Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation - Archive ouverte HAL Access content directly
Reports (Research Report) Year : 2008

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

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Benjamin Bouvier
Raik Gruenberg
• Function : Author
• PersonId : 846123
Michael Nilges
• Function : Author
• PersonId : 846124
Frédéric Cazals
• Function : Author
• PersonId : 905122

#### 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.

### Dates and versions

inria-00206173 , version 1 (16-01-2008)
inria-00206173 , version 2 (17-01-2008)
inria-00206173 , version 3 (18-01-2008)

### Identifiers

• HAL Id : inria-00206173 , version 3

### Cite

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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