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

(1) , (2) , (3) , (1)
1
2
3
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.
Fichier principal
Vignette du fichier
RR-6415.pdf (14.99 Mo) Télécharger le fichier
Origin : Files produced by the author(s)
Loading...

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⟩
274 View
258 Download

Share

Gmail Facebook Twitter LinkedIn More