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

Published online by Cambridge University Press:  03 June 2015

Sergio Decherchi ,
Jose Colmenares ,
Chiara Eva Catalano ,
Michela Spagnuolo ,
Emil Alexov  and
Walter Rocchia
Sergio Decherchi*
Affiliation:
Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy
Jose Colmenares*
Affiliation:
Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy
Chiara Eva Catalano*
Affiliation:
Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy
Michela Spagnuolo*
Affiliation:
Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy
Emil Alexov*
Affiliation:
Department of Physics, Clemson University, Clemson, South Carolina, USA
Walter Rocchia*
Affiliation:
Department of Drug Discovery and Development, Istituto Italiano di Tecnologia, via Morego, 30, 16163 Genova, Italy
*
Email:[email protected]
Email:[email protected]
Email:[email protected]
Email:[email protected]
Email:[email protected]
Corresponding author.Email:[email protected]
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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.

Keywords

65D1865Z0592-0835Q9278A70Molecular surfaceConnolly surfaceblobby surfaceskin surfacePoisson-Boltzmann
Type
Research Article
Information
Communications in Computational Physics , Volume 13 , Issue 1 , January 2013 , pp. 61 - 89
Copyright
Copyright © Global Science Press Limited 2013

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