Classification of β-hairpin repeat proteins

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

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

Abstract

In recent years, a number of new protein structures that possess tandem repeats have emerged. Many of these proteins are comprised of tandem arrays of β-hairpins. Today, the amount and variety of the data on these β-hairpin repeat (BHR) structures have reached a level that requires detailed analysis and further classification. In this paper, we classified the BHR proteins, compared structures, sequences of repeat motifs, functions and distribution across the major taxonomic kingdoms of life and within organisms. As a result, we identified six different BHR folds in tandem repeat proteins of Class III (elongated structures) and one BHR fold (up-and-down β-barrel) in Class IV ("closed" structures). Our survey reveals the high incidence of the BHR proteins among bacteria and viruses and their possible relationship to the structures of amyloid fibrils. It indicates that BHR folds will be an attractive target for future structural studies, especially in the context of age-related amyloidosis and emerging infectious diseases. This work allowed us to update the RepeatsDB database, which contains annotated tandem repeat protein structures and to construct sequence profiles based on BHR structural alignments.

Original languageEnglish
Pages (from-to)130-138
Number of pages9
JournalJournal of Structural Biology
Volume201
Issue number2
DOIs
Publication statusPublished - 1 Feb 2018

Keywords

  • Beta-barrel
  • Beta-structure
  • Porin
  • Proteins with repeats
  • Sequence-structure relationship
  • Structural classification
  • CRYSTAL-STRUCTURE
  • BINDING-PROTEIN
  • BARREL MEMBRANE-PROTEINS
  • ATOMIC-RESOLUTION
  • SOLENOID PROTEINS
  • BACTERIAL OUTER-MEMBRANE
  • STRUCTURAL BASIS
  • TANDEM REPEATS
  • PASSENGER DOMAIN
  • SALMONELLA-TYPHIMURIUM
  • Prions/chemistry
  • Humans
  • Repetitive Sequences, Amino Acid
  • Viral Proteins/chemistry
  • Databases, Protein
  • Bacterial Proteins/chemistry
  • Amyloid/chemistry
  • Models, Molecular
  • Protein Folding
  • Amino Acid Motifs
  • Proteins/chemistry
  • Protein Conformation, beta-Strand
  • Protein Conformation
  • Internet
  • Zinc/metabolism

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