Commun. Comput. Phys., 13 (2013), pp. 61-89.


Between Algorithm and Model: Different Molecular Surface Definitions for the Poisson-Boltzmann Based Electrostatic Characterization of Biomolecules in Solution

Sergio Decherchi 1, Jose Colmenares 1, Chiara Eva Catalano 2, Michela Spagnuolo 2, Emil Alexov 3, Walter Rocchia 1*

1 Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy.
2 Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy.
3 Department of Physics, Clemson University, Clemson, South Carolina, USA.

Received 5 July 2011; Accepted (in revised version) 11 November 2011
Available online 12 June 2012
doi:10.4208/cicp.050711.111111s

Abstract

The definition of a molecular surface which is physically sound and computationally efficient is a very interesting and long standing problem in the implicit solvent continuum modeling of biomolecular systems as well as in the molecular graphics field. In this work, two molecular surfaces are evaluated with respect to their suitability for electrostatic computation as alternatives to the widely used Connolly-Richards surface: the blobby surface, an implicit Gaussian atom centered surface, and the skin surface. As figures of merit, we considered surface differentiability and surface area continuity with respect to atom positions, and the agreement with explicit solvent simulations. Geometric analysis seems to privilege the skin to the blobby surface, and points to an unexpected relationship between the non connectedness of the surface, caused by interstices in the solute volume, and the surface area dependence on atomic centers. In order to assess the ability to reproduce explicit solvent results, specific software tools have been developed to enable the use of the skin surface in Poisson-Boltzmann calculations with the DelPhi solver. The results indicate that the skin and Connolly surfaces have a comparable performance from this last point of view.

AMS subject classifications: 65D18, 65Z05, 92-08, 35Q92, 78A70

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Key words: Molecular surface, Connolly surface, blobby surface, skin surface, Poisson-Boltzmann.

*Corresponding author.
Email: sergio.decherchi@iit.it (S. Decherchi), jose.colmenares@iit.it (J. Colmenares), chiara@ge.imati.cnr.it (C.E. Catalano), michela.spagnuolo@ge.imati.cnr.it (M. Spagnuolo), ealexov@clemson.edu (E. Alexov), walter.rocchia@iit.it (W. Rocchia)
 

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