On the occurrence of linear groups in proteins

Abstract

Linear groups-polypeptide conformations based on a single repeating phi,psi-pair-are a foundational concept in protein structure, yet how they are presented in textbooks is based largely on theoretical studies from the early days of protein structure analysis. Now, ultra-high resolution protein structures provide a resource for an accurate empirical and systematic assessment of the linear groups that truly exist in proteins. Here, a purely conformation-based survey of linear groups shows that only three distinct phi,psi-regions occur: a diverse set of extended conformations mostly present as beta-strands, a broad population of polyproline-II-like spirals, and a tight cluster that includes the highly populated alpha-helix and the conformationally-similar but much less populated 3(10)-helix. Rare, short left-handed alpha-/3(10)-helical turns with repeating phi,psi-angles occur, but none are longer than three residues. Misperceptions dispelled by this study are the existence of 2.2(7)- and pi-helices as linear groups, the existence of specific ideal phi,psi-angles for each linear group, and the existence of a substantive difference in the phi,psi-preferences for parallel versus antiparallel beta-strands. This study provides a concrete basis for updating and enhancing how we think about and teach the basics of protein structure.