Large-scale determination of previously unsolved protein structures using evolutionary information

ELife
Sergey OvchinnikovDavid Baker

Abstract

The prediction of the structures of proteins without detectable sequence similarity to any protein of known structure remains an outstanding scientific challenge. Here we report significant progress in this area. We first describe de novo blind structure predictions of unprecendented accuracy we made for two proteins in large families in the recent CASP11 blind test of protein structure prediction methods by incorporating residue-residue co-evolution information in the Rosetta structure prediction program. We then describe the use of this method to generate structure models for 58 of the 121 large protein families in prokaryotes for which three-dimensional structures are not available. These models, which are posted online for public access, provide structural information for the over 400,000 proteins belonging to the 58 families and suggest hypotheses about mechanism for the subset for which the function is known, and hypotheses about function for the remainder.

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Citations

May 5, 2016·Nature·Jyh-Yeuan LeeDaniel M Rosenbaum
Feb 3, 2016·Protein Science : a Publication of the Protein Society·Tyler N Starr, Joseph W Thornton
Aug 16, 2016·Journal of Molecular Biology·Christopher P ZschiedrichHendrik Szurmant
Aug 5, 2016·Biochemistry·Brian J BenderRocco Moretti
Nov 4, 2016·The Journal of Physical Chemistry. B·Jeffrey Skolnick, Hongyi Zhou
Nov 3, 2016·Briefings in Bioinformatics·Qiqige WuyunJianyi Yang
Jan 21, 2017·Science·Johannes Söding
Jan 21, 2017·Science·Sergey OvchinnikovDavid Baker
Jan 17, 2017·Nature Biotechnology·Thomas A HopfDebora S Marks
Nov 12, 2016·PLoS Computational Biology·Sophia S LiuLuís A N Amaral
Apr 4, 2017·Bioinformatics·Felix SimkovicDaniel J Rigden
May 18, 2017·IUCrJ·Felix SimkovicDaniel J Rigden
Nov 15, 2017·Bioinformatics·Saulo H P de OliveiraCharlotte M Deane
Oct 7, 2017·Scientific Reports·Zahra ShamsiDiwakar Shukla
Nov 6, 2018·PLoS Computational Biology·Susann VorbergJohannes Söding
Nov 14, 2018·PLoS Computational Biology·Anne-Florence Bitbol
Oct 20, 2018·The Journal of Biological Chemistry·Pengcheng SunDong Deng
Jan 1, 2019·PLoS Computational Biology·Andrew F Neuwald, Stephen F Altschul
Mar 11, 2018·The Biochemical Journal·Alexander S Moffett, Diwakar Shukla
Jun 9, 2016·Nature Structural & Molecular Biology·Patrick Barth, Alessandro Senes
Sep 16, 2016·Nature·Po-Ssu HuangDavid Baker
Jun 23, 2019·BMC Molecular and Cell Biology·R Dustin SchaefferNick Grishin
Dec 23, 2017·Molecular Biology and Evolution·Cristina M AlexandreChristin Queitsch
Dec 12, 2018·Bioinformatics·Claire Marks, Charlotte M Deane
Oct 12, 2019·Proteins·Davide SalaGaetano T Montelione
Dec 6, 2019·Nature Communications·Mayuko TakakuraTsutomu Suzuki

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Methods Mentioned

BETA
X-ray

Software Mentioned

SatP
GDT
SPARKS
EmrE
HHblits
TM
HHsuite
web server
RosettaCM
GREMLIN

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