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On the Dielectric Boundary in Poisson−Boltzmann Calculations
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Abstract
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 reparametrization 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 parametrized against either experimental solvation data or data obtained from explicit-solvent simulations on small compounds, for PB calculations on proteins. The second is the parametrization of vdW-based generalized Born models against MS-based PB results.
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This article has been cited by 2 ACS Journal articles (2 most recent appear below).
Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson−Boltzmann Equation Over a Broad Range of Salt Concentration
Marcia O. Fenley, Michael Mascagni, James McClain, Alexander R. J. Silalahi and Nikolai A. SimonovJournal of Chemical Theory and Computation2010 6 (1), 300-314Using Correlated Monte Carlo Sampling for Efficiently Solving the Linearized Poisson−Boltzmann Equation Over a Broad Range of Salt Concentration
Marcia O. Fenley, Michael Mascagni, James McClain, Alexander R. J. Silalahi and Nikolai A. SimonovJournal of Chemical Theory and Computation2010 6 (1), 300-314Dielectric continuum or implicit solvent models provide a significant reduction in computational cost when accounting for the salt-mediated electrostatic interactions of biomolecules immersed in an ionic environment. These models, in which the solvent and ...
On the Balance of Simplification and Reality in Molecular Modeling of the Electron Density
Peter L. Warburton, Jenna L. Wang and Paul G. MezeyJournal of Chemical Theory and Computation2008 4 (10), 1627-1636On the Balance of Simplification and Reality in Molecular Modeling of the Electron Density
Peter L. Warburton, Jenna L. Wang and Paul G. MezeyJournal of Chemical Theory and Computation2008 4 (10), 1627-1636Fused-sphere (van der Waals) surfaces and their variants such as solvent accessible surfaces and molecular surfaces are simple molecular models that are commonly used for many diverse purposes across a broad range of scientific disciplines due to their ...
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History
- Published In Issue March 11, 2008
- Received November 21, 2007
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