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Literature DB >> 11030939

Voronoï tessellation reveals the condensed matter character of folded proteins.

A Soyer¹, J Chomilier, J P Mornon, R Jullien, J F Sadoc.

Abstract

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.

Mesh：

Substances：
Proteins

Year: 2000 PMID： 11030939 DOI： 10.1103/PhysRevLett.85.3532

Source DB: PubMed Journal: Phys Rev Lett ISSN： 0031-9007 Impact factor: 9.161

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Cited

13 in total

1. Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.

Authors: S R Brych; S I Blaber; T M Logan; M Blaber
Journal: Protein Sci Date: 2001-12 Impact factor: 6.725

9. Characterization of non-trivial neighborhood fold constraints from protein sequences using generalized topohydrophobicity.

Authors: Guillaume Fourty; Isabelle Callebaut; Jean-Paul Mornon
Journal: Bioinform Biol Insights Date: 2008-01-31

10. Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.

Authors: Amir Shahmoradi; Claus O Wilke
Journal: Proteins Date: 2016-04-09

Voronoï tessellation reveals the condensed matter character of folded proteins.

1. Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.

2. Small-world communication of residues and significance for protein dynamics.

3. Revisiting the Voronoi description of protein-protein interfaces.

4. Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication.

5. The role of entropy and polarity in intermolecular contacts in protein crystals.

6. LAGUERRE-INTERSECTION METHOD FOR IMPLICIT SOLVATION.

7. Spectral properties of contact matrix: application to proteins.

8. Optimized null model for protein structure networks.

9. Characterization of non-trivial neighborhood fold constraints from protein sequences using generalized topohydrophobicity.

10. Dissecting the roles of local packing density and longer-range effects in protein sequence evolution.