Structural and sequence patterns in the loops of βαβ units

Abstract

The conformation and sequences of the 129 loops of 70 βαβ units from 17 β/β proteins were analysed for patterns. Many different conformations of the loop regions were observed, but 18 of the loops could be classified into one of four loop families with distinctive conformation and sequence patterns. (i) Adjacent αβ loops with one residue between the α-helix and β-strand. The residue is a glycine with conformationally restricted φ/ψ angles; (II) adjacent αβ loops of three residues with a conformationally restricted glycine as the first of the loop followed by an analine or histidine residue and a third residue with helical φ/ψ angles; (iii) adjacent βα loops of 3/4 residues previously reported to bind nucleotides and which have three glycine residues in the loop region; (iv) non adjacent βα loops of 0 residues with a serine or threonine as the last residue of the β-strand. The analysis provides in formation for the model building of loops and prediction of secondary structure from amino acid sequences.