Automated structure modeling of large protein assemblies using crosslinks as distance restraints.
Crosslinking mass spectrometry is increasingly used for structural characterization of multisubunit protein complexes. Chemical crosslinking captures conformational heterogeneity, which typically results in conflicting crosslinks that cannot be satisfied in a single model, making detailed modeling a challenging task. Here we introduce an automated modeling method dedicated to large protein assemblies ('XL-MOD' software is available at http://aria.pasteur.fr/supplementary-data/x-links) that (i) uses a form of spatial restraints that realistically reflects the distribution of experimentally observed crosslinked distances; (ii) automatically deals with ambiguous and/or conflicting crosslinks and identifies alternative conformations within a Bayesian framework; and (iii) allows subunit structures to be flexible during conformational sampling. We demonstrate our method by testing it on known structures and available crosslinking data. We also crosslinked and modeled the 17-subunit yeast RNA polymerase III at atomic resolution; the resulting model agrees remarkably well with recently published cryoelectron microscopy structures and provides additional insights into the polymerase structure.
Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France.
Mathias
M
Ferber
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Jan
0000-0002-3641-0322
J
Kosinski
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Alessandro
0000-0002-3046-0871
A
Ori
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Umar J
UJ
Rashid
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
María
M
Moreno-Morcillo
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Bernd
B
Simon
Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France.
Guillaume
G
Bouvier
Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France.
Paulo Ricardo
0000-0002-3399-174X
PR
Batista
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Christoph W
0000-0003-2176-8337
CW
Müller
European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
Martin
0000-0002-7397-1321
M
Beck
Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France.
Michael
0000-0002-1451-8092
M
Nilges
D001499:Bayes Theorem; D003432:Cross-Linking Reagents / Q000737:chemistry*; D013058:Mass Spectrometry; D008962:Models, Theoretical; D046912:Multiprotein Complexes / Q000737:chemistry*; D011487:Protein Conformation; D021122:Protein Subunits / Q000737:chemistry*; D012320:RNA Polymerase III / Q000737:chemistry; D015203:Reproducibility of Results; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D012680:Sensitivity and Specificity
D003432:Cross-Linking Reagents; D046912:Multiprotein Complexes; D021122:Protein Subunits; D029701:Saccharomyces cerevisiae Proteins; D012320:RNA Polymerase III