Deduction and systematic classification of spatial motifs of the antiparallel β structure in globular proteins

A systematic classification of complex topological types for polypeptide-chain folding in the antiparallel β form is proposed. Three well known simple topological types, β, m, g, were chosen as the basic ones: single β strand, hairpin of two strands and simple Greek key type of four strands. The new topologically allowed motifs are formed of a combination of the three basic motifs. All spatial motif types possible with this basis were considered for more complicated double Greek key motifs. This was done on the basis of a complete set of 14 basic spatial motifs of simple Greek key topology. Analysis of about 20 globular proteins shows that some spatial motifs appear to be realized as the main part of the chain fold of the molecule. This suggests that chain folds of antiparallel β proteins are necessarily conditioned by simple topological requirements.