Commun. Comput. Phys., 13 (2013), pp. 1-12.


Poisson-Boltzmann Calculations: van der Waals or Molecular Surface?

Xiaodong Pang 1, Huan-Xiang Zhou 2*

1 State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai 200433, China; and Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.
2 Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA.

Received 27 July 2011; Accepted (in revised version) 14 September 2011
Available online 12 June 2012
doi:10.4208/cicp.270711.140911s

Abstract

The Poisson-Boltzmann equation is widely used for modeling the electrostatics of biomolecules, but the calculation results are sensitive to the choice of the boundary between the low solute dielectric and the high solvent dielectric. The default choice for the dielectric boundary has been the molecular surface, but the use of the van der Waals surface has also been advocated. Here we review recent studies in which the two choices are tested against experimental results and explicit-solvent calculations. The assignment of the solvent high dielectric constant to interstitial voids in the solute is often used as a criticism against the van der Waals surface. However, this assignment may not be as unrealistic as previously thought, since hydrogen exchange and other NMR experiments have firmly established that all interior parts of proteins are transiently accessible to the solvent.


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PACS: 41.20.Cv
Key words: Poisson-Boltzmann calculation, biomolecular electrostatics, dielectric boundary, van der Waals surface, molecular surface.

*Corresponding author.
Email: hzhou4@fsu.edu (H.-X. Zhou)
 

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