# Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation

1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent molecular dynamics simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be dry', that is, insulated from water fluctuations. We show that patterns of dry' residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom's depth inside an interface. We analyze the correlation between Voronoi shelling order, dryness, and conservation on a set of 54 protein-protein complexes. Residues with high shelling order tend to be dry; evolutionary conservation also correlates with dryness and shelling order but, perhaps not surprisingly, is a much less accurate predictor of either property. Voronoi shelling order thus seems a meaningful and efficient descriptor of protein interfaces. Moreover, the strong correlation with dryness suggests that water dynamics within protein interfaces may, in first approximation, be described by simple diffusion models.
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Rapport
[Research Report] RR-6415, INRIA. 2008
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https://hal.inria.fr/inria-00206173
Contributeur : Frederic Cazals <>
Soumis le : vendredi 18 janvier 2008 - 09:03:36
Dernière modification le : jeudi 11 janvier 2018 - 16:24:50
Document(s) archivé(s) le : vendredi 25 novembre 2016 - 20:07:35

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• HAL Id : inria-00206173, version 3

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Benjamin Bouvier, Raik Gruenberg, Michael Nilges, Frédéric Cazals. Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation. [Research Report] RR-6415, INRIA. 2008. 〈inria-00206173v3〉

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