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

Authors:
Wenxiao Pan
Wenxiao Pan
Shandong University
China
Michael Daily
Michael Daily
Pacific Northwest National Laboratory
Nathan A Baker
Nathan A Baker
Washington University in St. Louis
United States

BMC Biophys 2015 7;8. Epub 2015 May 7.

Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, MSID K7-20, 99352, Richland, PO Box 999 WA USA.

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 ligand binding to a mouse acetylcholinesterase (mAChE) monomer. Rates for inhibitor binding to mAChE are calculated at various ionic strengths and compared with experiment and other numerical methods. We find that imposition of the Robin BC improves agreement between calculated and experimental reaction rates.

Conclusions: Although this initial application focuses on a single monomer system, our new method provides a framework to explore broader applications of SPH in larger-scale biomolecular complexes by taking advantage of its Lagrangian particle-based nature.

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http://dx.doi.org/10.1186/s13628-015-0021-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4438506PMC
May 2015
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