inria-00206173, version 2
Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
N° RR-6415 (2008)
Résumé : 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.
- a – INRIA
- b – EMBL
- c – Institut Pasteur
- 1 :
- INRIA
- 2 :
- EMBL
- 3 :
- CNRS : URA2185 – Institut Pasteur de Paris
- Domaine : Informatique/Bio-informatique
Sciences du Vivant/Bio-Informatique, Biologie Systémique
Informatique/Géométrie algorithmique - Mots-clés : Protein-protein complex – interface activity – hotspots – conservation – Voronoi models
- Référence interne : RR-6415
- Versions disponibles : v1 (16-01-2008) v2 (17-01-2008) v3 (18-01-2008)
- inria-00206173, version 2
- http://hal.inria.fr/inria-00206173
- oai:hal.inria.fr:inria-00206173
- Contributeur :
- Soumis le : Jeudi 17 Janvier 2008, 09:23:19
- Dernière modification le : Jeudi 17 Janvier 2008, 09:24:12





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