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


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.

SUBMITTER: Berezhkovskii AM 

PROVIDER: S-EPMC3172035 | biostudies-other | 2011 Aug

REPOSITORIES: biostudies-other

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