title: Nonatomic solvent-driven Voronoi tessellation of proteins: an open tool to analyze protein folds.
abstract: A three-dimensional Voronoi tessellation of folded proteins is used to analyze geometrical and topological properties of a set of proteins. To each amino acid is associated a central point surrounded by a Voronoi cell. Voronoi cells describe the packing of the amino acids. Special attention is given to reproduction of the protein surface. Once the Voronoi cells are built, a lot of tools from geometrical analysis can be applied to investigate the protein structure; volume of cells, number of faces per cell, and number of sides per face are the usual signatures of the protein structure. A distinct difference between faces related to primary, secondary, and tertiary structures has been observed. Faces threaded by the main-chain have on average more than six edges, whereas those related to helical packing of the amino acid chain have less than five edges. The faces on the protein surface have on average five edges within 1% error. The average number of faces on the protein surface for a given type of amino acid brings a new point of view in the characterization of the exposition to the solvent and the classification of amino acid as hydrophilic or hydrophobic. It may be a convenient tool for model validation.
authors.affiliation: Laboratoire de Physique des Solides, Université Paris 11, Orsay, France.
authors.forename: Borislav
authors.initials: B
authors.lastname: Angelov
authors.forename: Jean-François
authors.initials: JF
authors.lastname: Sadoc
authors.forename: Rémi
authors.initials: R
authors.lastname: Jullien
authors.forename: Alain
authors.initials: A
authors.lastname: Soyer
authors.forename: Jean-Paul
authors.initials: JP
authors.lastname: Mornon
authors.forename: Jacques
authors.initials: J
authors.lastname: Chomilier
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins; D019295:Computational Biology / Q000379:methods*; D029968:Escherichia coli Proteins / Q000737:chemistry; D057927:Hydrophobic and Hydrophilic Interactions; D008565:Membrane Proteins / Q000737:chemistry; D000072236:Methyl-Accepting Chemotaxis Proteins; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012997:Solvents; D055672:Static Electricity; D016008:Statistical Distributions
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; D000072236:Methyl-Accepting Chemotaxis Proteins; D011506:Proteins; D012997:Solvents