title: Up, down, and around: identifying recurrent interactions within and between super-secondary structures in β-propellers.
abstract: The examination and analysis of super-secondary structures or other specific structural patterns associated with particular functions, sequence motifs, or structural contexts require that the set of structures examined shares the same feature. This seems obvious but in practice this may often present problems such as identifying complete sets of data avoiding false positives. In the case of the β-propeller structures the symmetry of the propeller creates problems for many structure similarity search programs. Here we present a procedure that will identify propeller structures in PDB and assign them to the different N-propeller types. In addition we outline methods to examine similarities and differences within and between the four stranded up-and-down blades of the β-propeller.
authors.affiliation: Department of Molecular Biology, MIND Centre, CARB Centre, Aarhus University, Aarhus, Denmark. sth@mb.au.dk
authors.forename: Søren
authors.initials: S
authors.lastname: Thirup
authors.forename: Vikas
authors.initials: V
authors.lastname: Gupta
authors.forename: Esben M
authors.initials: EM
authors.lastname: Quistgaard
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment
chemical_list: D011506:Proteins