Abstract
Protein loops connect regular secondary structures and contain 4-residue beta turns which represent 63% of the residues in loops. The commonly used classification of beta turns (Type I, I’, II, II’, VIa1, VIa2, VIb, and VIII) was developed in the 1970s and 1980s from analysis of a small number of proteins of average resolution, and represents only two thirds of beta turns observed in proteins (with a generic class Type IV representing the rest). We present a new clustering of beta-turn conformations from a set of 13,030 turns from 1074 ultra-high resolution protein structures (≤1.2 Å). Our clustering is derived from applying the DBSCAN and k-medoids algorithms to this data set with a metric commonly used in directional statistics applied to the set of dihedral angles from the second and third residues of each turn. We define 18 turn types compared to the 8 classical turn types in common use. We propose a new 2-letter nomenclature for all 18 beta-turn types using Ramachandran region names for the two central residues (e.g., ‘A’ and ‘D’ for alpha regions on the left side of the Ramachandran map and ‘a’ and ‘d’ for equivalent regions on the right-hand side; classical Type I turns are ‘AD’ turns and Type I’ turns are ‘ad’). We identify 11 new types of beta turn, 5 of which are sub-types of classical beta-turn types. Up-to-date statistics, probability densities of conformations, and sequence profiles of beta turns in loops were collected and analyzed. A library of turn types, BetaTurnLib18, and cross-platform software, BetaTurnTool18, which identifies turns in an input protein structure, are freely available and redistributable from dunbrack.fccc.edu/betaturn and github.com/sh-maxim/BetaTurn18. Given the ubiquitous nature of beta turns, this comprehensive study updates understanding of beta turns and should also provide useful tools for protein structure determination, refinement, and prediction programs.
Highlights
Ordered protein structures consist of elements of regular secondary structure, such as alpha helices and beta-sheet strands, and irregular elements of structure referred to as loops or coil regions
Folded proteins consist of elements of regular secondary structure, such as alpha helices and beta sheets connected by irregular structures called loops
Beta turns are formed by four sequential amino acid residues and adopt specific conformations which have been classified into eight types since the 1970s
Summary
Ordered protein structures consist of elements of regular secondary structure, such as alpha helices and beta-sheet strands, and irregular elements of structure referred to as loops or coil regions. Due to the globular nature of folded proteins, the direction of the peptide chain often has to change radically within a few short residues within loops. Turns consist of segments between 2 and 6 amino acids (delta, gamma, beta, alpha and pi turns respectively), and are identified by the distance between the Cα atoms of the first and last residues and sometimes by the existence of specific hydrogen bonds within the segment [1,2,3,4,5,6] These turn fragments are often hydrophilic, since loops are usually on the protein surface [7,8,9]
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