Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness.

ABSTRACT: We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided by results obtained on exactly solvable model problems, we transform the problem of diffusion in a potential into free diffusion in the presence of an absorbing zone spanning the entrance to the binding funnel. The free diffusion problem is solved using a recently derived analytic expression for the rate of association of asymmetrically oriented molecules. Despite the required high steric specificity and the absence of long-range attractive interactions, the computed rates are typically on the order of 10(4)-10(6) M(-1) sec(-1), several orders of magnitu

SUBMITTER: Schlosshauer M 

PROVIDER: S-EPMC2279981 | biostudies-literature | 2004 Jun

REPOSITORIES: biostudies-literature