Structural trees for proteins containing φ-motifs

In the present study, a novel structural motif of proteins referred to as the φ-motif is considered, and two novel structural trees in which the φ-motif is taken as the root structure have been constructed. The simplest φ-motif is formed by three adjacent β-strands connected by loops and packed in one β-sheet so that its overall fold resembles the Greek letter φ. Construction of the structural trees and modeling of folding pathways have shown that all structures of the protein superfamilies can be obtained by stepwise addition of α-helices and/or β-strands to the root φ-motif taking into account a restricted set of rules inferred from known principles of protein structure. The structural trees are a good tool for structure comparison, structural classification of proteins, as well as for searching for all possible protein folds and folding pathways.