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      A mass spectrometry-based hybrid method for structural modelling of protein complexes

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          Abstract

          We describe a method that integrates data derived from different mass spectrometric (MS) techniques with a modelling strategy for structural characterization of protein assemblies. We encoded structural data derived from native MS, bottom-up proteomics, ion mobility-MS and chemical cross-linking MS into modelling restraints to compute the most likely structure of a protein assembly. We used the method to generate near-native models for three known structures and characterized an assembly intermediate of the proteasomal base.

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          Hierarchical clustering schemes.

          S. C. Johnson (1967)
          Article 0 comments Cited 621 times – based on 0 reviews     Review now
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            Complete subunit architecture of the proteasome regulatory particle

            Gabriel C. Lander, Eric Estrin, Mary E. Matyskiela … (2012)
            The proteasome is the major ATP-dependent protease in eukaryotic cells, but limited structural information strongly restricts a mechanistic understanding of its activities. The proteasome regulatory particle, consisting of the lid and base subcomplexes, recognizes and processes poly-ubiquitinated substrates. We used electron microscopy and a newly-developed heterologous expression system for the lid to delineate the complete subunit architecture of the regulatory particle. Our studies reveal the spatial arrangement of ubiquitin receptors, deubiquitinating enzymes, and the protein unfolding machinery at subnanometer resolution, outlining the substrate’s path to degradation. Unexpectedly, the ATPase subunits within the base unfoldase are arranged in a spiral staircase, providing insight into potential mechanisms for substrate translocation through the central pore. Large conformational rearrangements of the lid upon holoenzyme formation suggest allosteric regulation of deubiquitination. We provide a structural basis for the ability of the proteasome to degrade a diverse set of substrates and thus regulate vital cellular processes.
            Article 0 comments Cited 200 times – based on 0 reviews     Review now
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              Ion mobility-mass spectrometry analysis of large protein complexes.

              Brandon T Ruotolo, Justin L. P. Benesch, Alan M. Sandercock … (2008)
              Here we describe a detailed protocol for both data collection and interpretation with respect to ion mobility-mass spectrometry analysis of large protein assemblies. Ion mobility is a technique that can separate gaseous ions based on their size and shape. Specifically, within this protocol, we cover general approaches to data interpretation, methods of predicting whether specific model structures for a given protein assembly can be separated by ion mobility, and generalized strategies for data normalization and modeling. The protocol also covers basic instrument settings and best practices for both observation and detection of large noncovalent protein complexes by ion mobility-mass spectrometry.
              Article 0 comments Cited 199 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101215604
                Journal ID (pubmed-jr-id): 32338
                Journal ID (nlm-ta): Nat Methods
                Journal ID (iso-abbrev): Nat. Methods
                Title: Nature methods
                ISSN (Print): 1548-7091
                ISSN (Electronic): 1548-7105
                Publication date Nihms-submitted: 18 February 2014
                Publication date (Electronic): 09 February 2014
                Publication date (Print): April 2014
                Publication date PMC-release: 01 October 2014
                Volume: 11
                Issue: 4
                Pages: 403-406
                Affiliations
                [1 ]Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom.
                [2 ]Department of Biology, Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule (ETH) Zurich, Zurich, Switzerland.
                [3 ]Faculty of Science, University of Zurich, Zurich, Switzerland
                Author notes

                Author Contributions F.S. and A.P. conceived the study; A.P., F.S., C.V.R. and R.A. designed the research; A.P. performed all modelling and developed the software; F.S. carried out the experiments; Z.H and H.H. performed part of the IM-MS and native MS experiments. A.L. and T.W. supported CX-MS experiments and analysis; F.S. and A.P. analysed the data; A.P., F.S, C.V.R. and R.A. wrote the paper; All authors commented on and edited the final version of the paper.

                [4]

                Current address: Department of Life and Health Sciences, School of Biomedical Sciences, University of Ulster, Londonderry, United Kingdom

                [6 ]Correspondence should be addressed to: Ruedi Aebersold: aebersold@ 123456imsb.biol.ethz.ch and Carol V. Robinson: carol.robinson@ 123456chem.ox.ac.uk
                Article
                Manuscript ID: EMS56762
                DOI: 10.1038/nmeth.2841
                PMC ID: 3972104
                PubMed ID: 24509631
                SO-VID: 32602e84-4b54-4bc2-95d1-79dd490e20fa
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                ScienceOpen disciplines: Life sciences
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                ScienceOpen disciplines: Life sciences

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