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Orbán-Németh Z, Beveridge R, Hollenstein DM, Rampler E, Stranzl T, Hudecz O, Doblmann J, Schlögelhofer P, Mechtler K. Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data. Nat Protoc 2018; 13:478-494. [PMID: 29419816 PMCID: PMC5999019 DOI: 10.1038/nprot.2017.146] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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Affiliation(s)
- Zsuzsanna Orbán-Németh
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Rebecca Beveridge
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - David M. Hollenstein
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Evelyn Rampler
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Thomas Stranzl
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Otto Hudecz
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Johannes Doblmann
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- Mass Spectrometry and Protein Chemistry, Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Peter Schlögelhofer
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Karl Mechtler
- Mass Spectrometry and Protein Chemistry, Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
- 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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Orbán-Németh Z, Henen MA, Geist L, Żerko S, Saxena S, Stanek J, Koźmiński W, Propst F, Konrat R. Backbone and partial side chain assignment of the microtubule binding domain of the MAP1B light chain. Biomol NMR Assign 2014; 8:123-127. [PMID: 23339032 PMCID: PMC3955483 DOI: 10.1007/s12104-013-9466-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/12/2013] [Indexed: 06/01/2023]
Abstract
Microtubule-associated protein 1B (MAP1B) is a classical high molecular mass microtubule-associated protein expressed at high levels in the brain. It confers specific properties to neuronal microtubules and is essential for neuronal differentiation, brain development and synapse maturation. Misexpression of the protein contributes to the development of brain disorders in humans. However, despite numerous reports demonstrating the importance of MAP1B in regulation of the neuronal cytoskeleton during neurite extension and axon guidance, its mechanism of action is still elusive. Here we focus on the intrinsically disordered microtubule binding domain of the light chain of MAP1B. In order to obtain more detailed structural information about this domain we assigned NMR chemical shifts of backbone and aliphatic side chain atoms.
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Affiliation(s)
- Zsuzsanna Orbán-Németh
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 1, 1030 Vienna, Austria
| | - Morkos A. Henen
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Leonhard Geist
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
| | - Szymon Żerko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Saurabh Saxena
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Jan Stanek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Friedrich Propst
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 1, 1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, 1030 Vienna, Austria
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Orbán-Németh Z, Simader H, Badurek S, Tranciková A, Propst F. Microtubule-associated protein 1S, a short and ubiquitously expressed member of the microtubule-associated protein 1 family. J Biol Chem 2004; 280:2257-65. [PMID: 15528209 DOI: 10.1074/jbc.m408984200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The related high molecular mass microtubule-associated proteins (MAPs) MAP1A and MAP1B are predominantly expressed in the nervous system and are involved in axon guidance and synaptic function. MAP1B is implicated in fragile X mental retardation, giant axonal neuropathy, and ataxia type 1. We report the functional characterization of a novel member of the microtubule-associated protein 1 family, which we termed MAP1S (corresponding to sequence data bank entries for VCY2IP1 and C19ORF5). MAP1S contains the three hallmark domains of the microtubule-associated protein 1 family but hardly any additional sequences. It decorates neuronal microtubules and copurifies with tubulin from brain. MAP1S is synthesized as a precursor protein that is partially cleaved into heavy and light chains in a tissue-specific manner. Heavy and light chains interact to form the MAP1S complex. The light chain binds, bundles, and stabilizes microtubules and binds to actin. The heavy chain appears to regulate light chain activity. In contrast to MAP1A and MAP1B, MAP1S is expressed in a wide range of tissues in addition to neurons and represents the non-neuronal counterpart of this cytolinker family.
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Affiliation(s)
- Zsuzsanna Orbán-Németh
- Institute of Biochemistry and Molecular Cell Biology, Vienna Biocenter, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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