title: Detection of spatial correlations in protein structures and molecular complexes.
abstract: 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.
authors.affiliation: Division of Bioinformatics, Department of Molecular Biology, University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria. sippl@came.sbg.ac.at
authors.forename: Manfred J
authors.initials: MJ
authors.lastname: Sippl
authors.forename: Markus
authors.initials: M
authors.lastname: Wiederstein
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D017122:Bacteriophage T4 / Q000737:chemistry / Q000235:genetics; D036022:Capsid Proteins / Q000737:chemistry* / Q000235:genetics; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D005288:Ferredoxins / Q000737:chemistry / Q000235:genetics; D005293:Ferritins / Q000737:chemistry / Q000235:genetics; D005656:Fungal Proteins / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D008958:Models, Molecular; D010088:Oxidoreductases / Q000737:chemistry / Q000235:genetics; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D011550:Pseudomonas aeruginosa / Q000737:chemistry / Q000235:genetics; D017386:Sequence Homology, Amino Acid; D040681:Structural Homology, Protein
chemical_list: D001426:Bacterial Proteins; D036022:Capsid Proteins; D005288:Ferredoxins; D005656:Fungal Proteins; D004247:DNA; D005293:Ferritins; D010088:Oxidoreductases