ArticleProtein science : a publication of the Protein Society2013
β-Bulges: extensive structural analyses of β-sheets irregularities.
Article in Protein science : a publication of the Protein Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
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- Structure and self-association of Arrestin-1.Journal of structural biology · 2025Review
- 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
- De Novo Synthesis and Structural Elucidation of CDR-H3 Loop Mimics.ACS chemical biology · 2024Article
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- STR-based feature extraction and selection for genetic feature discovery in neurological disease genes.Scientific reports · 2023Article
- Human antibodies to SARS-CoV-2 with a recurring YYDRxG motif retain binding and neutralization to variants of concern including Omicron.Communications biology · 2022Article
- Secondary Structure of the Novel Myosin Binding Domain WYR and Implications within Myosin Structure.Biology · 2021Article
- De novo design of transmembrane β barrels.Science (New York, N.Y.) · 2021Article
- Identification and characterization of two classes of G1 β-bulge.Acta crystallographica. Section D, Structural biology · 2021Article
- MARK3-mediated phosphorylation of ARHGEF2 couples microtubules to the actin cytoskeleton to establish cell polarity.Science signaling · 2017Article
- Principles for designing proteins with cavities formed by curved β sheets.Science (New York, N.Y.) · 2017Article
- The origin of β-strand bending in globular proteins.BMC structural biology · 2015Article
- Structure of a CutA1 divalent-cation tolerance protein from Cryptosporidium parvum, the protozoal parasite responsible for cryptosporidiosis.Acta crystallographica. Section F, Structural biology communications · 2015Article
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4 authors.
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Abstract
β-Sheets are quite frequent in protein structures and are stabilized by regular main-chain hydrogen bond patterns. Irregularities in β-sheets, named β-bulges, are distorted regions between two consecutive hydrogen bonds. They disrupt the classical alternation of side chain direction and can alter the directionality of β-strands. They are implicated in protein-protein interactions and are introduced to avoid β-strand aggregation. Five different types of β-bulges are defined. Previous studies on β-bulges were performed on a limited number of protein structures or one specific family. These studies evoked a potential conservation during evolution. In this work, we analyze the β-bulge distribution and conservation in terms of local backbone conformations and amino acid composition. Our dataset consists of 66 times more β-bulges than the last systematic study (Chan et al. Protein Science 1993, 2:1574-1590). Novel amino acid preferences are underlined and local structure conformations are highlighted by the use of a structural alphabet. We observed that β-bulges are preferably localized at the N- and C-termini of β-strands, but contrary to the earlier studies, no significant conservation of β-bulges was observed among structural homologues. Displacement of β-bulges along the sequence was also investigated by Molecular Dynamics simulations.
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