The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations

Tjong, Harianto; Zhou, Huang-Xiang

doi:10.1063/1.2393243

Cited by 16 publications

(16 citation statements)

References 9 publications

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“…More recently, the combination formula (4.13) was proposed to incorporate the effect of dielectric environments; this formula is extremely precise for sphere-like shapes and also very accurate for arbitrary geometries after introducing a correction parameter. Recently, Still's equation was treated by introducing a scaling formula [177, 187] in order to incorporate the dependence of dielectrics.…”

Section: Generalized Born Methodsmentioning

confidence: 99%

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

Xu¹,

Cai²

2011

SIAM Rev.

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We review recent developments of fast analytical methods for macroscopic electrostatic calculations in biological applications, including the Poisson–Boltzmann (PB) and the generalized Born models for electrostatic solvation energy. The focus is on analytical approaches for hybrid solvation models, especially the image charge method for a spherical cavity, and also the generalized Born theory as an approximation to the PB model. This review places much emphasis on the mathematical details behind these methods.

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Section: Generalized Born Methodsmentioning

confidence: 99%

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

Xu¹,

Cai²

2011

SIAM Rev.

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“…We found that these dependences can be modeled accurately by a scaling formula. 41 Based on that formula, the result of Eq. ͑1͒ is scaled to…”

Section: A Gbrmentioning

confidence: 98%

G Br 6 NL : A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation

Tjong

Zhou

2007

The Journal of Chemical Physics

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The nonlinear Poisson-Boltzmann (NLPB) equation can provide accurate modeling of electrostatic effects for nucleic acids and highly charged proteins. Generalized Born methods have been developed to mimic the linearized Poisson-Boltzmann (LPB) equation at substantially reduced cost. The computer time for solving the NLPB equation is approximately fivefold longer than for the LPB equation, thus presenting an even greater obstacle. Here we present the first generalized Born method, GBr(6)NL, for mimicking the NLPB equation. GBr(6)NL is adapted from GBr(6), a generalized Born method recently developed to reproduce the solvation energy of the LPB equation [Tjong and Zhou, J. Phys. Chem. B 111, 3055 (2007)]. Salt effects predicted by GBr(6)NL on 55 proteins overall deviate from NLPB counterparts by 0.5 kcal/mol from ionic strengths from 10 to 1000 mM, which is approximately 10% of the average magnitudes of the salt effects. GBr(6)NL predictions for the salts effects on the electrostatic interaction energies of two protein:RNA complexes are very promising.

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“…The 55 test proteins have been used in our previous studies to find an empirical dependence of Δ G solv on solute and solvent dielectric constants 21 and to develop GB methods as substitutes of the linearized and full PB equation. 48,49 These proteins were collected from the Protein Data Bank (http://www.rcsb.org/pdb) using the following criteria: sequence identity less than 10%, resolution better than 1.0 Å, and number of residues less than 250.…”

Section: Calculation Detailsmentioning

confidence: 99%

On the Dielectric Boundary in Poisson−Boltzmann Calculations

Tjong

Zhou

2008

J. Chem. Theory Comput.

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In applying the Poisson-Boltzmann (PB) equation for calculating the electrostatic free energies of solute molecules, an open question is how to specify the boundary between the low-dielectric solute and the high-dielectric solvent. Two common specifications of the dielectric boundary, as the molecular surface (MS) or the van der Waals (vdW) surface of the solute, give very different results for the electrostatic free energy of the solute. With the same atomic radii, the solute is more solvent-exposed in the vdW specification. One way to resolve the difference is to use different sets of atomic radii for the two surfaces. The radii for the vdW surface would be larger in order to compensate for the higher solvent exposure. Here we show that radius re-parameterization required for bringing MS-based and vdW-based PB results to agreement is solute-size dependent. The difference in atomic radii for individual amino acids as solutes is only 2-5% but increases to over 20% for proteins with ~200 residues. Therefore two sets of radii that yield identical MS-based and vdW-based PB results for small solutes will give very different PB results for large solutes. This finding raises issues about two common practices. The first is the use of atomic radii, which are parameterized against either experimental solvation data or data obtained from explicit-solvent simulations on small compounds, for PB calculations on proteins. The second is the parameterization of vdW-based generalized Born models against MS-based PB results.

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The dependence of electrostatic solvation energy on dielectric constants in Poisson-Boltzmann calculations

Cited by 16 publications

References 9 publications

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

Fast Analytical Methods for Macroscopic Electrostatic Models in Biomolecular Simulations

G Br 6 NL : A generalized Born method for accurately reproducing solvation energy of the nonlinear Poisson-Boltzmann equation

On the Dielectric Boundary in Poisson−Boltzmann Calculations

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