Structure-based characterization of multiprotein complexes

Summary 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.
Graphical Abstract
Highlights • Tool enables efficient exploration of structure similarities among protein assemblies • Multiprotein complexes show structural correlations concealed on the level of chains • Hexamer of unknown function from Salmonella matches Hcp3 protein from Pseudomonas • Strikingly similar DNA clamp complexes assemble from highly different subunits
Wiederstein et al. introduce a fast protein structure search tool that scans the complete database of multiprotein complexes. It reveals structural correlations among multiprotein complexes that are concealed on the level of single chains and supports the characterization of newly determined protein structures.