Nonatomic Solvent-Driven Voronoi Tessellation of Proteins: An Open Tool to Analyze Protein Folds
Résumé
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.