Research output: Contribution to journal › Article › peer-review
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 output: Contribution to journal › Article › peer-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
C2 - 29444233
VL - 34
SP - 599
EP - 608
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 4
ER -
ID: 9349320