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Shelling the Voronoi interface of protein–protein complexes reveals patterns of residue conservation, dynamics, and composition
Author(s) -
Bouvier Benjamin,
Grünberg Raik,
Nilges Michael,
Cazals Frédéric
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22381
Subject(s) - voronoi diagram , biological system , molecular dynamics , protein dynamics , interface (matter) , protein structure , geometry , chemical physics , computer science , statistical physics , physics , chemistry , mathematics , biology , computational chemistry , thermodynamics , biochemistry , surface tension , gibbs isotherm
The accurate description and analysis of protein–protein interfaces remains a challenging task. Traditional definitions, 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. We here extend a fast, parameter‐free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom's depth inside the interface. Our analysis of 54 protein–protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Orders coincide with residues that were found shielded from bulk water fluctuations in a recent molecular dynamics study. Yet, VSO predicts such “dry” residues without consideration of forcefields or dynamics at a dramatically reduced cost. The interface center is enriched in hydrophobic residues. Yet, this hydrophobic centering is not universal and does not mirror the far stronger geometric bias of water fluxes. The seemingly complex water dynamics at protein interfaces appears thus largely controlled by geometry. Sequence analysis supports the functional relevance of dry residues and residues with high VSO, both of which tend to be more conserved. On closer inspection, the spatial distribution of conservation argues against the arbitrary dissection into core or rim and thus refines previous results. Voronoi Shelling Order reveals clear geometric patterns in protein interface composition, function and dynamics and facilitates the comparative analysis of protein–protein interactions. Proteins 2009. © 2009 Wiley‐Liss, Inc.