TY - JOUR

T1 - Classification of β-hairpin repeat proteins

AU - Roche, Daniel B.

AU - Viet, Phuong Do

AU - Bakulina, Anastasia

AU - Hirsh, Layla

AU - Tosatto, Silvio C.E.

AU - Kajava, Andrey V.

N1 - Publisher Copyright: © 2017 Elsevier Inc.

PY - 2018/2/1

Y1 - 2018/2/1

N2 - 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.

AB - 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.

KW - Beta-barrel

KW - Beta-structure

KW - Porin

KW - Proteins with repeats

KW - Sequence-structure relationship

KW - Structural classification

KW - CRYSTAL-STRUCTURE

KW - BINDING-PROTEIN

KW - BARREL MEMBRANE-PROTEINS

KW - ATOMIC-RESOLUTION

KW - SOLENOID PROTEINS

KW - BACTERIAL OUTER-MEMBRANE

KW - STRUCTURAL BASIS

KW - TANDEM REPEATS

KW - PASSENGER DOMAIN

KW - SALMONELLA-TYPHIMURIUM

KW - Prions/chemistry

KW - Humans

KW - Repetitive Sequences, Amino Acid

KW - Viral Proteins/chemistry

KW - Databases, Protein

KW - Bacterial Proteins/chemistry

KW - Amyloid/chemistry

KW - Models, Molecular

KW - Protein Folding

KW - Amino Acid Motifs

KW - Proteins/chemistry

KW - Protein Conformation, beta-Strand

KW - Protein Conformation

KW - Internet

KW - Zinc/metabolism

UR - http://www.scopus.com/inward/record.url?scp=85031328493&partnerID=8YFLogxK

U2 - 10.1016/j.jsb.2017.10.001

DO - 10.1016/j.jsb.2017.10.001

M3 - Article

C2 - 29017817

AN - SCOPUS:85031328493

VL - 201

SP - 130

EP - 138

JO - Journal of Structural Biology

JF - Journal of Structural Biology

SN - 1047-8477

IS - 2

ER -