Cross-link guided molecular modeling with ROSETTA.

Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these dis...

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Autores principales:	Abdullah Kahraman, Franz Herzog, Alexander Leitner, George Rosenberger, Ruedi Aebersold, Lars Malmström
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3d4e1533f747432d843a487f147ebd2e
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spelling	oai:doaj.org-article:3d4e1533f747432d843a487f147ebd2e2021-11-18T08:54:58ZCross-link guided molecular modeling with ROSETTA.1932-620310.1371/journal.pone.0073411https://doaj.org/article/3d4e1533f747432d843a487f147ebd2e2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24069194/?tool=EBIhttps://doaj.org/toc/1932-6203Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.Abdullah KahramanFranz HerzogAlexander LeitnerGeorge RosenbergerRuedi AebersoldLars MalmströmPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 9, p e73411 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Abdullah Kahraman Franz Herzog Alexander Leitner George Rosenberger Ruedi Aebersold Lars Malmström Cross-link guided molecular modeling with ROSETTA.
description	Chemical cross-links identified by mass spectrometry generate distance restraints that reveal low-resolution structural information on proteins and protein complexes. The technology to reliably generate such data has become mature and robust enough to shift the focus to the question of how these distance restraints can be best integrated into molecular modeling calculations. Here, we introduce three workflows for incorporating distance restraints generated by chemical cross-linking and mass spectrometry into ROSETTA protocols for comparative and de novo modeling and protein-protein docking. We demonstrate that the cross-link validation and visualization software Xwalk facilitates successful cross-link data integration. Besides the protocols we introduce XLdb, a database of chemical cross-links from 14 different publications with 506 intra-protein and 62 inter-protein cross-links, where each cross-link can be mapped on an experimental structure from the Protein Data Bank. Finally, we demonstrate on a protein-protein docking reference data set the impact of virtual cross-links on protein docking calculations and show that an inter-protein cross-link can reduce on average the RMSD of a docking prediction by 5.0 Å. The methods and results presented here provide guidelines for the effective integration of chemical cross-link data in molecular modeling calculations and should advance the structural analysis of particularly large and transient protein complexes via hybrid structural biology methods.
format	article
author	Abdullah Kahraman Franz Herzog Alexander Leitner George Rosenberger Ruedi Aebersold Lars Malmström
author_facet	Abdullah Kahraman Franz Herzog Alexander Leitner George Rosenberger Ruedi Aebersold Lars Malmström
author_sort	Abdullah Kahraman
title	Cross-link guided molecular modeling with ROSETTA.
title_short	Cross-link guided molecular modeling with ROSETTA.
title_full	Cross-link guided molecular modeling with ROSETTA.
title_fullStr	Cross-link guided molecular modeling with ROSETTA.
title_full_unstemmed	Cross-link guided molecular modeling with ROSETTA.
title_sort	cross-link guided molecular modeling with rosetta.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/3d4e1533f747432d843a487f147ebd2e
work_keys_str_mv	AT abdullahkahraman crosslinkguidedmolecularmodelingwithrosetta AT franzherzog crosslinkguidedmolecularmodelingwithrosetta AT alexanderleitner crosslinkguidedmolecularmodelingwithrosetta AT georgerosenberger crosslinkguidedmolecularmodelingwithrosetta AT ruediaebersold crosslinkguidedmolecularmodelingwithrosetta AT larsmalmstrom crosslinkguidedmolecularmodelingwithrosetta
_version_	1718421135240986624

Cross-link guided molecular modeling with ROSETTA.

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