Classification of β-hairpin repeat proteins

Roche, Daniel B.; Viet, Phuong Do; Bakulina, Anastasia; Hirsh, Layla; Tosatto, Silvio C. E.; Kajava, Andrey V.

doi:10.1016/j.jsb.2017.10.001

Cited by 21 publications

(30 citation statements)

References 74 publications

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“…Since both sides of the β‐sheet are exposed to solvent, these SLBPs do not possess a hydrophobic core, as commonly observed in globular proteins. SLBPs can be categorized as a member of the “curved single‐layer subfold” according to the classification defined by Roche et al…”

Section: Resultsmentioning

confidence: 99%

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Structures of single‐layer β‐sheet proteins evolved from β‐hairpin repeats

Biancalana

Grant

et al. 2019

Protein Science

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Free‐standing single‐layer β‐sheets are extremely rare in naturally occurring proteins, even though β‐sheet motifs are ubiquitous. Here we report the crystal structures of three homologous, single‐layer, anti‐parallel β‐sheet proteins, comprised of three or four twisted β‐hairpin repeats. The structures reveal that, in addition to the hydrogen bond network characteristic of β‐sheets, additional hydrophobic interactions mediated by small clusters of residues adjacent to the turns likely play a significant role in the structural stability and compensate for the lack of a compact hydrophobic core. These structures enabled identification of a family of secreted proteins that are broadly distributed in bacteria from the human gut microbiome and are putatively involved in the metabolism of complex carbohydrates. A conserved surface patch, rich in solvent‐exposed tyrosine residues, was identified on the concave surface of the β‐sheet. These new modular single‐layer β‐sheet proteins may serve as a new model system for studying folding and design of β‐rich proteins.

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Section: Resultsmentioning

confidence: 99%

“…One of the simplest, yet most uncommon, forms of β‐repeat proteins consists of multiple β‐hairpins assembled into a single‐layer antiparallel β‐sheet, linked together by inter‐strand hydrogen bonds . Unlike other folds, no conventional hydrophobic core can exist in single layer β‐sheet proteins.…”

Section: Introductionmentioning

confidence: 99%

Structures of single‐layer β‐sheet proteins evolved from β‐hairpin repeats

Biancalana

Grant

et al. 2019

Protein Science

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“…This can be considered as a shortcoming of these double β‐sheet models. The other experimental data led to the hypothesis that the amyloid pores have single‐layer β‐barrel structures similar to the arrangement found in the bacterial pore‐forming toxins . Typically, the polypeptide chain of the bacterial porins folds into a β‐barrel structure formed by a circular β‐sheet with antiparallel arrangement of β‐strands .…”

Section: Introductionmentioning

confidence: 88%

“…An initial set of proteins containing arrays of tandemly repeated β‐hairpins was obtained as described in ref. . The main criteria for the BHR protein selection were: 1) a repetitive unit is a β‐hairpin and 2) neighboring β‐hairpins interact with each other in an equivalent manner.…”

Section: Methodsmentioning

confidence: 99%

“…Recently, we developed a program ArchCandy for detection of amino acid sequences that are able to form the amyloidogenic β‐arcade structures . In the other work, we selected and classified the known β‐hairpin repeat (BHR) structures . Our analysis has shown that the known BHR structures have at least six different elongated folds and one compact β‐barrel fold.…”

Section: Introductionmentioning

confidence: 99%

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Porins and Amyloids are Coded by Similar Sequence Motifs

2018

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The relationship between amino acid sequences of the β‐hairpin structures and amyloidogenic β‐arcade‐forming motifs are of special interest because, similar to amyloid fibrils, most of the β‐hairpin repeat (BHR) structures have the so‐called cross‐β arrangement. Moreover, β‐hairpin is considered as a probable intermediate structure in amyloidogenesis. In this work, a bioinformatics sequence analysis of the known BHR structures is performed in search of amylodogenic motifs able to form β‐arcade fibrils. The analysis shows that the occurrence of the predicted β‐arcade motifs in the BHR regions is very different depending on the BHR structural fold, cellular localization, and phylogeny. One of the most striking observations is the high level of sequence similarity between the BHRs of membranous porins and β‐arcade motifs. This sequence similarity provides additional evidence that the structure of the membranous porins and annular amyloid oligomers may bear a resemblance. Moreover, these results explain how some amyloidogenic sequence can fold in either the ring‐like shape oligomers or elongated amyloid fibrils. It has been also found that potentially lethal amyloidogenic β‐arcade motifs are absent in the elongated BHR structures of intracellular eukaryotic proteins. It allows to hypothesize that, in this case, the selective evolutionary pressure acts against aggregation.

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Pierce into the Native Structure of Ata, a Trimeric Autotransporter of Acinetobacter baumannii ATCC 17978

Rahbar

Zarei

Jahangiri

et al. 2019

Int J Pept Res Ther

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Acinetobacter baumannii is an important pathogen responsible for nosocomial infections worldwide. Trimeric autotransporters, the obligate homotrimeric adhesins, are involved in adherence of bacterial cells to various surfaces. These sorts of adhesins were shown to be expressed by A. baumannii. Trimeric autotransporters are modular virulence factors, containing numerous domains and structural architectures. The better understanding of the sequence and structural features of virulence factors are crucial in designing new therapeutic strategies. In this regard, with the aid of reliable in silico tools and the concept of "inherence through homology", some sequence and structural features of Ata A.baumannii were unveiled. Domain architectures such as the position of repetitive modules, and coiled-coils, along with the prediction of tertiary and quaternary structures, allows us to define some important landscapes of Ata A.baumannii virulence factor. In addition, through CLANS analysis of TAA sequences of Moraxellaceae family, it was concluded that Ata contains several conserved of structural blocks of TAAs. The protein is initiated with extended signal peptide region, a stalk of several head domains and a membrane anchoring region. The globular heads are connected to each other by neck mediators and coiled-coil regions. Several fibronectin and collagen binding sites were defined within the structures. Minimal and maximal frustrated contacts are distributed within the structure of Ata, which suggest both the flexibility and toughness. These are come together for creating an efficient adhesin which is able to bind and bend through multiple sites. The protein could be great target for designing new vaccines or anti-virulence drug.

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Classification of β-hairpin repeat proteins

Cited by 21 publications

References 74 publications

Structures of single‐layer β‐sheet proteins evolved from β‐hairpin repeats

Structures of single‐layer β‐sheet proteins evolved from β‐hairpin repeats

Porins and Amyloids are Coded by Similar Sequence Motifs

Pierce into the Native Structure of Ata, a Trimeric Autotransporter of Acinetobacter baumannii ATCC 17978

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