Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data

• Published in: Nature protocols Vol. 13; no. 3; p. 478
• Main Authors: Orbán-Németh, Zsuzsanna, Beveridge, Rebecca, Hollenstein, David M, Rampler, Evelyn, Stranzl, Thomas, Hudecz, Otto, Doblmann, Johannes, Schlögelhofer, Peter, Mechtler, Karl
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01.03.2018
• Subjects: Amino acid sequence; Computer applications; Computer Simulation; Constraints; Cross-Linking Reagents - chemistry; Crosslinking; Data processing; Forecasting - methods; Homology; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; Mathematical models; Models, Molecular; Predictions; Protein Structure, Tertiary - genetics; Protein Structure, Tertiary - physiology; Proteins; Proteins - genetics; Proteins - physiology; Scientific imaging; Source programs; Spectroscopy; Structural models; Workflow
• ISSN: 1754-2189; 1750-2799; 1750-2799
• DOI: 10.1038/nprot.2017.146

This protocol describes a workflow for creating structural models of proteins or protein complexes using distance restraints derived from cross-linking mass spectrometry experiments. The distance restraints are used (i) to adjust preliminary models that are calculated on the basis of a homologous template and primary sequence, and (ii) to select the model that is in best agreement with the experimental data. In the case of protein complexes, the cross-linking data are further used to dock the subunits to one another to generate models of the interacting proteins. Predicting models in such a manner has the potential to indicate multiple conformations and dynamic changes that occur in solution. This modeling protocol is compatible with many cross-linking workflows and uses open-source programs or programs that are free for academic users and do not require expertise in computational modeling. This protocol is an excellent additional application with which to use cross-linking results for building structural models of proteins. The established protocol is expected to take 6-12 d to complete, depending on the size of the proteins and the complexity of the cross-linking data.