La Jolla, CA 92093-0365, USA
BMC Biophysics 2011, 4:4 doi:10.1186/2046-1682-4-4Published: 2 March 2011
The binding and active sites of proteins are often dynamically occluded by motion of the nearby polypeptide. A variety of theoretical and computational methods have been developed to predict rates of ligand binding and reactivity in such cases. Two general approaches exist, "protein centric" approaches that explicitly treat only the protein target, and more detailed dynamical simulation approaches in which target and ligand are both treated explicitly. This mini-review describes recent work in this area and some of the biological implications.