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      Modular detergents tailor the purification and structural analysis of membrane proteins including G-protein coupled receptors

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          Abstract

          Detergents enable the purification of membrane proteins and are indispensable reagents in structural biology. Even though a large variety of detergents have been developed in the last century, the challenge remains to identify guidelines that allow fine-tuning of detergents for individual applications in membrane protein research. Addressing this challenge, here we introduce the family of oligoglycerol detergents (OGDs). Native mass spectrometry (MS) reveals that the modular OGD architecture offers the ability to control protein purification and to preserve interactions with native membrane lipids during purification. In addition to a broad range of bacterial membrane proteins, OGDs also enable the purification and analysis of a functional G-protein coupled receptor (GPCR). Moreover, given the modular design of these detergents, we anticipate fine-tuning of their properties for specific applications in structural biology. Seen from a broader perspective, this represents a significant advance for the investigation of membrane proteins and their interactions with lipids.

          Abstract

          Detergents are indispensable reagents in membrane protein structural biology. Here, L. H. Urner and co-workers introduce oligoglycerol detergents (OGDs) and use native mass spectrometry to show how interactions of membrane proteins with native membrane lipids can be preserved during purification.

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          Most cited references42

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          Bayesian deconvolution of mass and ion mobility spectra: from binary interactions to polydisperse ensembles.

          Interpretation of mass spectra is challenging because they report a ratio of two physical quantities, mass and charge, which may each have multiple components that overlap in m/z. Previous approaches to disentangling the two have focused on peak assignment or fitting. However, the former struggle with complex spectra, and the latter are generally computationally intensive and may require substantial manual intervention. We propose a new data analysis approach that employs a Bayesian framework to separate the mass and charge dimensions. On the basis of this approach, we developed UniDec (Universal Deconvolution), software that provides a rapid, robust, and flexible deconvolution of mass spectra and ion mobility-mass spectra with minimal user intervention. Incorporation of the charge-state distribution in the Bayesian prior probabilities provides separation of the m/z spectrum into its physical mass and charge components. We have evaluated our approach using systems of increasing complexity, enabling us to deduce lipid binding to membrane proteins, to probe the dynamics of subunit exchange reactions, and to characterize polydispersity in both protein assemblies and lipoprotein Nanodiscs. The general utility of our approach will greatly facilitate analysis of ion mobility and mass spectra.
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            The role of interfacial lipids in stabilizing membrane protein oligomers

            Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability. For the bacterial homologue of the eukaryotic biogenic transporters (LeuT, one of the proteins with the lowest oligomeric stability), we found a precise cohort of lipids within the dimer interface. Delipidation, mutation of lipid-binding sites or expression in cardiolipin-deficient Escherichia coli abrogated dimer formation. Molecular dynamics simulation revealed that cardiolipin acts as a bidentate ligand, bridging across subunits. Subsequently, we show that for the Vibrio splendidus sugar transporter SemiSWEET, another protein with low oligomeric stability, cardiolipin shifts the equilibrium from monomer to functional dimer. We hypothesized that lipids are essential for dimerization of the Na+/H+ antiporter NhaA from E. coli, which has the lowest oligomeric strength, but not for the substantially more stable homologous Thermus thermophilus protein NapA. We found that lipid binding is obligatory for dimerization of NhaA, whereas NapA has adapted to form an interface that is stable without lipids. Overall, by correlating interfacial strength with the presence of interfacial lipids, we provide a rationale for understanding the role of lipids in both transient and stable interactions within a range of α-helical membrane proteins, including G-protein-coupled receptors.
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              Mass spectrometry of intact membrane protein complexes.

              Mass spectrometry (MS) of intact soluble protein complexes has emerged as a powerful technique to study the stoichiometry, structure-function and dynamics of protein assemblies. Recent developments have extended this technique to the study of membrane protein complexes, where it has already revealed subunit stoichiometries and specific phospholipid interactions. Here we describe a protocol for MS of membrane protein complexes. The protocol begins with the preparation of the membrane protein complex, enabling not only the direct assessment of stoichiometry, delipidation and quality of the target complex but also the evaluation of the purification strategy. A detailed list of compatible nonionic detergents is included, along with a protocol for screening detergents to find an optimal one for MS, biochemical and structural studies. This protocol also covers the preparation of lipids for protein-lipid binding studies and includes detailed settings for a quadrupole time-of-flight (Q-TOF) mass spectrometer after the introduction of complexes from gold-coated nanoflow capillaries.
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                Author and article information

                Contributors
                haag@zedat.fu-berlin.de
                carol.robinson@chem.ox.ac.uk
                kevin.pagel@fu-berlin.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                28 January 2020
                28 January 2020
                2020
                : 11
                : 564
                Affiliations
                [1 ]ISNI 0000 0000 9116 4836, GRID grid.14095.39, Institute of Chemistry and Biochemistry, , Freie Universität Berlin, ; 14195 Berlin, Germany
                [2 ]ISNI 0000 0004 1936 8948, GRID grid.4991.5, Physical and Theoretical Chemistry Laboratory, , University of Oxford, ; Oxford, OX1 3QZ UK
                [3 ]OMass Therapeutics, The Schrödinger Building, Heatley Road, The Oxford Science Park, Oxford, OX4 4GE UK
                [4 ]ISNI 0000 0001 0565 1775, GRID grid.418028.7, Department of Molecular Physics, , Fritz Haber Institute of the Max Planck Society, ; 14195 Berlin, Germany
                Author information
                http://orcid.org/0000-0001-8144-8955
                http://orcid.org/0000-0003-4346-182X
                http://orcid.org/0000-0001-7686-2983
                http://orcid.org/0000-0001-7829-5505
                Article
                14424
                10.1038/s41467-020-14424-8
                6987200
                31992701
                881b1d4c-08fc-4bbf-a691-24c49c700c25
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 18 June 2019
                : 19 December 2019
                Funding
                Funded by: Fonds der Chemischen Industrie Focus Area Nanoscale of the Freie Universität Berlin
                Funded by: Junior Research Fellowship at The Queen´s College (Oxford)
                Funded by: ERC Advanced Grant No. 695511 (ENABLE)
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                lipids,g protein-coupled receptors,membrane proteins,structural biology,mass spectrometry

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