Hidden relationships between metalloproteins unveiled by structural comparison of their metal sites.

ABSTRACT: Metalloproteins account for a substantial fraction of all proteins. They incorporate metal atoms, which are required for their structure and/or function. Here we describe a new computational protocol to systematically compare and classify metal-binding sites on the basis of their structural similarity. These sites are extracted from the MetalPDB database of minimal functional sites (MFSs) in metal-binding biological macromolecules. Structural similarity is measured by the scoring function of the available MetalS2 program. Hierarchical clustering was used to organize MFSs into clusters, for each of which a representative MFS was identified. The comparison of all representative MFSs provided a thorough structure-based classification of the sites analyzed. As examples, the application of the

SUBMITTER: Valasatava Y 

PROVIDER: S-EPMC4377587 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature