BetaSerpentine

a bioinformatics tool for reconstruction of amyloid structures

Stanislav A Bondarev, Olga V Bondareva, Galina A Zhouravleva, Andrey V Kajava

Research outputpeer-review

2 Citations (Scopus)

Abstract

Motivation: Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics.

Results: We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments.

Availability and implementation: BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine).

Contact: stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr.

Supplementary information: Supplementary data are available at Bioinformatics online.

Original languageEnglish
Pages (from-to)599-608
Number of pages10
JournalBioinformatics
Volume34
Issue number4
DOIs
Publication statusPublished - 15 Feb 2018

Cite this

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title = "BetaSerpentine: a bioinformatics tool for reconstruction of amyloid structures",
abstract = "Motivation: Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics.Results: We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments.Availability and implementation: BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine).Contact: stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr.Supplementary information: Supplementary data are available at Bioinformatics online.",
keywords = "ALPHA-SYNUCLEIN, ATOMIC-STRUCTURE, DOMAIN, FIBRIL STRUCTURE, FULL-LENGTH, IN-REGISTER, PARALLEL BETA-SHEET, PRION STRAIN, PSI+ PRION, SUP35 PROTEIN",
author = "Bondarev, {Stanislav A} and Bondareva, {Olga V} and Zhouravleva, {Galina A} and Kajava, {Andrey V}",
note = "{\circledC} The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com",
year = "2018",
month = "2",
day = "15",
doi = "10.1093/bioinformatics/btx629",
language = "English",
volume = "34",
pages = "599--608",
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BetaSerpentine : a bioinformatics tool for reconstruction of amyloid structures. / Bondarev, Stanislav A; Bondareva, Olga V; Zhouravleva, Galina A; Kajava, Andrey V.

In: Bioinformatics, Vol. 34, No. 4, 15.02.2018, p. 599-608.

Research outputpeer-review

TY - JOUR

T1 - BetaSerpentine

T2 - a bioinformatics tool for reconstruction of amyloid structures

AU - Bondarev, Stanislav A

AU - Bondareva, Olga V

AU - Zhouravleva, Galina A

AU - Kajava, Andrey V

N1 - © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

PY - 2018/2/15

Y1 - 2018/2/15

N2 - Motivation: Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics.Results: We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments.Availability and implementation: BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine).Contact: stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr.Supplementary information: Supplementary data are available at Bioinformatics online.

AB - Motivation: Numerous experimental studies have suggested that polypeptide chains of large amyloidogenic regions zig-zag in β-serpentine arrangements. These β-serpentines are stacked axially and form the superpleated β-structure. Despite this progress in the understanding of amyloid folds, the determination of their 3D structure at the atomic level is still a problem due to the polymorphism of these fibrils and incompleteness of experimental structural data. Today, the way to get insight into the atomic structure of amyloids is a combination of experimental studies with bioinformatics.Results: We developed a computer program BetaSerpentine that reconstructs β-serpentine arrangements from individual β-arches predicted by ArchCandy program and ranks them in order of preference. It was shown that the BetaSerpentine program in combination with the experimental data can be used to gain insight into the detailed 3D structure of amyloids. It opens avenues to the structure-based interpretation and design of the experiments.Availability and implementation: BetaSerpentine webserver can be accessed through website: http://bioinfo.montp.cnrs.fr/b-serpentine. Source code is available in git.hub repository (github.com/stanislavspbgu/BetaSerpentine).Contact: stanislavspbgu@gmail.com or andrey.kajava@crbm.cnrs.fr.Supplementary information: Supplementary data are available at Bioinformatics online.

KW - ALPHA-SYNUCLEIN

KW - ATOMIC-STRUCTURE

KW - DOMAIN

KW - FIBRIL STRUCTURE

KW - FULL-LENGTH

KW - IN-REGISTER

KW - PARALLEL BETA-SHEET

KW - PRION STRAIN

KW - PSI+ PRION

KW - SUP35 PROTEIN

U2 - 10.1093/bioinformatics/btx629

DO - 10.1093/bioinformatics/btx629

M3 - Article

VL - 34

SP - 599

EP - 608

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 4

ER -