Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.

ABSTRACT:

Background

The calculation of diffusion-controlled ligand binding rates is important for understanding enzyme mechanisms as well as designing enzyme inhibitors.

Methods

We demonstrate the accuracy and effectiveness of a Lagrangian particle-based method, smoothed particle hydrodynamics (SPH), to study diffusion in biomolecular systems by numerically solving the time-dependent Smoluchowski equation for continuum diffusion. Unlike previous studies, a reactive Robin boundary condition (BC), rather than the absolute absorbing (Dirichlet) BC, is considered on the reactive boundaries. This new BC treatment allows for the analysis of enzymes with "imperfect" reaction rates.

Results

The numerical method is first verified in simple systems and then applied to the calculation of

SUBMITTER: Pan W 

PROVIDER: S-EPMC4438506 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature