Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies

Overview

Journal Chem Phys Lett

Date 2011 Nov 30

PMID 22125339

Citations 17

Authors

Qin Cai

Xiang Ye

Jun Wang

Ray Luo

Affiliations

Soon will be listed here.

Abstract

Continuum modeling of electrostatic interactions based upon the numerical solutions of the Poisson-Boltzmann equation has been widely adopted in biomolecular applications. To extend their applications to molecular dynamics and energy minimization, robust and efficient methodologies to compute solvation forces must be developed. In this study, we have first reviewed the theory for the computation of dielectric boundary forces based on the definition of the Maxwell stress tensor. This is followed by a new formulation of the dielectric boundary force suitable for the finite-difference Poisson-Boltzmann methods. We have validated the new formulation with idealized analytical systems and realistic molecular systems.

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References

Case D, Cheatham 3rd T, Darden T, Gohlke H, Luo R, Merz Jr K . The Amber biomolecular simulation programs. J Comput Chem. 2005; 26(16):1668-88. PMC: 1989667. DOI: 10.1002/jcc.20290. View

Cerutti D, Baker N, McCammon J . Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?. J Chem Phys. 2007; 127(15):155101. PMC: 2556216. DOI: 10.1063/1.2771171. View

Koehl P . Electrostatics calculations: latest methodological advances. Curr Opin Struct Biol. 2006; 16(2):142-51. DOI: 10.1016/j.sbi.2006.03.001. View

Gilson M . Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol. 1995; 5(2):216-23. DOI: 10.1016/0959-440x(95)80079-4. View

Klapper I, Hagstrom R, Fine R, Sharp K, Honig B . Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins. 1986; 1(1):47-59. DOI: 10.1002/prot.340010109. View

Che J, Dzubiella J, Li B, McCammon J . Electrostatic free energy and its variations in implicit solvent models. J Phys Chem B. 2008; 112(10):3058-69. DOI: 10.1021/jp7101012. View

Luo R, David L, Gilson M . Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem. 2002; 23(13):1244-53. DOI: 10.1002/jcc.10120. View

Zauhar R, Morgan R . A new method for computing the macromolecular electric potential. J Mol Biol. 1985; 186(4):815-20. DOI: 10.1016/0022-2836(85)90399-7. View

Lee M, Olson M . Evaluation of Poisson solvation models using a hybrid explicit/implicit solvent method. J Phys Chem B. 2006; 109(11):5223-36. DOI: 10.1021/jp046377z. View

10.

Cai Q, Hsieh M, Wang J, Luo R . Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. J Chem Theory Comput. 2014; 6(1):203-211. PMC: 3979552. DOI: 10.1021/ct900381r. View

11.

Honig B, Nicholls A . Classical electrostatics in biology and chemistry. Science. 1995; 268(5214):1144-9. DOI: 10.1126/science.7761829. View

12.

Prabhu N, Zhu P, Sharp K . Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method. J Comput Chem. 2004; 25(16):2049-64. DOI: 10.1002/jcc.20138. View

13.

Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B . Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem. 2002; 23(1):128-37. DOI: 10.1002/jcc.1161. View

14.

Tan C, Yang L, Luo R . How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis. J Phys Chem B. 2006; 110(37):18680-7. DOI: 10.1021/jp063479b. View

15.

Wang J, Cai Q, Li Z, Zhao H, Luo R . Achieving Energy Conservation in Poisson-Boltzmann Molecular Dynamics: Accuracy and Precision with Finite-Difference Algorithms. Chem Phys Lett. 2010; 468(4-6):112-118. PMC: 2663913. DOI: 10.1016/j.cplett.2008.12.049. View

16.

Wang J, Luo R . Assessment of linear finite-difference Poisson-Boltzmann solvers. J Comput Chem. 2010; 31(8):1689-98. PMC: 2854862. DOI: 10.1002/jcc.21456. View

17.

Cramer C, Truhlar D . Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev. 2002; 99(8):2161-2200. DOI: 10.1021/cr960149m. View

18.

Roux B, Simonson T . Implicit solvent models. Biophys Chem. 2006; 78(1-2):1-20. DOI: 10.1016/s0301-4622(98)00226-9. View

19.

Bashford D, Case D . Generalized born models of macromolecular solvation effects. Annu Rev Phys Chem. 2000; 51:129-52. DOI: 10.1146/annurev.physchem.51.1.129. View

20.

Wagoner J, Baker N . Solvation forces on biomolecular structures: a comparison of explicit solvent and Poisson-Boltzmann models. J Comput Chem. 2004; 25(13):1623-9. DOI: 10.1002/jcc.20089. View