Search

Multiprotein complexes govern virtually all cellular processes. Their 3D structures provide important clues to their biological roles, especially through structural correlations among protein molecules and complexes. The detection of such correlations generally requires comprehensive searches in databases of known protein structures by means of appropriate structure-matching techniques. Here, we present a high-speed structure search engine capable of instantly matching large protein oligomers against the complete and up-to-date database of biologically functional assemblies of protein molecules. We use this tool to reveal unseen structural correlations on the level of protein quaternary structure and demonstrate its general usefulness for efficiently exploring complex structural relationships among known protein assemblies. [ABSTRACT FROM AUTHOR]

Summary: Protein structures are frequently related by spectacular and often surprising similarities. Structural correlations among protein chains are routinely detected by various structure-matching techniques, but the comparison of oligomers and molecular complexes is largely uncharted territory. Here we solve the structure-matching problem for oligomers and large molecular aggregates, including the largest molecular complexes known today. We provide several challenging examples that cannot be handled by conventional structure-matching techniques and we report on a number of remarkable correlations. The examples cover the cell-puncturing device of bacteriophage T4, the secretion system of P. aeruginosa, members of the dehydrogenase family, DNA clamps, ferredoxin iron-storage cages, and virus capsids. [Copyright &y& Elsevier]

They map the atomic three-dimensional structures of proteins participating in protein-protein interactions to compact representations based on 26 residue cluster classes (RCCs). Here, SSFs are used (in addition to other methods) to predict disordered proteins/protein regions in Camelus species and Homo sapiens. Such SSFs are employed in numerous bioinformatics methods, e.g., for the assessment of experimentally determined structures or in the prediction of 3D protein structures, protein-protein interactions, protein-ligand interactions, protein stability, etc. [Extracted from the article]