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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| Published in: | Nature protocols Vol. 13; no. 3; p. 478 |
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| Main Authors: | , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
| Published: |
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Nature Publishing Group
01.03.2018
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| ISSN: | 1754-2189, 1750-2799, 1750-2799 |
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| Abstract | 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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| AbstractList | 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. 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.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. |
| Author | Rampler, Evelyn Orbán-Németh, Zsuzsanna Hollenstein, David M Stranzl, Thomas Mechtler, Karl Beveridge, Rebecca Schlögelhofer, Peter Doblmann, Johannes Hudecz, Otto |
| Author_xml | – sequence: 1 givenname: Zsuzsanna surname: Orbán-Németh fullname: Orbán-Németh, Zsuzsanna organization: Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria – sequence: 2 givenname: Rebecca surname: Beveridge fullname: Beveridge, Rebecca organization: Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria – sequence: 3 givenname: David M orcidid: 0000-0002-1977-1556 surname: Hollenstein fullname: Hollenstein, David M organization: Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria – sequence: 4 givenname: Evelyn surname: Rampler fullname: Rampler, Evelyn organization: Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria – sequence: 5 givenname: Thomas surname: Stranzl fullname: Stranzl, Thomas organization: Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria – sequence: 6 givenname: Otto surname: Hudecz fullname: Hudecz, Otto organization: Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria – sequence: 7 givenname: Johannes surname: Doblmann fullname: Doblmann, Johannes organization: Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria – sequence: 8 givenname: Peter surname: Schlögelhofer fullname: Schlögelhofer, Peter organization: Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria – sequence: 9 givenname: Karl surname: Mechtler fullname: Mechtler, Karl organization: Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria |
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| SubjectTerms | 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 |
| Title | Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data |
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