Literature DB >> 23504509

Image Charge Method for Reaction Fields in a Hybrid Ion-Channel Model.

Zhenli Xu1, Wei Cai, Xiaolin Cheng.   

Abstract

A multiple-image method is proposed to approximate the reaction-field potential of a source charge inside a finite length cylinder due to the electric polarization of the surrounding membrane and bulk water. When applied to a hybrid ion-channel model, this method allows a fast and accurate treatment of the electrostatic interactions of protein with membrane and solvent. To treat the channel/membrane interface boundary conditions of the electric potential, an optimization approach is used to derive image charges by fitting the reaction-field potential expressed in terms of cylindric harmonics. Meanwhile, additional image charges are introduced to satisfy the boundary conditions at the planar membrane interfaces. In the end, we convert the electrostatic interaction problem in a complex inhomogeneous system of ion channel/membrane/water into one in a homogeneous free space embedded with discrete charges (the source charge and image charges). The accuracy of this method is then validated numerically in calculating the solvation self-energy of a point charge.

Entities:  

Keywords:  Ion channels; cylindrical harmonics; electrostatic interactions; image charges

Year:  2010        PMID: 23504509      PMCID: PMC3596020          DOI: 10.4208/cicp.160410.200910a

Source DB:  PubMed          Journal:  Commun Comput Phys        ISSN: 1815-2406            Impact factor:   3.246


  14 in total

Review 1.  Simulation approaches to ion channel structure-function relationships.

Authors:  D P Tieleman; P C Biggin; G R Smith; M S Sansom
Journal:  Q Rev Biophys       Date:  2001-11       Impact factor: 5.318

Review 2.  The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology.

Authors:  F Fogolari; A Brigo; H Molinari
Journal:  J Mol Recognit       Date:  2002 Nov-Dec       Impact factor: 2.137

3.  An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions.

Authors:  Yuchun Lin; Andrij Baumketner; Shaozhong Deng; Zhenli Xu; Donald Jacobs; Wei Cai
Journal:  J Chem Phys       Date:  2009-10-21       Impact factor: 3.488

Review 4.  Theoretical and computational models of biological ion channels.

Authors:  Benoît Roux; Toby Allen; Simon Bernèche; Wonpil Im
Journal:  Q Rev Biophys       Date:  2004-02       Impact factor: 5.318

Review 5.  Modeling of ion channels.

Authors:  D G Levitt
Journal:  J Gen Physiol       Date:  1999-06       Impact factor: 4.086

Review 6.  Classical electrostatics in biology and chemistry.

Authors:  B Honig; A Nicholls
Journal:  Science       Date:  1995-05-26       Impact factor: 47.728

7.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins.

Authors:  R Abagyan; M Totrov
Journal:  J Mol Biol       Date:  1994-01-21       Impact factor: 5.469

8.  Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Authors:  Zhenli Xu; Wei Cai
Journal:  SIAM Rev Soc Ind Appl Math       Date:  2011-11-07       Impact factor: 10.780

9.  Implicit solvent simulations of peptide interactions with anionic lipid membranes.

Authors:  Themis Lazaridis
Journal:  Proteins       Date:  2005-02-15

10.  An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins.

Authors:  Wonpil Im; Michael Feig; Charles L Brooks
Journal:  Biophys J       Date:  2003-11       Impact factor: 4.033

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  1 in total

1.  Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations.

Authors:  Zhenli Xu; Wei Cai
Journal:  SIAM Rev Soc Ind Appl Math       Date:  2011-11-07       Impact factor: 10.780

  1 in total

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