期刊
NATURE PROTOCOLS
卷 13, 期 3, 页码 478-494出版社
NATURE PORTFOLIO
DOI: 10.1038/nprot.2017.146
关键词
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资金
- Austrian Science Fund [SFB F3402, P24685-B24, TRP 308-N15]
- NIGMS [P41-GM103311]
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA)
- Research Institute of Molecular Pathology (IMP)
- EU FP7 project MEIOsys [222883-2]
- Austrian Science Fund (FWF) [P 24685, TRP 308] Funding Source: researchfish
- Austrian Science Fund (FWF) [P24685] Funding Source: Austrian Science Fund (FWF)
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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