Deficiency of the Coulomb-field approximation in the generalized Born model: An improved formula for Born radii evaluation

The weaknesses of the widely used Coulomb-field (CF) approximation in the generalized Born model are discussed from the standpoint of the Kirkwood model of biopolymer electrostatics. It is shown that the effective Born radii are overestimated by up to a factor of 2 because of the CF approximation. The problem is made worse by the fact that these critical parameters are used not only to model the self-contributions to the free enthalpy of solvation but they also appear in the analytical function for a pairwise contribution. A new simple formula for the effective Born radii evaluation overcoming some limits of the CF approximation is proposed and then tested on a model of a biopolymer with nonspherical symmetry. Some conclusions regarding the pairwise contribution are also formulated.

[1]  B Honig,et al.  Electrostatic interaction of myristoylated proteins with membranes: simple physics, complicated biology. , 1997, Structure.

[2]  J. A. V. BUTLER,et al.  Theory of the Stability of Lyophobic Colloids , 1948, Nature.

[3]  S. Harvey.  Treatment of electrostatic effects in macromolecular modeling , 1989, Proteins.

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

[5]  N. J. A. Sloane,et al.  Sphere Packings, Lattices and Groups , 1987, Grundlehren der mathematischen Wissenschaften.

[6]  P. Chaikin,et al.  Charge renormalization, osmotic pressure, and bulk modulus of colloidal crystals: Theory , 1984 .

[7]  C. Tanford,et al.  Theory of Protein Titration Curves. I. General Equations for Impenetrable Spheres , 1957 .

[8]  M. Gilson,et al.  Computing ionization states of proteins with a detailed charge model , 1996, J. Comput. Chem..

[9]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[10]  J. Kirkwood,et al.  Theory of Solutions of Molecules Containing Widely Separated Charges with Special Application to Zwitterions , 1934 .

[11]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[12]  B Honig,et al.  Electrostatic binding of proteins to membranes. Theoretical predictions and experimental results with charybdotoxin and phospholipid vesicles. , 1997, Biophysical journal.

[13]  T. Grycuk.  Revision of the Model System Concept for the Prediction of pKa's in Proteins , 2002 .

[14]  K. Sharp,et al.  Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models , 1994 .

[15]  An-Suei Yang,et al.  Electrostatic effects on protein stability: Current Opinion in Structural Biology 1992, 2:40…-45 , 1992 .

[16]  Huan‐Xiang Zhou,et al.  Modeling of protein conformational fluctuations in pKa predictions. , 1997, Journal of molecular biology.

[17]  Carmay Lim,et al.  Absolute pKa calculations with continuum dielectric methods , 1991 .

[18]  L. R. Scott,et al.  Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program , 1995 .

[19]  N. Ben-Tal,et al.  Electrostatic properties of membranes containing acidic lipids and adsorbed basic peptides: theory and experiment. , 1999, Biophysical journal.

[20]  R. Constanciel,et al.  Self consistent field theory of solvent effects representation by continuum models: Introduction of desolvation contribution , 1984 .

[21]  N. Ben-Tal,et al.  Electrostatics and the membrane association of Src: theory and experiment. , 1998, Biochemistry.

[22]  B Honig,et al.  Binding of small basic peptides to membranes containing acidic lipids: theoretical models and experimental results. , 1996, Biophysical journal.

[23]  B. Honig,et al.  Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis , 1988, Proteins.

[24]  Barry Honig,et al.  Salt Effects on Protein-DNA Interactions: The λcI Repressor and EcoRI Endonuclease , 1994 .

[25]  M. Born.  Volumen und Hydratationswärme der Ionen , 1920 .

[26]  K. Sharp,et al.  On the calculation of pKas in proteins , 1993, Proteins.

[27]  E. M. Lifshitz,et al.  Electrodynamics of continuous media , 1961 .

[28]  W. C. Still,et al.  Semianalytical treatment of solvation for molecular mechanics and dynamics , 1990 .

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

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

[31]  B Honig,et al.  Salt effects on polyelectrolyte–ligand binding: Comparison of Poisson–Boltzmann, and limiting law/counterion binding models , 1995, Biopolymers.