Electrostatic forces in the Poisson-Boltzmann systems.

Continuum modeling of electrostatic interactions based upon numerical solutions of the Poisson-Boltzmann equation has been widely used in structural and functional analyses of biomolecules. A limitation of the numerical strategies is that it is conceptually difficult to incorporate these types of models into molecular mechanics simulations, mainly because of the issue in assigning atomic forces. In this theoretical study, we first derived the Maxwell stress tensor for molecular systems obeying the full nonlinear Poisson-Boltzmann equation. We further derived formulations of analytical electrostatic forces given the Maxwell stress tensor and discussed the relations of the formulations with those published in the literature. We showed that the formulations derived from the Maxwell stress tensor require a weaker condition for its validity, applicable to nonlinear Poisson-Boltzmann systems with a finite number of singularities such as atomic point charges and the existence of discontinuous dielectric as in the widely used classical piece-wise constant dielectric models.

[1]  H. Scheraga,et al.  A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent , 1997 .

[2]  A. Rashin Electrostatics of ion-ion interactions in solution , 1989 .

[3]  Ruhong Zhou,et al.  Poisson−Boltzmann Analytical Gradients for Molecular Modeling Calculations , 1999 .

[4]  H. Zhou,et al.  Boundary element solution of macromolecular electrostatics: interaction energy between two proteins. , 1993, Biophysical journal.

[5]  Klaus Schulten,et al.  Molecular Dynamics Simulations in Heterogeneous Dielectrica and Debye-Hückel Media - Application to the Protein Bovine Pancreatic Trypsin Inhibitor , 1992 .

[6]  B. Honig,et al.  A rapid finite difference algorithm, utilizing successive over‐relaxation to solve the Poisson–Boltzmann equation , 1991 .

[7]  Nathan A. Baker,et al.  Adaptive multilevel finite element solution of the Poisson–Boltzmann equation I. Algorithms and examples , 2000 .

[8]  K. Sharp,et al.  Macroscopic models of aqueous solutions : biological and chemical applications , 1993 .

[9]  Nathan A. Baker,et al.  Improving implicit solvent simulations: a Poisson-centric view. , 2005, Current opinion in structural biology.

[10]  Michael J. Holst,et al.  Numerical solution of the nonlinear Poisson–Boltzmann equation: Developing more robust and efficient methods , 1995, J. Comput. Chem..

[11]  M. Karplus,et al.  pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model. , 1990, Biochemistry.

[12]  Y. C. Zhou,et al.  Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes II: size effects on ionic distributions and diffusion-reaction rates. , 2011, Biophysical journal.

[13]  Richard A. Friesner,et al.  Numerical solution of the Poisson–Boltzmann equation using tetrahedral finite‐element meshes , 1997 .

[14]  R. Zauhar,et al.  The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations , 1991 .

[15]  Benzhuo Lu,et al.  Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations. , 2007, Journal of chemical theory and computation.

[16]  Bo Li,et al.  Dielectric Boundary Force in Molecular Solvation with the Poisson-Boltzmann Free Energy: A Shape Derivative Approach , 2011, SIAM J. Appl. Math..

[17]  Barry Honig,et al.  Extending the Applicability of the Nonlinear Poisson−Boltzmann Equation: Multiple Dielectric Constants and Multivalent Ions† , 2001 .

[18]  Barry Honig,et al.  Focusing of electric fields in the active site of Cu‐Zn superoxide dismutase: Effects of ionic strength and amino‐acid modification , 1986, Proteins.

[19]  Evgenii Mikhailovich Lifshitz,et al.  ELECTROSTATICS OF CONDUCTORS , 1984 .

[20]  D. Case,et al.  Generalized born models of macromolecular solvation effects. , 2000, Annual review of physical chemistry.

[21]  H. Berendsen,et al.  The electric potential of a macromolecule in a solvent: A fundamental approach , 1991 .

[22]  Ray Luo,et al.  Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies. , 2011, Chemical physics letters.

[23]  Anna Tempczyk,et al.  Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations , 1991 .

[24]  J. Milovich,et al.  Solution of the nonlinear Poisson-Boltzmann equation using pseudo-transient continuation and the finite element method. , 2002, Journal of colloid and interface science.

[25]  Barry Honig,et al.  Calculating total electrostatic energies with the nonlinear Poisson-Boltzmann equation , 1990 .

[26]  B. J. Yoon,et al.  A boundary element method for molecular electrostatics with electrolyte effects , 1990 .

[27]  R. Luo,et al.  Reducing grid-dependence in finite-difference Poisson-Boltzmann calculations. , 2012, Journal of chemical theory and computation.

[28]  Ray Luo,et al.  Performance of Nonlinear Finite-Difference Poisson-Boltzmann Solvers. , 2010, Journal of chemical theory and computation.

[29]  Enrico O. Purisima,et al.  A simple yet accurate boundary element method for continuum dielectric calculations , 1995, J. Comput. Chem..

[30]  Donald Bashford,et al.  An Object-Oriented Programming Suite for Electrostatic Effects in Biological Molecules , 1997, ISCOPE.

[31]  Dexuan Xie,et al.  A new minimization protocol for solving nonlinear Poisson–Boltzmann mortar finite element equation , 2007 .

[32]  Marcia O. Fenley,et al.  Fast Boundary Element Method for the Linear Poisson-Boltzmann Equation , 2002 .

[33]  Ray Luo,et al.  Assessment of linear finite‐difference Poisson–Boltzmann solvers , 2010, J. Comput. Chem..

[34]  Benzhuo Lu,et al.  Computation of electrostatic forces between solvated molecules determined by the Poisson-Boltzmann equation using a boundary element method. , 2005, The Journal of chemical physics.

[35]  Ray Luo,et al.  Accelerated Poisson–Boltzmann calculations for static and dynamic systems , 2002, J. Comput. Chem..

[36]  R. Zauhar,et al.  The rigorous computation of the molecular electric potential , 1988 .

[37]  S Subramaniam,et al.  Computation of molecular electrostatics with boundary element methods. , 1997, Biophysical journal.

[38]  Kim A. Sharp,et al.  Incorporating solvent and ion screening into molecular dynamics using the finite‐difference Poisson–Boltzmann method , 1991 .

[39]  K. Sharp,et al.  Electrostatic interactions in macromolecules: theory and applications. , 1990, Annual review of biophysics and biophysical chemistry.

[40]  B. Honig,et al.  Classical electrostatics in biology and chemistry. , 1995, Science.

[41]  J. Warwicker,et al.  Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. , 1982, Journal of molecular biology.

[42]  Nathan A. Baker,et al.  Adaptive multilevel finite element solution of the Poisson–Boltzmann equation II. Refinement at solvent‐accessible surfaces in biomolecular systems , 2000 .

[43]  Michael Feig,et al.  Extending the horizon: towards the efficient modeling of large biomolecular complexes in atomic detail , 2006 .

[44]  C. Cramer,et al.  Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. , 1999, Chemical reviews.

[45]  R Abagyan,et al.  Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide. , 2001, Biopolymers.

[46]  J. Andrew McCammon,et al.  Electrostatic energy calculations by a Finite‐difference method: Rapid calculation of charge–solvent interaction energies , 1992 .

[47]  James Andrew McCammon,et al.  Molecular dynamics simulation with a continuum electrostatic model of the solvent , 1995, J. Comput. Chem..

[48]  J. A. McCammon,et al.  Calculating electrostatic forces from grid‐calculated potentials , 1990 .

[49]  Jacob K. White,et al.  Accurate solution of multi‐region continuum biomolecule electrostatic problems using the linearized Poisson–Boltzmann equation with curved boundary elements , 2009, J. Comput. Chem..

[50]  S. Sriharan,et al.  The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems , 1995, J. Comput. Chem..

[51]  Ray Luo,et al.  Dielectric pressure in continuum electrostatic solvation of biomolecules. , 2012, Physical chemistry chemical physics : PCCP.

[52]  Eric C. Cyr,et al.  A first‐order system least‐squares finite element method for the Poisson‐Boltzmann equation , 2009, J. Comput. Chem..

[53]  M K Gilson,et al.  Theory of electrostatic interactions in macromolecules. , 1995, Current opinion in structural biology.

[54]  Benzhuo Lu,et al.  Order N algorithm for computation of electrostatic interactions in biomolecular systems , 2006, Proceedings of the National Academy of Sciences.

[55]  J. Andrew McCammon,et al.  Solving the finite‐difference non‐linear Poisson–Boltzmann equation , 1992 .

[56]  Chandrajit L. Bajaj,et al.  An Efficient Higher-Order Fast Multipole Boundary Element Solution for Poisson-Boltzmann-Based Molecular Electrostatics , 2011, SIAM J. Sci. Comput..

[57]  C. Brooks,et al.  Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. , 2006, Journal of the American Chemical Society.

[58]  P. Koehl Electrostatics calculations: latest methodological advances. , 2006, Current opinion in structural biology.

[59]  C. Brooks,et al.  Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. , 2005, Advances in protein chemistry.

[60]  Benzhuo Lu,et al.  An Adaptive Fast Multipole Boundary Element Method for Poisson−Boltzmann Electrostatics , 2009, Journal of chemical theory and computation.

[61]  Ray Luo,et al.  Chapter Six - Poisson–Boltzmann Implicit Solvation Models , 2012 .

[62]  Malcolm E. Davis,et al.  Electrostatics in biomolecular structure and dynamics , 1990 .

[63]  Alexander A. Rashin,et al.  Hydration phenomena, classical electrostatics, and the boundary element method , 1990 .

[64]  R. Zauhar,et al.  A new method for computing the macromolecular electric potential. , 1985, Journal of molecular biology.

[65]  J Andrew McCammon,et al.  Electrostatic Free Energy and Its Variations in Implicit Solvent Models , 2022 .

[66]  Robert E. Bruccoleri,et al.  Grid positioning independence and the reduction of self‐energy in the solution of the Poisson—Boltzmann equation , 1993, J. Comput. Chem..

[67]  Benoît Roux,et al.  Solvation of complex molecules in a polar liquid: An integral equation theory , 1996 .

[68]  J. Andrew McCammon,et al.  Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation , 1993 .

[69]  J. Tomasi,et al.  Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects , 1981 .

[70]  Michael J. Holst,et al.  Multigrid solution of the Poisson—Boltzmann equation , 1992, J. Comput. Chem..

[71]  W. Im,et al.  Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation , 1998 .

[72]  Douglas A. Lauffenburger,et al.  NUMERICAL SOLUTION OF THE NONLINEAR POISSON-BOLTZMANN EQUATION FOR A MEMBRANE-ELECTROLYTE SYSTEM , 1994 .

[73]  J. Andrew McCammon,et al.  Dielectric boundary smoothing in finite difference solutions of the poisson equation: An approach to improve accuracy and convergence , 1991 .

[74]  Minoru Sakurai,et al.  Medium effects on the molecular electronic structure. I. The formulation of a theory for the estimation of a molecular electronic structure surrounded by an anisotropic medium , 1987 .

[75]  Harold A. Scheraga,et al.  A combined iterative and boundary-element approach for solution of the nonlinear Poisson-Boltzmann equation , 1992 .

[76]  Michael J. Holst,et al.  Poisson-Nernst-Planck equations for simulating biomolecular diffusion-reaction processes I: Finite element solutions , 2010, J. Comput. Phys..

[77]  Holger Gohlke,et al.  The Amber biomolecular simulation programs , 2005, J. Comput. Chem..

[78]  J. A. McCammon,et al.  Solving the finite difference linearized Poisson‐Boltzmann equation: A comparison of relaxation and conjugate gradient methods , 1989 .

[79]  Richard A. Friesner,et al.  An automatic three‐dimensional finite element mesh generation system for the Poisson–Boltzmann equation , 1997 .

[80]  Richard A. Friesner,et al.  Solvation Free Energies of Peptides: Comparison of Approximate Continuum Solvation Models with Accurate Solution of the Poisson−Boltzmann Equation , 1997 .

[81]  B. J. Yoon,et al.  Computation of the electrostatic interaction energy between a protein and a charged surface , 1992 .

[82]  J. Andrew Grant,et al.  A smooth permittivity function for Poisson–Boltzmann solvation methods , 2001, J. Comput. Chem..

[83]  Michael J. Holst,et al.  The Finite Element Approximation of the Nonlinear Poisson-Boltzmann Equation , 2007, SIAM J. Numer. Anal..