Literature DB >> 26273581

Nonlocal Electrostatics in Spherical Geometries Using Eigenfunction Expansions of Boundary-Integral Operators.

Jaydeep P Bardhan1, Matthew G Knepley2, Peter Brune3.   

Abstract

In this paper, we present an exact, infinite-series solution to Lorentz nonlocal continuum electrostatics for an arbitrary charge distribution in a spherical solute. Our approach relies on two key steps: (1) re-formulating the PDE problem using boundary-integral equations, and (2) diagonalizing the boundary-integral operators using the fact that their eigenfunctions are the surface spherical harmonics. To introduce this uncommon approach for calculations in separable geometries, we first re-derive Kirkwood's classic results for a protein surrounded concentrically by a pure-water ion-exclusion (Stern) layer and then a dilute electrolyte, which is modeled with the linearized Poisson-Boltzmann equation. The eigenfunction-expansion approach provides a computationally efficient way to test some implications of nonlocal models, including estimating the reasonable range of the nonlocal length-scale parameter λ. Our results suggest that nonlocal solvent response may help to reduce the need for very high dielectric constants in calculating pH-dependent protein behavior, though more sophisticated nonlocal models are needed to resolve this question in full. An open-source MATLAB implementation of our approach is freely available online.

Entities:  

Year:  2015        PMID: 26273581      PMCID: PMC4530806          DOI: 10.1515/mlbmb-2015-0001

Source DB:  PubMed          Journal:  Mol Based Math Biol        ISSN: 2299-3266


  29 in total

1.  Tanford-Kirkwood electrostatics for protein modeling.

Authors:  J J Havranek; P B Harbury
Journal:  Proc Natl Acad Sci U S A       Date:  1999-09-28       Impact factor: 11.205

Review 2.  What are the dielectric "constants" of proteins and how to validate electrostatic models?

Authors:  C N Schutz; A Warshel
Journal:  Proteins       Date:  2001-09-01

3.  Electrostatics of nanosystems: application to microtubules and the ribosome.

Authors:  N A Baker; D Sept; S Joseph; M J Holst; J A McCammon
Journal:  Proc Natl Acad Sci U S A       Date:  2001-08-21       Impact factor: 11.205

4.  Size dependent ion hydration, its asymmetry, and convergence to macroscopic behavior.

Authors:  Sowmianarayanan Rajamani; Tuhin Ghosh; Shekhar Garde
Journal:  J Chem Phys       Date:  2004-03-01       Impact factor: 3.488

5.  Mathematical analysis of the boundary-integral based electrostatics estimation approximation for molecular solvation: exact results for spherical inclusions.

Authors:  Jaydeep P Bardhan; Matthew G Knepley
Journal:  J Chem Phys       Date:  2011-09-28       Impact factor: 3.488

6.  Treating entropy and conformational changes in implicit solvent simulations of small molecules.

Authors:  David L Mobley; Ken A Dill; John D Chodera
Journal:  J Phys Chem B       Date:  2008-01-03       Impact factor: 2.991

7.  Computation of molecular electrostatics with boundary element methods.

Authors:  J Liang; S Subramaniam
Journal:  Biophys J       Date:  1997-10       Impact factor: 4.033

8.  Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

Authors:  Jaydeep P Bardhan; Pavel Jungwirth; Lee Makowski
Journal:  J Chem Phys       Date:  2012-09-28       Impact factor: 3.488

9.  The dielectric constant of a folded protein.

Authors:  M K Gilson; B H Honig
Journal:  Biopolymers       Date:  1986-11       Impact factor: 2.505

10.  Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

Authors:  In Suk Joung; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2008-07-02       Impact factor: 2.991

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