Work

Diffusion-influenced ligand binding to buried sites in macromolecules and transmembrane channels

Year: 2011

Type: article

Abstract: We consider diffusion-influenced binding to a buried binding site that is connected to the surface by a narrow tunnel. Under the single assumption of an equilibrium distribution of ligands over the tunnel cross section, we reduce the calculation of the time-dependent rate coefficient to the solution of a one-dimensional diffusion equation with appropriate boundary conditions. We obtain a simple analytical expression for the steady-state rate that depends on the potential of mean force in the tunnel and the diffusion-controlled rate of binding to the tunnel entrance. Potential applications of our theory include substrate binding to a buried active site of an enzyme and permeant ion binding to an internal site in a transmembrane channel.

Source: The Journal of Chemical Physics

DOI: 10.1063/1.3609973

Authors: Alexander M. Berezhkovskii, Attila Szabo, Huan-Xiang Zhou

Institutions: National Institutes of Health, Center for Information Technology, National Institute of Diabetes and Digestive and Kidney Diseases, Florida State University

Language: English

Topic: Diffusion and Search Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Institute of General Medical Sciences, National Institute of Allergy and Infectious Diseases, National Institute of Diabetes and Digestive and Kidney Diseases

Awards: G1197277349, G1773173006, Theory of Protein-Protein Association, G59170538, G9000041719