Universality in protein residue networks.

ABSTRACT: Residue networks representing 595 nonhomologous proteins are studied. These networks exhibit universal topological characteristics as they belong to the topological class of modular networks formed by several highly interconnected clusters separated by topological cavities. There are some networks that tend to deviate from this universality. These networks represent small-size proteins having <200 residues. This article explains such differences in terms of the domain structure of these proteins. On the other hand, the topological cavities characterizing proteins residue networks match very well with protein binding sites. This study investigates the effect of the cutoff value used in building the residue network. For small cutoff values, <5 A, the cavities found are very large correspondi

SUBMITTER: Estrada E 

PROVIDER: S-EPMC2830435 | biostudies-literature | 2010 Mar

REPOSITORIES: biostudies-literature