The modular organization of domain structures: insights into protein-protein binding.

ABSTRACT: Domains are the building blocks of proteins and play a crucial role in protein-protein interactions. Here, we propose a new approach for the analysis and prediction of domain-domain interfaces. Our method, which relies on the representation of domains as residue-interacting networks, finds an optimal decomposition of domain structures into modules. The resulting modules comprise highly cooperative residues, which exhibit few connections with other modules. We found that non-overlapping binding sites in a domain, involved in different domain-domain interactions, are generally contained in different modules. This observation indicates that our modular decomposition is able to separate protein domains into regions with specialized functions. Our results show that modules with high modularity

SUBMITTER: del Sol A 

PROVIDER: S-EPMC2134966 | biostudies-literature | 2007 Dec

REPOSITORIES: biostudies-literature