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

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 te...

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Vydáno v:Nature protocols Ročník 13; číslo 3; s. 478
Hlavní autoři: Orbán-Németh, Zsuzsanna, Beveridge, Rebecca, Hollenstein, David M, Rampler, Evelyn, Stranzl, Thomas, Hudecz, Otto, Doblmann, Johannes, Schlögelhofer, Peter, Mechtler, Karl
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Nature Publishing Group 01.03.2018
Témata:
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
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Popis
Shrnutí: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.
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ISSN:1754-2189
1750-2799
1750-2799
DOI:10.1038/nprot.2017.146