ArticlePLoS computational biology2019
A new clustering and nomenclature for beta turns derived from high-resolution protein structures.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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27 citing papers in PubMed.
- Thermodynamic and Structural Determinants of Ni(II), Co(II), and Zn(II) Binding to an XHXXHXH Peptide Motif.Journal of peptide science : an official publication of the European Peptide Society · 2026Article
- Defining the Active Conformation of Typical Protein Kinase Domains from Substrate-Bound PDB Structures Enables Active-State AlphaFold2 Models for All 437 Human Catalytic Protein Kinases.bioRxiv : the preprint server for biology · 2026Article
- Proline/sidechain C-H/O interactions stabilizePhysical chemistry chemical physics : PCCP · 2026Article
- Structural and functional properties ofFood production, processing and nutrition · 2026Article
- Chemical and ribosomal synthesis of atropisomeric and macrocyclic peptides with embedded quinolines.Nature chemistry · 2026Article
- Genome-wide identification and expression analysis of the MBD gene family in Broomcorn millet (Panicum miliaceum) and its response to abiotic stress.BMC genomics · 2025Article
- ExploreTurns: A web tool for the exploration, analysis, and classification of beta turns and structured loops in proteins; application to beta-bulge and Schellman loops, Asx helix caps, beta hairpins, and other hydrogen-bonded motifs.Protein science : a publication of the Protein Society · 2025Article
- MapTurns: mapping the structure, H-bonding, and contexts of beta turns in proteins.Bioinformatics (Oxford, England) · 2024Article
- Exquisite selectivity of griselimycin extends to beta subunit of DNA polymerases from Gram-negative bacterial pathogens.Communications biology · 2024Article
- Sequence and structural determinants of RNAPII CTD phase-separation and phosphorylation by CDK7.Nature communications · 2024Article
- Geometric descriptors for beta turns.Protein science : a publication of the Protein Society · 2024Article
- Protein folding, protein dynamics and the topology of self-motions.Royal Society open science · 2024Article
- Emerging role of carbonyl-carbonyl interactions in the classification of beta turns.Protein science : a publication of the Protein Society · 2024Article
- Structural Analyses of Designed α-Helix and β-Sheet Peptide Nanofibers Using Solid-State Nuclear Magnetic Resonance and Cryo-Electron Microscopy and Introduction of Structure-Based Metal-Responsive Properties.International journal of molecular sciences · 2024Article
- HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes.Nature communications · 2023Article
- An active site loop toggles between conformations to control antibiotic hydrolysis and inhibition potency for CTX-M β-lactamase drug-resistance enzymes.Nature communications · 2022Article
- A Perspective on the (Rise and Fall of) Protein β-Turns.International journal of molecular sciences · 2022Review
- Structure-activity relationships of mitochondria-targeted tetrapeptide pharmacological compounds.eLife · 2022Article
- Delineating the RAS Conformational Landscape.Cancer research · 2022Article
- Quantitative Assessment of Chirality of Protein Secondary Structures and Phenylalanine Peptide Nanotubes.Nanomaterials (Basel, Switzerland) · 2021Article
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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.
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