Structural mass spectrometry comes of age: new insight into protein structure, function and interactions.

Mass spectrometry (MS) provides an impressive array of information about the structure, function and interactions of proteins. In recent years, many new developments have been in the field of native MS and these exemplify a new coming of age of this field. In this mini review, we connect the latest methodological and instrumental developments in native MS to the new insights these have enabled. We highlight the prominence of an increasingly common strategy of using hybrid approaches, where multiple MS-based techniques are used in combination, and integrative approaches, where MS is used alongside other techniques such as ion-mobility spectrometry. We also review how the emergence of a native top-down approach, which combines native MS with top-down proteomics into a single experiment, is the pièce de résistance of structural mass spectrometry's coming of age. Finally, we outline key developments that have enabled membrane protein native MS to shift from being extremely challenging to routine, and how this technique is uncovering inaccessible details of membrane protein-lipid interactions.

[1]  N. Kelleher,et al.  Top Down proteomics: facts and perspectives. , 2014, Biochemical and biophysical research communications.

[2]  Weston B. Struwe,et al.  The role of interfacial lipids in stabilizing membrane protein oligomers , 2017, Nature.

[3]  A. Heck,et al.  Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity , 2016, Nature Communications.

[4]  Thomas G. Watkinson,et al.  Systematic analysis of the use of amphipathic polymers for studies of outer membrane proteins using mass spectrometry , 2015, International journal of mass spectrometry.

[5]  A. Laganowsky,et al.  Fourier Transform-Ion Mobility-Orbitrap Mass Spectrometer: A Next-Generation Instrument for Native Mass Spectrometry. , 2018, Analytical chemistry.

[6]  C. Robinson,et al.  Crystal structure of an invertebrate cytolysin pore reveals unique properties and mechanism of assembly , 2016, Nature Communications.

[7]  C. Robinson,et al.  Integrative modelling coupled with ion mobility mass spectrometry reveals structural features of the clamp loader in complex with single-stranded DNA binding protein. , 2013, Journal of molecular biology.

[8]  R. Linhardt,et al.  Dimerization interface of osteoprotegerin revealed by hydrogen–deuterium exchange mass spectrometry , 2018, The Journal of Biological Chemistry.

[9]  A. Heck,et al.  Comprehensive Proteoform Characterization of Plasma Complement Component C8αβγ by Hybrid Mass Spectrometry Approaches , 2018, Journal of The American Society for Mass Spectrometry.

[10]  R. Hausinger,et al.  A Structural Model of the Urease Activation Complex Derived from Ion Mobility-Mass Spectrometry and Integrative Modeling. , 2018, Structure.

[11]  Daniel A. Polasky,et al.  Collision induced unfolding of isolated proteins in the gas phase: past, present, and future. , 2018, Current opinion in chemical biology.

[12]  Gianluca Damonte,et al.  Achievements and perspectives of top‐down proteomics , 2010, Proteomics.

[13]  Ying Ge,et al.  Top‐down proteomics in health and disease: Challenges and opportunities , 2014, Proteomics.

[14]  N. Kelleher,et al.  From protein complexes to subunit backbone fragments: a multi-stage approach to native mass spectrometry. , 2013, Analytical chemistry.

[15]  Carol V Robinson,et al.  Mass spectrometry of intact membrane protein complexes , 2013, Nature Protocols.

[16]  Friedrich Förster,et al.  Structures of the cyanobacterial circadian oscillator frozen in a fully assembled state , 2017, Science.

[17]  M. Gross,et al.  Native electrospray and electron-capture dissociation FTICR mass spectrometry for top-down studies of protein assemblies. , 2011, Analytical chemistry.

[18]  A. Frank,et al.  Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment , 2017, Journal of The American Society for Mass Spectrometry.

[19]  William M. McGee,et al.  Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. , 2017, Analytical chemistry.

[20]  Sheng Yin,et al.  Native Top-Down Mass Spectrometry and Ion Mobility MS for Characterizing the Cobalt and Manganese Metal Binding of α-Synuclein Protein , 2018, Journal of The American Society for Mass Spectrometry.

[21]  Andrea Sinz,et al.  Cross-Linking/Mass Spectrometry for Studying Protein Structures and Protein-Protein Interactions: Where Are We Now and Where Should We Go from Here? , 2018, Angewandte Chemie.

[22]  R. Zubarev,et al.  Electron ionization dissociation of singly and multiply charged peptides. , 2009, Journal of the American Chemical Society.

[23]  A. Makarov,et al.  Engineering Nanodisc Scaffold Proteins for Native Mass Spectrometry. , 2017, Analytical chemistry.

[24]  Carla Schmidt,et al.  A comparative cross-linking strategy to probe conformational changes in protein complexes , 2014, Nature Protocols.

[25]  C. Huber,et al.  Native mass spectrometry combined with enzymatic dissection unravels glycoform heterogeneity of biopharmaceuticals , 2018, Nature Communications.

[26]  S. Mohammed,et al.  Ligand binding to a G protein–coupled receptor captured in a mass spectrometer , 2017, Science Advances.

[27]  J. Brodbelt,et al.  Multistage Ultraviolet Photodissociation Mass Spectrometry To Characterize Single Amino Acid Variants of Human Mitochondrial BCAT2. , 2018, Analytical chemistry.

[28]  P. Hoskisson,et al.  The lipid environment determines the activity of the Escherichia coli ammonium transporter AmtB , 2018, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[29]  Lars Konermann,et al.  Hydrogen exchange mass spectrometry for studying protein structure and dynamics. , 2011, Chemical Society reviews.

[30]  A. Laganowsky,et al.  Characterization of Membrane Protein–Lipid Interactions by Mass Spectrometry Ion Mobility Mass Spectrometry , 2017, Journal of The American Society for Mass Spectrometry.

[31]  Mikhail E. Belov,et al.  An informatic framework for decoding protein complexes by top-down mass spectrometry , 2015, Nature Methods.

[32]  Ruedi Aebersold,et al.  A mass spectrometry-based hybrid method for structural modelling of protein complexes , 2014, Nature Methods.

[33]  Carol V Robinson,et al.  Quantifying the stabilizing effects of protein–ligand interactions in the gas phase , 2015, Nature Communications.

[34]  D. Rees,et al.  The Effect of Detergent, Temperature, and Lipid on the Oligomeric State of MscL Constructs: Insights from Mass Spectrometry. , 2015, Chemistry & biology.

[35]  Brandon T Ruotolo,et al.  The growing role of structural mass spectrometry in the discovery and development of therapeutic antibodies. , 2018, The Analyst.

[36]  A. Laganowsky,et al.  Allosteric modulation of protein-protein interactions by individual lipid binding events , 2017, Nature Communications.

[37]  Gongyu Li,et al.  Reliable Tracking In-Solution Protein Unfolding via Ultrafast Thermal Unfolding/Ion Mobility-Mass Spectrometry. , 2018, Analytical chemistry.

[38]  A. Heck,et al.  Resolving the micro-heterogeneity and structural integrity of monoclonal antibodies by hybrid mass spectrometric approaches , 2017, mAbs.

[39]  S. Cianférani,et al.  Native Mass Spectrometry, Ion Mobility, and Collision-Induced Unfolding for Conformational Characterization of IgG4 Monoclonal Antibodies. , 2018, Analytical chemistry.

[40]  M. Crispin,et al.  Signature of Antibody Domain Exchange by Native Mass Spectrometry and Collision-Induced Unfolding. , 2018, Analytical chemistry.

[41]  Lukasz G. Migas,et al.  Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding , 2016, Nature Communications.

[42]  Z. Hall,et al.  Uncovering the Early Assembly Mechanism for Amyloidogenic β2-Microglobulin Using Cross-linking and Native Mass Spectrometry* , 2015, The Journal of Biological Chemistry.

[43]  E. Marklund,et al.  Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters , 2017, Nature Communications.

[44]  C. Robinson,et al.  Identifying key membrane protein lipid interactions using mass spectrometry , 2018, Nature Protocols.

[45]  Alexandre M. J. J. Bonvin,et al.  Insight into cyanobacterial circadian timing from structural details of the KaiB–KaiC interaction , 2014, Proceedings of the National Academy of Sciences.

[46]  S. Matthews,et al.  Protein assemblies ejected directly from native membranes yield complexes for mass spectrometry , 2018, Science.

[47]  A. Ellington,et al.  Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry. , 2015, Journal of the American Chemical Society.

[48]  R. Aebersold,et al.  Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines. , 2016, Trends in biochemical sciences.

[49]  Huilin Li,et al.  Revealing Ligand Binding Sites and Quantifying Subunit Variants of Noncovalent Protein Complexes in a Single Native Top-Down FTICR MS Experiment , 2014, Journal of The American Society for Mass Spectrometry.

[50]  C. D. Boone,et al.  Allostery revealed within lipid binding events to membrane proteins , 2018, Proceedings of the National Academy of Sciences.

[51]  Gérald Larrouy-Maumus,et al.  Hybrid Mass Spectrometry Approaches to Determine How L-Histidine Feedback Regulates the Enzyzme MtATP-Phosphoribosyltransferase , 2017, Structure.

[52]  Liangliang Sun,et al.  Native Proteomics in Discovery Mode Using Size-Exclusion Chromatography-Capillary Zone Electrophoresis-Tandem Mass Spectrometry. , 2018, Analytical chemistry.

[53]  C. Ihling,et al.  An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor. , 2017, Angewandte Chemie.

[54]  C. Robinson,et al.  Membrane proteins bind lipids selectively to modulate their structure and function , 2014, Nature.

[55]  S. Young,et al.  Mass spectrometry captures off-target drug binding and provides mechanistic insights into the human metalloprotease ZMPSTE24 , 2016, Nature chemistry.

[56]  Carol V Robinson,et al.  The role of the detergent micelle in preserving the structure of membrane proteins in the gas phase. , 2015, Angewandte Chemie.

[57]  A. Heck,et al.  Dissecting ribosomal particles throughout the kingdoms of life using advanced hybrid mass spectrometry methods , 2018, Nature Communications.

[58]  Albert J. R. Heck,et al.  Native Mass Spectrometry: What is in the Name? , 2016, Journal of The American Society for Mass Spectrometry.

[59]  J. Brodbelt,et al.  Characterization of native protein complexes using ultraviolet photodissociation mass spectrometry. , 2014, Journal of the American Chemical Society.

[60]  G. Anand,et al.  HDX‐MS reveals orthosteric and allosteric changes in apolipoprotein‐D structural dynamics upon binding of progesterone , 2018, Protein science : a publication of the Protein Society.

[61]  Carol V. Robinson,et al.  Mass Spectrometry of Intact V-Type ATPases Reveals Bound Lipids and the Effects of Nucleotide Binding , 2011, Science.

[62]  K. Pagel,et al.  Oligomerisation of Synaptobrevin-2 Studied by Native Mass Spectrometry and Chemical Cross-Linking , 2018, Journal of The American Society for Mass Spectrometry.

[63]  Frank Sobott,et al.  Top‐down mass spectrometry of intact membrane protein complexes reveals oligomeric state and sequence information in a single experiment , 2015, Protein science : a publication of the Protein Society.

[64]  John R. Engen,et al.  Applications of Hydrogen/Deuterium Exchange MS from 2012 to 2014 , 2014, Analytical chemistry.

[65]  Structural Lipids Enable the Formation of Functional Oligomers of the Eukaryotic Purine Symporter UapA , 2018, Cell chemical biology.

[66]  Walter Fast,et al.  Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. , 2016, Journal of the American Chemical Society.

[67]  C. Robinson,et al.  Interfacing Membrane Mimetics with Mass Spectrometry. , 2016, Accounts of chemical research.

[68]  Albert J R Heck,et al.  High-sensitivity Orbitrap mass analysis of intact macromolecular assemblies , 2012, Nature Methods.

[69]  A. Heck Native mass spectrometry: a bridge between interactomics and structural biology , 2008, Nature Methods.

[70]  R. Tampé,et al.  A subset of annular lipids is linked to the flippase activity of an ABC transporter. , 2015, Nature chemistry.

[71]  Z. Yao,et al.  Protein dynamics revealed by hydrogen/deuterium exchange mass spectrometry: Correlation between experiments and simulation. , 2019, Rapid communications in mass spectrometry : RCM.

[72]  Albert J R Heck,et al.  Expanding the structural analysis capabilities on an Orbitrap-based mass spectrometer for large macromolecular complexes. , 2017, The Analyst.

[73]  J. Brodbelt,et al.  Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. , 2018, Analytical chemistry.

[74]  Andreas Plückthun,et al.  PIP2 stabilises active states of GPCRs and enhances the selectivity of G-protein coupling , 2018, Nature.

[75]  A. Konijnenberg,et al.  Native ion mobility-mass spectrometry and related methods in structural biology. , 2013, Biochimica et biophysica acta.

[76]  G. R. Malmirchegini,et al.  Native Top-down Mass Spectrometry for the Structural Characterization of Human Hemoglobin , 2015, European journal of mass spectrometry.

[77]  C. Robinson,et al.  New vehicles allow detergent-free mass spectrometry of membrane protein complexes , 2013, Nature Methods.

[78]  J. Burke,et al.  An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery , 2017, Expert opinion on drug discovery.

[79]  T. Burzykowski,et al.  Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry. , 2017, Mass spectrometry reviews.

[80]  C. Robinson,et al.  Direct observation of the influence of cardiolipin and antibiotics on lipid II binding to MurJ. , 2018, Nature chemistry.

[81]  N. Kelleher,et al.  Native GELFrEE: a new separation technique for biomolecular assemblies. , 2015, Analytical chemistry.

[82]  S. Cianférani,et al.  Insights from native mass spectrometry approaches for top- and middle- level characterization of site-specific antibody-drug conjugates , 2017, mAbs.

[83]  Erik Marklund,et al.  Fundamentals of ion mobility spectrometry. , 2017, Current opinion in chemical biology.

[84]  L. Martens,et al.  Cross-linked peptide identification: A computational forest of algorithms. , 2018, Mass spectrometry reviews.

[85]  P. Eyers,et al.  Understanding protein-drug interactions using ion mobility-mass spectrometry. , 2018, Current opinion in chemical biology.

[86]  Michal Sharon,et al.  The application of ion-mobility mass spectrometry for structure/function investigation of protein complexes. , 2018, Current opinion in chemical biology.

[87]  G. Bitan,et al.  Native Top-Down Mass Spectrometry and Ion Mobility Spectrometry of the Interaction of Tau Protein with a Molecular Tweezer Assembly Modulator , 2018, Journal of The American Society for Mass Spectrometry.

[88]  O. Dym,et al.  Triple-Stage Mass Spectrometry Unravels the Heterogeneity of an Endogenous Protein Complex. , 2017, Analytical chemistry.

[89]  Weston B Struwe,et al.  High-resolution mass spectrometry of small molecules bound to membrane proteins , 2016, Nature Methods.

[90]  Huilin Li,et al.  Native top-down electrospray ionization-mass spectrometry of 158 kDa protein complex by high-resolution Fourier transform ion cyclotron resonance mass spectrometry. , 2014, Analytical chemistry.

[91]  Iain D G Campuzano,et al.  An Integrated Native Mass Spectrometry and Top-Down Proteomics Method that Connects Sequence to Structure and Function of Macromolecular Complexes , 2017, Nature chemistry.