Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data
Antonio Rosato
(1, 2)
,
James M. Aramini
(3)
,
Cheryl Arrowsmith
(4)
,
Anurag Bagaria
(5, 6)
,
David Baker
(7)
,
Andrea Cavalli
(8)
,
Jurgen F. Doreleijers
(9)
,
Alexander Eletsky
(10)
,
Andrea Giachetti
(10)
,
Paul Guerry
(11)
,
Aleksandras Gutmanas
(4)
,
Peter Güntert
(5, 12)
,
Yunfen He
(10)
,
Torsten Herrmann
(11)
,
Yuanpeng J. Huang
(3)
,
Victor Jaravine
(5, 12)
,
Hendrik R.A. Jonker
(13, 14)
,
Michael A. Kennedy
(15)
,
Olivier F. Lange
(7)
,
Gaohua Liu
(3)
,
Thérèse E. Malliavin
(16)
,
Rajeswari Mani
(3)
,
Binchen Mao
(3)
,
Gaetano T. Montelione
(3)
,
Michael Nilges
(16)
,
Paolo Rossi
(3)
,
Gijs van Der Schot
(17)
,
Harald Schawlbe
(13, 14)
,
Thomas A. Szyperski
(10)
,
Michele Vendruscolo
(8)
,
Robert Vernon
(7)
,
Wim F. Vranken
(18, 19)
,
Sjored de Vries
(17)
,
Geerten W. Vuister
(9, 20)
,
Bin Wu
(4)
,
Yunhuang Yang
(15)
,
Alexandre M.J.J. Bonvin
(17)
1
UniFI -
Università degli Studi di Firenze = University of Florence = Université de Florence
2 DICUS UniFI - Dipartimento di Chimica 'Ugo Schiff' [Sesto Fiorentino]
3 Center for Advanced Biotechnology and Medicine
4 Ontario Cancer Institute
5 Institute of Biophysical Chemistry and Frankfurt Institute for Advanced Studies
6 Goethe-Universität Frankfurt am Main
7 Department of Biochemistry [Washington ]
8 Department of Chemistry
9 Protein Biophysics - Institute of Molecules and Materials
10 SUNY - State University of New York
11 ISA - Centre de RMN à très hauts champs
12 Center for Biomolecular Magnetic Resonance
13 Center for Biomolecular Magnetic Resonance
14 Institute of Organic Chemistry and Chemical Biology
15 department of Chemistry and Biochemistry and NESG
16 Bioinformatique Structurale
17 Bijvoet Center of Biomolecular Research [Utrecht]
18 Department of Structural Biology
19 SBB - Structural Biology Brussels
20 Department of Biochemistry [Leicester]
2 DICUS UniFI - Dipartimento di Chimica 'Ugo Schiff' [Sesto Fiorentino]
3 Center for Advanced Biotechnology and Medicine
4 Ontario Cancer Institute
5 Institute of Biophysical Chemistry and Frankfurt Institute for Advanced Studies
6 Goethe-Universität Frankfurt am Main
7 Department of Biochemistry [Washington ]
8 Department of Chemistry
9 Protein Biophysics - Institute of Molecules and Materials
10 SUNY - State University of New York
11 ISA - Centre de RMN à très hauts champs
12 Center for Biomolecular Magnetic Resonance
13 Center for Biomolecular Magnetic Resonance
14 Institute of Organic Chemistry and Chemical Biology
15 department of Chemistry and Biochemistry and NESG
16 Bioinformatique Structurale
17 Bijvoet Center of Biomolecular Research [Utrecht]
18 Department of Structural Biology
19 SBB - Structural Biology Brussels
20 Department of Biochemistry [Leicester]
Antonio Rosato
- Fonction : Auteur
- PersonId : 762605
- ORCID : 0000-0002-5263-8386
David Baker
- Fonction : Auteur
- PersonId : 760695
- ORCID : 0000-0002-7184-6594
Torsten Herrmann
- Fonction : Auteur
- PersonId : 742391
- IdHAL : torsten-herrmann
- ORCID : 0000-0003-2115-4781
Michael Nilges
- Fonction : Auteur
- PersonId : 757144
- ORCID : 0000-0002-1451-8092
- IdRef : 139250018
Alexandre M.J.J. Bonvin
- Fonction : Auteur
- PersonId : 918243
Résumé
The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for deposition in the Protein Data Bank, we gathered 10 experimental data sets with unassigned nuclear Overhauser effect spectroscopy (NOESY) peak lists for various proteins of unknown structure, computed structures for each of them using different, fully automatic programs, and compared the results to each other and to the manually solved reference structures that were not available at the time the data were provided. This constitutes a stringent "blind" assessment similar to the CASP and CAPRI initiatives. This study demonstrates the feasibility of routine, fully automated protein structure determination by NMR. Highlights Automated assignment and structure calculation from NMR NOESY spectra were assessed Routine, fully automated determination of protein structures is feasible Good stereochemical and geometric quality alone does not indicate structure accuracy