Highly accurate biomolecular electrostatics in continuum dielectric environments

Authors

  • Y. C. Zhou,

    1. Department of Mathematics, Michigan State University, East Lansing, Michigan 48824
    Current affiliation:
    1. Department of Mathematics, University of California, San Diego, La Jolla, CA 92093-0112, USA
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  • Michael Feig,

    1. Department of Chemistry, Michigan State University, East Lansing, Michigan 48824
    2. Department of Biochemistry and Molecular Biology, 4223 Biomedical Physical Sciences Building, Michigan State University, East Lansing, Michigan 48824
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  • G. W. Wei

    Corresponding author
    1. Department of Mathematics, Michigan State University, East Lansing, Michigan 48824
    2. Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824
    • Department of Mathematics, Michigan State University, East Lansing, Michigan 48824
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Abstract

Implicit solvent models based on the Poisson-Boltzmann (PB) equation are frequently used to describe the interactions of a biomolecule with its dielectric continuum environment. A novel, highly accurate Poisson-Boltzmann solver is developed based on the matched interface and boundary (MIB) method, which rigorously enforces the continuity conditions of both the electrostatic potential and its flux at the molecular surface. The MIB based PB solver attains much better convergence rates as a function of mesh size compared to conventional finite difference and finite element based PB solvers. Consequently, highly accurate electrostatic potentials and solvation energies are obtained at coarse mesh sizes. In the context of biomolecular electrostatic calculations it is demonstrated that the MIB method generates substantially more accurate solutions of the PB equation than other established methods, thus providing a new level of reference values for such models. Initial results also indicate that the MIB method can significantly improve the quality of electrostatic surface potentials of biomolecules that are frequently used in the study of biomolecular interactions based on experimental structures. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008

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