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Voronoï Tessellation Reveals the Condensed Matter Character of Folded Proteins

2000; American Physical Society; Volume: 85; Issue: 16 Linguagem: Inglês

10.1103/physrevlett.85.3532

1092-0145

Alain Soyer, Jacques Chomilier, Jean‐Paul Mornon, R. Jullien, Jean‐François Sadoc,

RNA and protein synthesis mechanisms

The packing geometry of amino acids in folded proteins is analyzed via a modified Voronoï tessellation method which distinguishes bulk and surface. From a statistical analysis of the Voronoï cells over 40 representative proteins, it appears that the packings are in average similar to random packings of hard spheres encountered in condensed matter physics, with a quite strong fivefold local symmetry. Moreover, the statistics permits one to establish a classification of amino acids in terms of increasing propensity to be buried in agreement with what is known from chemical considerations.