Introduction of a new scheme for classifying β-turns in protein structures

Protein beta-turn classification remains an area of ongoing development in structural biology research. While the commonly used nomenclature defining type I, type II and type IV beta-turns was introduced in the 1970s and 1980s, refinements of beta-turn type definitions have been introduced as recently as 2019 by Dunbrack, Jr and co-workers who expanded the number of beta-turn types to 18 (Shapovalov et al, PLOS Computat. Biol., 15, e1006844, 2019). Based on their analysis of 13 030 turns from 1074 ultrahigh resolution (<= 1.2 angstrom) protein structures, they used a new clustering algorithm to expand the definitions used to classify protein beta-turns and introduced a new nomenclature system. We recently encountered a specific problem when classifying beta-turns in crystal structures of pentapeptide repeat proteins (PRPs) determined in our lab that are largely composed of beta-turns that often lie close to, but just outside of, canonical beta-turn regions. To address this problem, we devised a new scheme that merges the Klyne-Prelog stereochemistry nomenclature and definitions with the Ramachandran plot. The resulting Klyne-Prelog-modified Ramachandran plot scheme defines 1296 distinct potential beta-turn classifications that cover all possible protein beta-turn space with a nomenclature that indicates the stereochemistry of i + 1 and i + 2 backbone dihedral angles. The utility of the new classification scheme was illustrated by re-classification of the beta-turns in all known protein structures in the PRP superfamily and further assessed using a database of 16 657 high-resolution protein structures (<= 1.5 angstrom) from which 522 776 beta-turns were identified and classified.

Automated summary

Classification of protein beta-turns is an area of ongoing development in structural biology research, with 18 different classifications introduced as recently as 2019 along with a new clustering algorithm and nomenclature system. A new scheme combining Klyne-Prelog stereochemistry nomenclature and Ramachandran plot was devised to address specific classification problems, leading to the definition of 1296 distinct potential beta-turn classifications covering all possible protein beta-turn space. The utility of the new classification scheme was demonstrated through re-classification of beta-turns in known protein structures and assessment using a database of high-resolution protein structures.