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Bioinformatics Advance Access published online on April 12, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti444
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received February 9, 2005
Revised March 30, 2005
Accepted April 7, 2005

Article

Three-dimensional computation of atom depth in complex molecular structures

Daniele Varrazzo 1, Andrea Bernini 2, Ottavia Spiga 2, Arianna Ciutti 3, Stefano Chiellini 3, Vincenzo Venditti 1, Luisa Bracci 1, and Neri Niccolai 2*

1 Biomolecular Structure Research Center and Department of Molecular Biology, Università di Siena, I-53100 Siena, Italy
2 Biomolecular Structure Research Center and Department of Molecular Biology, Università di Siena, I-53100 Siena, Italy; SienaBioGrafix Srl, I-53100 Siena, Italy
3 SienaBioGrafix Srl, I-53100 Siena, Italy

* To whom correspondence should be addressed.
Neri Niccolai, E-mail: niccolai{at}unisi.it


  Abstract

Motivation: For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the three-dimensional character of depth is largely lost. To calculate atom depths in a way that the molecular shape can be taken into account, a new approach is here proposed.

Results: An algorithm has been developed to calculate intersections between the molecular volume and spheres centered on the atoms whose depth has to be quantified. Many proteins with different size and shape have been chosen to compare the results obtained from distance-based and volume-based depth calculations. From the wealth of experimental data available for hen egg white lysozyme, H/D exchange rates and TEMPOL induced paramagnetic perturbations have been analyzed both in terms of depth indexes and of atom distances to the solvent accessible surface. The algorithm here proposed yields better correlations between experimental data and atom depth, particularly for those atoms which are located near to the protein surface.

Availability: Instructions to obtain source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.net.


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