1
|
Harvey SR, Gadkari VV, Ruotolo BT, Russell DH, Wysocki VH, Zhou M. Expanding Native Mass Spectrometry to the Masses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:646-652. [PMID: 38303101 DOI: 10.1021/jasms.3c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
At the 33rd ASMS Sanibel Meeting, on Membrane Proteins and Their Complexes, a morning roundtable discussion was held discussing the current challenges facing the field of native mass spectrometry and approaches to expanding the field to nonexperts. This Commentary summarizes the discussion and current initiatives to address these challenges.
Collapse
Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77844, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, Ohio, 43210, United States
| | - Mowei Zhou
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310058, China
| |
Collapse
|
2
|
Zhu Y, Yun SD, Zhang T, Chang JY, Stover L, Laganowsky A. Native mass spectrometry of proteoliposomes containing integral and peripheral membrane proteins. Chem Sci 2023; 14:14243-14255. [PMID: 38098719 PMCID: PMC10718073 DOI: 10.1039/d3sc04938h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/18/2023] [Indexed: 12/17/2023] Open
Abstract
Cellular membranes are critical to the function of membrane proteins, whether they are associated (peripheral) or embedded (integral) within the bilayer. While detergents have contributed to our understanding of membrane protein structure and function, there remains challenges in characterizing protein-lipid interactions within the context of an intact membrane. Here, we developed a method to prepare proteoliposomes for native mass spectrometry (MS) studies. We first use native MS to detect the encapsulation of soluble proteins within liposomes. We then find the peripheral Gβ1γ2 complex associated with the membrane can be ejected and analyzed using native MS. Four different integral membrane proteins (AmtB, AqpZ, TRAAK, and TREK2), all of which have previously been characterized in detergent, eject from the proteoliposomes as intact complexes bound to lipids that have been shown to tightly associate in detergent, drawing a correlation between the two approaches. We also show the utility of more complex lipid environments, such as a brain polar lipid extract, and show TRAAK ejects from liposomes of this extract bound to lipids. These findings underscore the capability to eject protein complexes from membranes bound to both lipids and metal ions, and this approach will be instrumental in the identification of key protein-lipid interactions.
Collapse
Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Sangho D Yun
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Tianqi Zhang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Lauren Stover
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University College Station TX 77843 USA
| |
Collapse
|
3
|
Le J, Loo JA. Detection of Lipid-Bound Bacteriorhodopsin Trimer Complex Directly from Purple Membrane by Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2620-2624. [PMID: 37975648 PMCID: PMC10947533 DOI: 10.1021/jasms.3c00314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Native mass spectrometry (MS) was used to detect the membrane protein, bacteriorhodopsin (bR), in its 27 kDa monomeric form and trimeric assemblies directly from lipid-containing purple membranes (PMs) from the halophilic archaeon, Halobacterium salinarum. Trimer bR ion populations bound to lipid molecules were detected with n-octyl β-d-glucopyranoside as the solubilizing detergent; the use of octyl tetraethylene glycol monooctyl ether or n-dodecyl-β-d-maltopyranoside resulted in only detection of monomeric bR. The archaeal lipids phosphotidylglycerolphosphate methyl ester and 3-HSO3-Galp-β1,6-Manp-α1,2-Glcp-α1,1-sn-2,3-diphytanylglycerol were the only lipids in the PMs found to bind to bR, consistent with previous high-resolution structural studies. Removal of the lipids from the sample resulted in the detection of only the bR monomer, highlighting the importance of specific lipids for stabilizing the bR trimer. To the best of our knowledge, this is the first report of the detection of the bR trimer with resolved lipid-bound species by MS.
Collapse
Affiliation(s)
- Jessie Le
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, University of California-Los Angeles, Los Angeles, CA 90095 USA
- Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, 90095 USA
| |
Collapse
|
4
|
Campuzano IDG. A Research Journey: Over a Decade of Denaturing and Native-MS Analyses of Hydrophobic and Membrane Proteins in Amgen Therapeutic Discovery. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2413-2431. [PMID: 37643331 DOI: 10.1021/jasms.3c00175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane proteins and associated complexes currently comprise the majority of therapeutic targets and remain among the most challenging classes of proteins for analytical characterization. Through long-term strategic collaborations forged between industrial and academic research groups, there has been tremendous progress in advancing membrane protein mass spectrometry (MS) analytical methods and their concomitant application to Amgen therapeutic project progression. Herein, I will describe a detailed and personal account of how electrospray ionization (ESI) native mass spectrometry (nMS), ion mobility-MS (IM-MS), reversed phase liquid chromatographic mass spectrometry (RPLC-MS), high-throughput solid phase extraction mass spectrometry, and matrix-assisted laser desorption ionization mass spectrometry methods were developed, optimized, and validated within Amgen Research, and importantly, how these analytical methods were applied for membrane and hydrophobic protein analyses and ultimately therapeutic project support and progression. Additionally, I will discuss all the highly important and productive collaborative efforts, both internal Amgen and external academic, which were key in generating the samples, methods, and associated data described herein. I will also describe some early and previously unpublished nano-ESI (nESI) native-MS data from Amgen Research and the highly productive University of California Los Angeles (UCLA) collaboration. I will also present previously unpublished examples of real-life Amgen biotherapeutic membrane protein projects that were supported by all the MS (and IM) analytical techniques described herein. I will start by describing the initial nESI nMS experiments performed at Amgen in 2011 on empty nanodisc molecules, using a quadrupole time-of-flight MS, and how these experiments progressed on to the 15 Tesla Fourier transform ion cyclotron resonance MS at UCLA. Then described are monomeric and multimeric membrane protein data acquired in both nESI nMS and tandem-MS modes, using multiple methods of ion activation, resulting in dramatic spectral simplification. Also described is how we investigated the far less established and less published subject, that is denaturing RPLC-MS analysis of membrane proteins, and how we developed a highly robust and reproducible RPLC-MS method capable of effective separation of membrane proteins differing in only the presence or absence of an N-terminal post translational modification. Also described is the evolution of the aforementioned RPLC-MS method into a high-throughput solid phase extraction MS method. Finally, I will give my opinion on key developments and how the area of nMS of membrane proteins needs to evolve to a state where it can be applied within the biopharmaceutical research environment for routine therapeutic project support.
Collapse
Affiliation(s)
- Iain D G Campuzano
- Amgen Research, Center for Research Acceleration by Digital Innovation, Molecular Analytics, Thousand Oaks, California 91320, United States
| |
Collapse
|
5
|
Panda A, Brown C, Gupta K. Studying Membrane Protein-Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1917-1927. [PMID: 37432128 PMCID: PMC10932607 DOI: 10.1021/jasms.3c00110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Native mass spectrometry (nMS) has emerged as a key analytical tool to study the organizational states of proteins and their complexes with both endogenous and exogenous ligands. Specifically, for membrane proteins, it provides a key analytical dimension to determine the identity of bound lipids and to decipher their effects on the observed structural assembly. We recently developed an approach to study membrane proteins directly from intact and tunable lipid membranes where both the biophysical properties of the membrane and its lipid compositions can be customized. Extending this, we use our liposome-nMS platform to decipher the lipid specificity of membrane proteins through their multiorganelle trafficking pathways. To demonstrate this, we used VAMP2 and reconstituted it in the endoplasmic reticulum (ER), Golgi, synaptic vesicle (SV), and plasma membrane (PM) mimicking liposomes. By directly studying VAMP2 from these customized liposomes, we show how the same transmembrane protein can bind to different sets of lipids in different organellar-mimicking membranes. Considering that the cellular trafficking pathway of most eukaryotic integral membrane proteins involves residence in multiple organellar membranes, this study highlights how the lipid-specificity of the same integral membrane protein may change depending on the membrane context. Further, leveraging the capability of the platform to study membrane proteins from liposomes with curated biophysical properties, we show how we can disentangle chemical versus biophysical properties, of individual lipids in regulating membrane protein assembly.
Collapse
Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, United States
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, United States
| |
Collapse
|
6
|
Panda A, Giska F, Duncan AL, Welch AJ, Brown C, McAllister R, Hariharan P, Goder JND, Coleman J, Ramakrishnan S, Pincet F, Guan L, Krishnakumar S, Rothman JE, Gupta K. Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nat Methods 2023; 20:891-897. [PMID: 37106230 PMCID: PMC10932606 DOI: 10.1038/s41592-023-01864-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 03/23/2023] [Indexed: 04/29/2023]
Abstract
Hierarchical organization of integral membrane proteins (IMP) and lipids at the membrane is essential for regulating myriad downstream signaling. A quantitative understanding of these processes requires both detections of oligomeric organization of IMPs and lipids directly from intact membranes and determination of key membrane components and properties that regulate them. Addressing this, we have developed a platform that enables native mass spectrometry (nMS) analysis of IMP-lipid complexes directly from intact and customizable lipid membranes. Both the lipid composition and membrane properties (such as curvature, tension, and fluidity) of these bilayers can be precisely customized to a target membrane. Subsequent direct nMS analysis of these intact proteolipid vesicles can yield the oligomeric states of the embedded IMPs, identify bound lipids, and determine the membrane properties that can regulate the observed IMP-lipid organization. Applying this method, we show how lipid binding regulates neurotransmitter release and how membrane composition regulates the functional oligomeric state of a transporter.
Collapse
Affiliation(s)
- Aniruddha Panda
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Fabian Giska
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford, UK
- Department of Chemistry, Aarhus University, Aarhus C, Denmark
| | | | - Caroline Brown
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Rachel McAllister
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Jean N D Goder
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeff Coleman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Sathish Ramakrishnan
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Frédéric Pincet
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Laboratoire de Physique de l'Ecole Normale Supérieure, ENS, CNRS, Université PSL, Sorbonne Université, Université Paris-Cité, Paris, France
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Shyam Krishnakumar
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Neurology, Yale University School of Medicine, New Haven, CT, USA
| | - James E Rothman
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Kallol Gupta
- Nanobiology Institute, Yale University, West Haven, CT, USA.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
| |
Collapse
|
7
|
Mass spectrometry of intact membrane proteins: shifting towards a more native-like context. Essays Biochem 2023; 67:201-213. [PMID: 36807530 PMCID: PMC10070488 DOI: 10.1042/ebc20220169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Integral membrane proteins are involved in a plethora of biological processes including cellular signalling, molecular transport, and catalysis. Many of these functions are mediated by non-covalent interactions with other proteins, substrates, metabolites, and surrounding lipids. Uncovering such interactions and deciphering their effect on protein activity is essential for understanding the regulatory mechanisms underlying integral membrane protein function. However, the detection of such dynamic complexes has proven to be challenging using traditional approaches in structural biology. Native mass spectrometry has emerged as a powerful technique for the structural characterisation of membrane proteins and their complexes, enabling the detection and identification of protein-binding partners. In this review, we discuss recent native mass spectrometry-based studies that have characterised non-covalent interactions of membrane proteins in the presence of detergents or membrane mimetics. We additionally highlight recent progress towards the study of membrane proteins within native membranes and provide our perspective on how these could be combined with recent developments in instrumentation to investigate increasingly complex biomolecular systems.
Collapse
|
8
|
Wang B, Tieleman DP. Release of nanodiscs from charged nano-droplets in the electrospray ionization revealed by molecular dynamics simulations. Commun Chem 2023; 6:21. [PMID: 36717705 PMCID: PMC9886951 DOI: 10.1038/s42004-023-00818-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
Electrospray ionization (ESI) is essential for application of mass spectrometry in biological systems, as it prevents the analyte being split into fragments. However, due to lack of a clear understanding of the mechanism of ESI, the interpretation of mass spectra is often ambiguous. This is a particular challenge for complex biological systems. Here, we focus on systems that include nanodiscs as membrane environment, which are essential for membrane proteins. We performed microsecond atomistic molecular dynamics simulations to study the release of nanodiscs from highly charged nano-droplets into the gas phase, the late stage of ESI. We observed two distinct major scenarios, highlighting the diversity of morphologies of gaseous product ions. Our simulations are in reasonable agreement with experimental results. Our work provides a detailed atomistic view of the ESI process of a heterogeneous system (lipid nanodisc), which may give insights into the interpretation of mass spectra of all lipid-protein systems.
Collapse
Affiliation(s)
- Beibei Wang
- grid.20513.350000 0004 1789 9964Centre for Advanced Materials Research, Beijing Normal University, Zhuhai, 519087 People’s Republic of China
| | - D. Peter Tieleman
- grid.22072.350000 0004 1936 7697Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, T2N 1N4 Canada
| |
Collapse
|
9
|
Gadkari VV, Juliano BR, Mallis CS, May JC, Kurulugama RT, Fjeldsted JC, McLean JA, Russell DH, Ruotolo BT. Performance evaluation of in-source ion activation hardware for collision-induced unfolding of proteins and protein complexes on a drift tube ion mobility-mass spectrometer. Analyst 2023; 148:391-401. [PMID: 36537590 PMCID: PMC10103148 DOI: 10.1039/d2an01452a] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) has emerged as an information-rich technique for gas phase protein structure characterization; however, IM resolution is currently insufficient for the detection of subtle structural differences in large biomolecules. This challenge has spurred the development of collision-induced unfolding (CIU) which utilizes incremental gas phase activation to unfold a protein in order to expand the number of measurable descriptors available for native protein ions. Although CIU is now routinely used in native mass spectrometry studies, the interlaboratory reproducibility of CIU has not been established. Here we evaluate the reproducibility of the CIU data produced across three laboratories (University of Michigan, Texas A&M University, and Vanderbilt University). CIU data were collected for a variety of protein ions ranging from 8.6-66 kDa. Within the same laboratory, the CIU fingerprints were found to be repeatable with root mean square deviation (RMSD) values of less than 5%. Collision cross section (CCS) values of the CIU intermediates were consistent across the laboratories, with most features exhibiting an interlaboratory reproducibility of better than 1%. In contrast, the activation potentials required to induce protein CIU transitions varied between the three laboratories. To address these differences, three source assemblies were constructed with an updated ion activation hardware design utilizing higher mechanical tolerance specifications. The production-grade assemblies were found to produce highly consistent CIU data for intact antibodies, exhibiting high precision ion CCS and CIU transition values, thus opening the door to establishing databases of CIU fingerprints to support future biomolecular classification efforts.
Collapse
Affiliation(s)
- Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | - Christopher S Mallis
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
| |
Collapse
|
10
|
Russell Lewis B, Lawrence R, Hammerschmid D, Reading E. Structural mass spectrometry approaches to understand multidrug efflux systems. Essays Biochem 2022; 67:255-267. [PMID: 36504255 PMCID: PMC10070475 DOI: 10.1042/ebc20220190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022]
Abstract
Multidrug efflux pumps are ubiquitous across both eukaryotes and prokaryotes, and have major implications in antimicrobial and multidrug resistance. They reside within cellular membranes and have proven difficult to study owing to their hydrophobic character and relationship with their compositionally complex lipid environment. Advances in structural mass spectrometry (MS) techniques have made it possible to study these systems to elucidate critical information on their structure-function relationships. For example, MS techniques can report on protein structural dynamics, stoichiometry, connectivity, solvent accessibility, and binding interactions with ligands, lipids, and other proteins. This information proving powerful when used in conjunction with complementary structural biology methods and molecular dynamics (MD) simulations. In the present review, aimed at those not experts in MS techniques, we report on the current uses of MS in studying multidrug efflux systems, practical considerations to consider, and the future direction of the field. In the first section, we highlight the importance of studying multidrug efflux proteins, and introduce a range of different MS techniques and explain what information they yield. In the second section, we review recent studies that have utilised MS techniques to study and characterise a range of different multidrug efflux systems.
Collapse
Affiliation(s)
- Benjamin Russell Lewis
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Ryan Lawrence
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Dietmar Hammerschmid
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Eamonn Reading
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| |
Collapse
|
11
|
Korn P, Schwieger C, Gruhle K, Garamus VM, Meister A, Ihling C, Drescher S. Azide- and diazirine-modified membrane lipids: Physicochemistry and applicability to study peptide/lipid interactions via cross-linking/mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184004. [PMID: 35841926 DOI: 10.1016/j.bbamem.2022.184004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Although the incorporation of photo-activatable lipids into membranes potentially opens new avenues for studying interactions with peptides and proteins, the question of whether azide- or diazirine-modified lipids are suitable for such studies remains controversial. We have recently shown that diazirine-modified lipids can indeed form cross-links to membrane peptides after UV activation and that these cross-links can be precisely determined in their position by mass spectrometry (MS). However, we also observed an unexpected backfolding of the lipid's diazirine-containing stearoyl chain to the membrane interface challenging the potential application of this modified lipid for future cross-linking (XL)-MS studies of protein/lipid interactions. In this work, we compared an azide- (AzidoPC) and a diazirine-modified (DiazPC) membrane lipid regarding their self-assembly properties, their mixing behavior with saturated bilayer-forming phospholipids, and their reactivity upon UV activation using differential scanning calorimetry (DSC), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and MS. Mixtures of both modified lipids with DMPC were further used for photo-chemically induced XL experiments with a transmembrane model peptide (KLAW23) to elucidate similarities and differences between the azide and the diazirine moiety. We showed that both photo-reactive lipids can be used to study lipid/peptide and lipid/protein interactions. The AzidoPC proved easier to handle, whereas the DiazPC had fewer degradation products and a higher cross-linking yield. However, the problem of backfolding occurs in both lipids; thus, it seems to be a general phenomenon.
Collapse
Affiliation(s)
- Patricia Korn
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Schwieger
- Institute of Chemistry, MLU Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany
| | - Vasil M Garamus
- Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502 Geesthacht, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg, Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Institute of Biochemistry and Biotechnology-Physical Biotechnology, Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Charles Tanford Protein Center, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120 Halle (Saale), Germany; Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120 Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120 Halle (Saale), Germany; Phospholipid Research Center, Im Neuenheimer Feld 515, 69120 Heidelberg, Germany.
| |
Collapse
|
12
|
Dafun AS, Marcoux J. Structural mass spectrometry of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140813. [PMID: 35750312 DOI: 10.1016/j.bbapap.2022.140813] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
The analysis of proteins and protein complexes by mass spectrometry (MS) has come a long way since the invention of electrospray ionization (ESI) in the mid 80s. Originally used to characterize small soluble polypeptide chains, MS has progressively evolved over the past 3 decades towards the analysis of samples of ever increasing heterogeneity and complexity, while the instruments have become more and more sensitive and resolutive. The proofs of concepts and first examples of most structural MS methods appeared in the early 90s. However, their application to membrane proteins, key targets in the biopharma industry, is more recent. Nowadays, a wealth of information can be gathered from such MS-based methods, on all aspects of membrane protein structure: sequencing (and more precisely proteoform characterization), but also stoichiometry, non-covalent ligand binding (metals, drug, lipids, carbohydrates), conformations, dynamics and distance restraints for modelling. In this review, we present the concept and some historical and more recent applications on membrane proteins, for the major structural MS methods.
Collapse
Affiliation(s)
- Angelique Sanchez Dafun
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| |
Collapse
|
13
|
Abstract
Native mass spectrometry (nMS) has emerged as an important tool in studying the structure and function of macromolecules and their complexes in the gas phase. In this review, we cover recent advances in nMS and related techniques including sample preparation, instrumentation, activation methods, and data analysis software. These advances have enabled nMS-based techniques to address a variety of challenging questions in structural biology. The second half of this review highlights recent applications of these technologies and surveys the classes of complexes that can be studied with nMS. Complementarity of nMS to existing structural biology techniques and current challenges in nMS are also addressed.
Collapse
Affiliation(s)
- Kelly R Karch
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Dalton T Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Sophie R Harvey
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA;
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
14
|
Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
Collapse
Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
| |
Collapse
|
15
|
Gavriilidou AFM, Sokratous K, Yen HY, De Colibus L. High-Throughput Native Mass Spectrometry Screening in Drug Discovery. Front Mol Biosci 2022; 9:837901. [PMID: 35495635 PMCID: PMC9047894 DOI: 10.3389/fmolb.2022.837901] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/15/2022] [Indexed: 12/15/2022] Open
Abstract
The design of new therapeutic molecules can be significantly informed by studying protein-ligand interactions using biophysical approaches directly after purification of the protein-ligand complex. Well-established techniques utilized in drug discovery include isothermal titration calorimetry, surface plasmon resonance, nuclear magnetic resonance spectroscopy, and structure-based drug discovery which mainly rely on protein crystallography and, more recently, cryo-electron microscopy. Protein-ligand complexes are dynamic, heterogeneous, and challenging systems that are best studied with several complementary techniques. Native mass spectrometry (MS) is a versatile method used to study proteins and their non-covalently driven assemblies in a native-like folded state, providing information on binding thermodynamics and stoichiometry as well as insights on ternary and quaternary protein structure. Here, we discuss the basic principles of native mass spectrometry, the field’s recent progress, how native MS is integrated into a drug discovery pipeline, and its future developments in drug discovery.
Collapse
|
16
|
Sun J, Li W, Gross ML. Advances in mass spectrometry-based footprinting of membrane proteins. Proteomics 2022; 22:e2100222. [PMID: 35290716 PMCID: PMC10493193 DOI: 10.1002/pmic.202100222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
Structural biology is entering an exciting time where many new high-resolution structures of large complexes and membrane proteins (MPs) are determined regularly. These advances have been driven by over 15 years of technological improvements, first in macromolecular crystallography, and recently in cryo-electron microscopy. Obtaining information about MP higher order structure and interactions is also a frontier, important but challenging owing to their unique properties and the need to choose suitable detergents/lipids for their study. The development of mass spectrometry (MS), both instruments and methodology in the past 10 years, has also advanced it as a complementary method to study MP structure and interactions. In this review, we discuss advances in MS-based footprinting for MPs and highlight recent methodologies that offer new promise for MP study by chemical footprinting and mass spectrometry.
Collapse
Affiliation(s)
- Jie Sun
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| |
Collapse
|
17
|
Harvey SR, O’Neale C, Schey KL, Wysocki VH. Native Mass Spectrometry and Surface Induced Dissociation Provide Insight into the Post-Translational Modifications of Tetrameric AQP0 Isolated from Bovine Eye Lens. Anal Chem 2022; 94:1515-1519. [PMID: 35015511 PMCID: PMC9161558 DOI: 10.1021/acs.analchem.1c04322] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Aquaporin-0 (AQP0) is a tetrameric membrane protein and the most abundant membrane protein in the eye lens. Interestingly, there is little to no cellular turnover once mature lens fiber cells are formed, and hence, age-related modifications accumulate with time. While bottom-up mass spectrometry-based approaches can provide identification of post-translational modifications, they cannot provide information on how these modifications coexist in a single chain or complex. Native mass spectrometry, however, enables the transfer of the intact complex into the gas-phase allowing modifications to be identified at the tetramer level. Here, we present the use of native mass spectrometry and surface-induced dissociation to study the post-translational modifications of AQP0 isolated and purified from bovine eye lens, existing as multiple forms due to the different modification states naturally present.
Collapse
Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Carla O’Neale
- Vanderbilt University Department of Biochemistry and Mass Spectrometry Research Center, Nashville, TN 37240
| | - Kevin L Schey
- Vanderbilt University Department of Biochemistry and Mass Spectrometry Research Center, Nashville, TN 37240
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,
| |
Collapse
|
18
|
Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition. Proc Natl Acad Sci U S A 2021; 118:2112651118. [PMID: 34911762 PMCID: PMC8713884 DOI: 10.1073/pnas.2112651118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2021] [Indexed: 11/30/2022] Open
Abstract
Molecular imaging at the single-molecule level of large and flexible proteins such as monoclonal IgG antibodies is possible by low-energy electron holography after chemically selective sample preparation by native electrospray ion beam deposition (ES-IBD) from native solution conditions. The single-molecule nature of the measurement allows the mapping of the structural variability of the molecules that originates from their intrinsic flexibility and from different adsorption geometries. Additionally, we can distinguish gas-phase–related conformations and conformations induced by the landing of the molecules on the surface. Our results underpin the relation between the gas-phase structure of protein ions created by native electrospray ionization (ESI) and the native protein structure and are of relevance for structural biology applications in the gas phase. Imaging of proteins at the single-molecule level can reveal conformational variability, which is essential for the understanding of biomolecules. To this end, a biologically relevant state of the sample must be retained during both sample preparation and imaging. Native electrospray ionization (ESI) can transfer even the largest protein complexes into the gas phase while preserving their stoichiometry and overall shape. High-resolution imaging of protein structures following native ESI is thus of fundamental interest for establishing the relation between gas phase and solution structure. Taking advantage of low-energy electron holography’s (LEEH) unique capability of imaging individual proteins with subnanometer resolution, we investigate the conformational flexibility of Herceptin, a monoclonal IgG antibody, deposited by native electrospray mass-selected ion beam deposition (ES-IBD) on graphene. Images reconstructed from holograms reveal a large variety of conformers. Some of these conformations can be mapped to the crystallographic structure of IgG, while others suggest that a compact, gas-phase–related conformation, adopted by the molecules during ES-IBD, is retained. We can steer the ratio of those two types of conformations by changing the landing energy of the protein on the single-layer graphene surface. Overall, we show that LEEH can elucidate the conformational heterogeneity of inherently flexible proteins, exemplified here by IgG antibodies, and thereby distinguish gas-phase collapse from rearrangement on surfaces.
Collapse
|
19
|
Sun J, Liu XR, Li S, He P, Li W, Gross ML. Nanoparticles and photochemistry for native-like transmembrane protein footprinting. Nat Commun 2021; 12:7270. [PMID: 34907205 PMCID: PMC8671412 DOI: 10.1038/s41467-021-27588-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
Mass spectrometry-based footprinting can probe higher order structure of soluble proteins in their native states and serve as a complement to high-resolution approaches. Traditional footprinting approaches, however, are hampered for integral membrane proteins because their transmembrane regions are not accessible to solvent, and they contain hydrophobic residues that are generally unreactive with most chemical reagents. To address this limitation, we bond photocatalytic titanium dioxide (TiO2) nanoparticles to a lipid bilayer. Upon laser irradiation, the nanoparticles produce local concentrations of radicals that penetrate the lipid layer, which is made permeable by a simultaneous laser-initiated Paternò-Büchi reaction. This approach achieves footprinting for integral membrane proteins in liposomes, helps locate both ligand-binding residues in a transporter and ligand-induced conformational changes, and reveals structural aspects of proteins at the flexible unbound state. Overall, this approach proves effective in intramembrane footprinting and forges a connection between material science and biology.
Collapse
Affiliation(s)
- Jie Sun
- grid.4367.60000 0001 2355 7002Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Box 1134, Saint Louis, MO 63130 USA
| | - Xiaoran Roger Liu
- grid.4367.60000 0001 2355 7002Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Box 1134, Saint Louis, MO 63130 USA
| | - Shuang Li
- grid.4367.60000 0001 2355 7002Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Box 8231, St. Louis, MO 63110 USA
| | - Peng He
- grid.4367.60000 0001 2355 7002Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Box 8231, St. Louis, MO 63110 USA
| | - Weikai Li
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave, Box 8231, St. Louis, MO, 63110, USA.
| | - Michael L. Gross
- grid.4367.60000 0001 2355 7002Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Box 1134, Saint Louis, MO 63130 USA
| |
Collapse
|
20
|
Dorner J, Korn P, Gruhle K, Ramsbeck D, Garamus VM, Lilie H, Meister A, Schwieger C, Ihling C, Sinz A, Drescher S. A Diazirine-Modified Membrane Lipid to Study Peptide/Lipid Interactions - Chances and Challenges. Chemistry 2021; 27:14586-14593. [PMID: 34406694 PMCID: PMC8597076 DOI: 10.1002/chem.202102048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Indexed: 01/19/2023]
Abstract
Although incorporation of photo‐activatable lipids into membranes potentially opens up novel avenues for investigating interactions with proteins, the question of whether diazirine‐modified lipids are suitable for such studies, remains under debate. Focusing on the potential for studying lipid/peptide interactions by cross‐linking mass spectrometry (XL‐MS), we developed a diazirine‐modified lipid (DiazPC), and examined its behaviour in membranes incorporating the model α‐helical peptide LAVA20. We observed an unexpected backfolding of the diazirine‐containing stearoyl chain of the lipid. This surprising behaviour challenges the potential application of DiazPC for future XL‐MS studies of peptide and protein/lipid interactions. The observations made for DiazPC most likely represent a general phenomenon for any type of membrane lipids with a polar moiety incorporated into the alkyl chain. Our finding is therefore of importance for future protein/lipid interaction studies relying on modified lipid probes.
Collapse
Affiliation(s)
- Julia Dorner
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Patricia Korn
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Kai Gruhle
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany
| | - Daniel Ramsbeck
- Fraunhofer Institute for Cell Therapy and Immunology IZI, Weinbergweg 22, 06120, Halle (Saale), Germany.,Institute of Pharmacy, University Leipzig, Brüderstr. 34, 04103, Leipzig, Germany
| | - Vasil M Garamus
- Helmholtz-Zentrum Hereon, Max-Planck-Str. 1, 21502, Geesthacht, Germany
| | - Hauke Lilie
- Institute for Biochemistry and Biotechnology-Technical Biochemistry, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Annette Meister
- Institute of Biochemistry and Biotechnology-Physical Biotechnology Charles Tanford Protein Center, MLU Halle-Wittenberg, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany.,Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Christian Schwieger
- Interdisciplinary Research Center HALOmem, MLU Halle-Wittenberg Charles Tanford Protein Center, Kurt-Mothes-Str. 3a, 06120, Halle (Saale), Germany
| | - Christian Ihling
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Andrea Sinz
- Institute of Pharmacy-Pharmaceutical Chemistry and Bioanalytics, Martin Luther University (MLU) Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany.,Center for Structural Mass Spectrometry, Kurt-Mothes-Str. 3, 06120, Halle (Saale), Germany
| | - Simon Drescher
- Institute of Pharmacy-Biophysical Pharmacy, MLU Halle-Wittenberg, Wolfgang-Langenbeck-Str. 4, 06120, Halle (Saale), Germany.,Phospholipid Research Center, Im Neuenheimer Feld 515, 69120, Heidelberg, Germany
| |
Collapse
|
21
|
Abstract
Native mass spectrometry (MS) is aimed at preserving and determining the native structure, composition, and stoichiometry of biomolecules and their complexes from solution after they are transferred into the gas phase. Major improvements in native MS instrumentation and experimental methods over the past few decades have led to a concomitant increase in the complexity and heterogeneity of samples that can be analyzed, including protein-ligand complexes, protein complexes with multiple coexisting stoichiometries, and membrane protein-lipid assemblies. Heterogeneous features of these biomolecular samples can be important for understanding structure and function. However, sample heterogeneity can make assignment of ion mass, charge, composition, and structure very challenging due to the overlap of tens or even hundreds of peaks in the mass spectrum. In this review, we cover data analysis, experimental, and instrumental advances and strategies aimed at solving this problem, with an in-depth discussion of theoretical and practical aspects of the use of available deconvolution algorithms and tools. We also reflect upon current challenges and provide a view of the future of this exciting field.
Collapse
Affiliation(s)
- Amber D Rolland
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States
| | - James S Prell
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403-1253, United States.,Materials Science Institute, University of Oregon, Eugene, Oregon 97403-1252, United States
| |
Collapse
|
22
|
Bennett JL, Nguyen GTH, Donald WA. Protein-Small Molecule Interactions in Native Mass Spectrometry. Chem Rev 2021; 122:7327-7385. [PMID: 34449207 DOI: 10.1021/acs.chemrev.1c00293] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Small molecule drug discovery has been propelled by the continual development of novel scientific methodologies to occasion therapeutic advances. Although established biophysical methods can be used to obtain information regarding the molecular mechanisms underlying drug action, these approaches are often inefficient, low throughput, and ineffective in the analysis of heterogeneous systems including dynamic oligomeric assemblies and proteins that have undergone extensive post-translational modification. Native mass spectrometry can be used to probe protein-small molecule interactions with unprecedented speed and sensitivity, providing unique insights into polydisperse biomolecular systems that are commonly encountered during the drug discovery process. In this review, we describe potential and proven applications of native MS in the study of interactions between small, drug-like molecules and proteins, including large multiprotein complexes and membrane proteins. Approaches to quantify the thermodynamic and kinetic properties of ligand binding are discussed, alongside a summary of gas-phase ion activation techniques that have been used to interrogate the structure of protein-small molecule complexes. We additionally highlight some of the key areas in modern drug design for which native mass spectrometry has elicited significant advances. Future developments and applications of native mass spectrometry in drug discovery workflows are identified, including potential pathways toward studying protein-small molecule interactions on a whole-proteome scale.
Collapse
Affiliation(s)
- Jack L Bennett
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Giang T H Nguyen
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| | - William A Donald
- School of Chemistry, University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
23
|
Abstract
![]()
Native mass spectrometry
(MS) involves the analysis and characterization
of macromolecules, predominantly intact proteins and protein complexes,
whereby as much as possible the native structural features of the
analytes are retained. As such, native MS enables the study of secondary,
tertiary, and even quaternary structure of proteins and other biomolecules.
Native MS represents a relatively recent addition to the analytical
toolbox of mass spectrometry and has over the past decade experienced
immense growth, especially in enhancing sensitivity and resolving
power but also in ease of use. With the advent of dedicated mass analyzers,
sample preparation and separation approaches, targeted fragmentation
techniques, and software solutions, the number of practitioners and
novel applications has risen in both academia and industry. This review
focuses on recent developments, particularly in high-resolution native
MS, describing applications in the structural analysis of protein
assemblies, proteoform profiling of—among others—biopharmaceuticals
and plasma proteins, and quantitative and qualitative analysis of
protein–ligand interactions, with the latter covering lipid,
drug, and carbohydrate molecules, to name a few.
Collapse
Affiliation(s)
- Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Maurits A den Boer
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
24
|
Frick M, Schwieger C, Schmidt C. Liposomes as Carriers of Membrane-Associated Proteins and Peptides for Mass Spectrometric Analysis. Angew Chem Int Ed Engl 2021; 60:11523-11530. [PMID: 33599387 PMCID: PMC8252038 DOI: 10.1002/anie.202101242] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Indexed: 12/11/2022]
Abstract
Membrane proteins are key players of the cell. Their structure and the interactions they form with their lipid environment are required to understand their function. Here we explore liposomes as membrane mimetics for mass spectrometric analysis of peripheral membrane proteins and peptides. Liposomes are advantageous over other membrane mimetics in that they are easy to prepare, can be varied in size and composition, and are suitable for functional assays. We demonstrate that they dissociate into lipid clusters in the gas phase of a mass spectrometer while intact protein and protein–lipid complexes are retained. We exemplify this approach by employing different liposomes including proteoliposomes of two model peptides/proteins differing in size. Our results pave the way for the general application of liposomes for mass spectrometric analysis of membrane‐associated proteins.
Collapse
Affiliation(s)
- Melissa Frick
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle, Germany
| | - Christian Schwieger
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle, Germany
| |
Collapse
|
25
|
Frick M, Schwieger C, Schmidt C. Liposomen als Überträger membranassoziierter Proteine und Peptide für die massenspektrometrische Analyse. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Melissa Frick
- Interdisziplinäre wissenschaftliche Einrichtung Charles-Tanford-Proteinzentrum Institut für Biochemie und Biotechnologie Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Straße 3a 06120 Halle Deutschland
| | - Christian Schwieger
- Interdisziplinäre wissenschaftliche Einrichtung Charles-Tanford-Proteinzentrum Institut für Biochemie und Biotechnologie Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Straße 3a 06120 Halle Deutschland
| | - Carla Schmidt
- Interdisziplinäre wissenschaftliche Einrichtung Charles-Tanford-Proteinzentrum Institut für Biochemie und Biotechnologie Martin-Luther-Universität Halle-Wittenberg Kurt-Mothes-Straße 3a 06120 Halle Deutschland
| |
Collapse
|
26
|
Oganesyan I, Lento C, Tandon A, Wilson DJ. Conformational Dynamics of α-Synuclein during the Interaction with Phospholipid Nanodiscs by Millisecond Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1169-1179. [PMID: 33784451 DOI: 10.1021/jasms.0c00463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Both normal and pathological functions of α-synuclein (αSN), an abundant protein in the central and peripheral nervous system, have been linked to its interaction with membrane lipid bilayers. The ability to characterize structural transitions of αSN upon membrane complexation will clarify molecular mechanisms associated with αSN-linked pathologies, including Parkinson's disease (PD), multiple systems atrophy, and other synucleinopathies. In this work, time-resolved electrospray ionization hydrogen/deuterium exchange mass spectrometry (TRESI-HDX-MS) was employed to acquire a detailed picture of αSN's conformational transitions as it undergoes complexation with nanodisc membrane mimics with different headgroup charges (zwitterionic DMPC and negative POPG). Using this approach, αSN interactions with DMPC nanodiscs were shown to be rapid exchanging and to have little impact on the αSN conformational ensemble. Interactions with nanodiscs containing lipids known to promote amyloidogenesis (e.g., POPG), on the other hand, were observed to induce substantial and specific changes in the αSN conformational ensemble. Ultimately, we identify a region corresponding residues 19-28 and 45-57 of the αSN sequence that is uniquely impacted by interactions with "amyloidogenic" lipid membranes, supporting the existing "broken-helix" model for α-synuclein/membrane interactions, but do not detect a "helical extension" that is also thought to play a role in αSN aggregation.
Collapse
Affiliation(s)
- Irina Oganesyan
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Cristina Lento
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
| | - Anurag Tandon
- Department of Medicine, University of Toronto, Toronto M5S 1A1, Canada
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto M3J 1P3, Canada
- Centre for Research in Mass Spectrometry, York University, Toronto M3J 1P3, Canada
| |
Collapse
|
27
|
Hoi KK, Bada Juarez JF, Judge PJ, Yen HY, Wu D, Vinals J, Taylor GF, Watts A, Robinson CV. Detergent-free Lipodisq Nanoparticles Facilitate High-Resolution Mass Spectrometry of Folded Integral Membrane Proteins. NANO LETTERS 2021; 21:2824-2831. [PMID: 33787280 PMCID: PMC8050825 DOI: 10.1021/acs.nanolett.0c04911] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/04/2021] [Indexed: 05/04/2023]
Abstract
Integral membrane proteins pose considerable challenges to mass spectrometry (MS) owing to the complexity and diversity of the components in their native environment. Here, we use native MS to study the post-translational maturation of bacteriorhodopsin (bR) and archaerhodopsin-3 (AR3), using both octyl-glucoside detergent micelles and lipid-based nanoparticles. A lower collision energy was required to obtain well-resolved spectra for proteins in styrene-maleic acid copolymer (SMA) Lipodisqs than in membrane scaffold protein (MSP) Nanodiscs. By comparing spectra of membrane proteins prepared using the different membrane mimetics, we found that SMA may favor selective solubilization of correctly folded proteins and better preserve native lipid interactions than other membrane mimetics. Our spectra reveal the correlation between the post-translation modifications (PTMs), lipid-interactions, and protein-folding states of bR, providing insights into the process of maturation of the photoreceptor proteins.
Collapse
Affiliation(s)
- Kin Kuan Hoi
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Juan Francisco Bada Juarez
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Peter J. Judge
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Hsin-Yung Yen
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
- OMass
Therapeutics, The Schrödinger
Building, Oxford Science Park, Oxford OX4
4GE, United Kingdom
| | - Di Wu
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Javier Vinals
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Garrick F. Taylor
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Anthony Watts
- Department
of Biochemistry, Biomembrane Structure Unit, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Carol V. Robinson
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| |
Collapse
|
28
|
Scratching the surface: native mass spectrometry of peripheral membrane protein complexes. Biochem Soc Trans 2021; 48:547-558. [PMID: 32129823 PMCID: PMC7192793 DOI: 10.1042/bst20190787] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/09/2020] [Accepted: 02/11/2020] [Indexed: 02/06/2023]
Abstract
A growing number of integral membrane proteins have been shown to tune their activity by selectively interacting with specific lipids. The ability to regulate biological functions via lipid interactions extends to the diverse group of proteins that associate only peripherally with the lipid bilayer. However, the structural basis of these interactions remains challenging to study due to their transient and promiscuous nature. Recently, native mass spectrometry has come into focus as a new tool to investigate lipid interactions in membrane proteins. Here, we outline how the native MS strategies developed for integral membrane proteins can be applied to generate insights into the structure and function of peripheral membrane proteins. Specifically, native MS studies of proteins in complex with detergent-solubilized lipids, bound to lipid nanodiscs, and released from native-like lipid vesicles all shed new light on the role of lipid interactions. The unique ability of native MS to capture and interrogate protein–protein, protein–ligand, and protein–lipid interactions opens exciting new avenues for the study of peripheral membrane protein biology.
Collapse
|
29
|
Hammerschmid D, van Dyck JF, Sobott F, Calabrese AN. Interrogating Membrane Protein Structure and Lipid Interactions by Native Mass Spectrometry. Methods Mol Biol 2021; 2168:233-261. [PMID: 33582995 DOI: 10.1007/978-1-0716-0724-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Native mass spectrometry and native ion mobility mass spectrometry are now established techniques in structural biology, with recent work developing these methods for the study of integral membrane proteins reconstituted in both lipid bilayer and detergent environments. Here we show how native mass spectrometry can be used to interrogate integral membrane proteins, providing insights into conformation, oligomerization, subunit composition/stoichiometry, and interactions with detergents/lipids/drugs. Furthermore, we discuss the sample requirements and experimental considerations unique to integral membrane protein native mass spectrometry research.
Collapse
Affiliation(s)
- Dietmar Hammerschmid
- Protein Chemistry, Proteomics and Epigenetic Signalling (PPES), Department of Biomedical Sciences, University of Antwerp, Wilrijk, Belgium.,Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Jeroen F van Dyck
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium
| | - Frank Sobott
- Biomolecular & Analytical Mass Spectrometry Group, Chemistry Department, University of Antwerp, Antwerp, Belgium.,Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Antonio N Calabrese
- Faculty of Biological Sciences, School of Molecular and Cellular Biology, University of Leeds, Leeds, UK. .,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
| |
Collapse
|
30
|
Lau AM, Politis A. Integrative Mass Spectrometry-Based Approaches for Modeling Macromolecular Assemblies. Methods Mol Biol 2021; 2247:221-241. [PMID: 33301120 DOI: 10.1007/978-1-0716-1126-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mass spectrometry (MS)-based strategies have emerged as key elements for structural modeling of proteins and their assemblies. In particular, merging together complementary MS tools, through the so-called hybrid approaches, has enabled structural characterization of proteins in their near-native states. Here, we describe how different MS techniques, such as native MS, chemical cross-linking MS, and ion mobility MS, are brought together using sophisticated computational algorithms and modeling restraints. We demonstrate the applicability of the strategy by building accurate models of multimeric protein assemblies. These strategies can practically be applied to any protein complex of interest and be readily integrated with other structural approaches such as electron density maps from cryo-electron microscopy.
Collapse
Affiliation(s)
- Andy M Lau
- Department of Chemistry, King's College London, London, UK
| | | |
Collapse
|
31
|
Harvey SR, VanAernum ZL, Kostelic MM, Marty MT, Wysocki VH. Probing the structure of nanodiscs using surface-induced dissociation mass spectrometry. Chem Commun (Camb) 2020; 56:15651-15654. [PMID: 33355562 PMCID: PMC7943047 DOI: 10.1039/d0cc05531j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
In the study of membrane proteins and antimicrobial peptides, nanodiscs have emerged as a valuable membrane mimetic to solubilze these molecules in a lipid bilayer. We present the structural characterization of nanodiscs using native mass spectrometry and surface-induced dissociation, which are powerful tools in structural biology.
Collapse
Affiliation(s)
- Sophie R Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA.
| | | | | | | | | |
Collapse
|
32
|
Marty MT. Nanodiscs and Mass Spectrometry: Making Membranes Fly. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2020; 458:116436. [PMID: 33100891 PMCID: PMC7584149 DOI: 10.1016/j.ijms.2020.116436] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Cells are surrounded by a protective lipid bilayer membrane, and membrane proteins in the bilayer control the flow of chemicals, information, and energy across this barrier. Many therapeutics target membrane proteins, and some directly target the lipid membrane itself. However, interactions within biological membranes are challenging to study due to their heterogeneity and insolubility. Mass spectrometry (MS) has become a powerful technique for studying membrane proteins, especially how membrane proteins interact with their surrounding lipid environment. Although detergent micelles are the most common membrane mimetic, nanodiscs are emerging as a promising platform for MS. Nanodiscs, nanoscale lipid bilayers encircled by two scaffold proteins, provide a controllable lipid bilayer for solubilizing membrane proteins. This Young Scientist Perspective focuses on native MS of intact nanodiscs and highlights the unique experiments enabled by making membranes fly, including studying membrane protein-lipid interactions and exploring the specificity of fragile transmembrane peptide complexes. It will also explore current challenges and future perspectives for interfacing nanodiscs with MS.
Collapse
Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, AZ 85721
| |
Collapse
|
33
|
Barth M, Schmidt C. Native mass spectrometry-A valuable tool in structural biology. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4578. [PMID: 32662584 DOI: 10.1002/jms.4578] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Accepted: 05/19/2020] [Indexed: 05/16/2023]
Abstract
Proteins and the complexes they form with their ligands are the players of cellular action. Their function is directly linked with their structure making the structural analysis of protein-ligand complexes essential. Classical techniques of structural biology include X-ray crystallography, nuclear magnetic resonance spectroscopy and recently distinguished cryo-electron microscopy. However, protein-ligand complexes are often dynamic and heterogeneous and consequently challenging for these techniques. Alternative approaches are therefore needed and gained importance during the last decades. One alternative is native mass spectrometry, which is the analysis of intact protein complexes in the gas phase. To achieve this, sample preparation and instrument conditions have to be optimised. Native mass spectrometry then reveals stoichiometry, protein interactions and topology of protein assemblies. Advanced techniques such as ion mobility and high-resolution mass spectrometry further add to the range of applications and deliver information on shape and microheterogeneity of the complexes. In this tutorial, we explain the basics of native mass spectrometry including sample requirements, instrument modifications and interpretation of native mass spectra. We further discuss the developments of native mass spectrometry and provide example spectra and applications.
Collapse
Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| |
Collapse
|
34
|
Lyu J, Liu Y, McCabe JW, Schrecke S, Fang L, Russell DH, Laganowsky A. Discovery of Potent Charge-Reducing Molecules for Native Ion Mobility Mass Spectrometry Studies. Anal Chem 2020; 92:11242-11249. [PMID: 32672445 DOI: 10.1021/acs.analchem.0c01826] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is growing interest in the characterization of protein complexes and their interactions with ligands using native ion mobility mass spectrometry. A particular challenge, especially for membrane proteins, is preserving noncovalent interactions and maintaining native-like structures. Different approaches have been developed to minimize activation of protein complexes by manipulating charge on protein complexes in solution and the gas-phase. Here, we report the utility of polyamines that have exceptionally high charge-reducing potencies with some molecules requiring 5-fold less than trimethylamine oxide to elicit the same effect. The charge-reducing molecules do not adduct to membrane protein complexes and are also compatible with ion-mobility mass spectrometry, paving the way for improved methods of charge reduction.
Collapse
Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| |
Collapse
|
35
|
Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
|
36
|
Chorev DS, Tang H, Rouse SL, Bolla JR, von Kügelgen A, Baker LA, Wu D, Gault J, Grünewald K, Bharat TAM, Matthews SJ, Robinson CV. The use of sonicated lipid vesicles for mass spectrometry of membrane protein complexes. Nat Protoc 2020; 15:1690-1706. [PMID: 32238951 PMCID: PMC7305028 DOI: 10.1038/s41596-020-0303-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/23/2020] [Indexed: 12/28/2022]
Abstract
Recent applications of mass spectrometry (MS) to study membrane protein complexes are yielding valuable insights into the binding of lipids and their structural and functional roles. To date, most native MS experiments with membrane proteins are based on detergent solubilization. Many insights into the structure and function of membrane proteins have been obtained using detergents; however, these can promote local lipid rearrangement and can cause fluctuations in the oligomeric state of protein complexes. To overcome these problems, we developed a method that does not use detergents or other chemicals. Here we report a detailed protocol that enables direct ejection of protein complexes from membranes for analysis by native MS. Briefly, lipid vesicles are prepared directly from membranes of different sources and subjected to sonication pulses. The resulting destabilized vesicles are concentrated, introduced into a mass spectrometer and ionized. The mass of the observed protein complexes is determined and this information, in conjunction with 'omics'-based strategies, is used to determine subunit stoichiometry as well as cofactor and lipid binding. Within this protocol, we expand the applications of the method to include peripheral membrane proteins of the S-layer and amyloid protein export machineries overexpressed in membranes from which the most abundant components have been removed. The described experimental procedure takes approximately 3 d from preparation to MS. The time required for data analysis depends on the complexity of the protein assemblies embedded in the membrane under investigation.
Collapse
Affiliation(s)
- Dror S Chorev
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Haiping Tang
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, London, UK
| | - Jani Reddy Bolla
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Microscopy Imaging Centre, Oxford, UK
| | - Lindsay A Baker
- Division of Structural Biology, University of Oxford, Oxford, UK
| | - Di Wu
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Joseph Gault
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Kay Grünewald
- Division of Structural Biology, University of Oxford, Oxford, UK
- Heinrich Pette Institute, Leibniz-Institut für Experimentelle Virologie, Centre for Structural Systems Biology, c/o DESY, Hamburg, Germany
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Microscopy Imaging Centre, Oxford, UK
| | | | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK.
| |
Collapse
|
37
|
Bender J, Schmidt C. Mass spectrometry of membrane protein complexes. Biol Chem 2020; 400:813-829. [PMID: 30956223 DOI: 10.1515/hsz-2018-0443] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022]
Abstract
Membrane proteins are key players in the cell. Due to their hydrophobic nature they require solubilising agents such as detergents or membrane mimetics during purification and, consequently, are challenging targets in structural biology. In addition, their natural lipid environment is crucial for their structure and function further hampering their analysis. Alternative approaches are therefore required when the analysis by conventional techniques proves difficult. In this review, we highlight the broad application of mass spectrometry (MS) for the characterisation of membrane proteins and their interactions with lipids. We show that MS unambiguously identifies the protein and lipid components of membrane protein complexes, unravels their three-dimensional arrangements and further provides clues of protein-lipid interactions.
Collapse
Affiliation(s)
- Julian Bender
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
| |
Collapse
|
38
|
Styrene maleic-acid lipid particles (SMALPs) into detergent or amphipols: An exchange protocol for membrane protein characterisation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183192. [PMID: 31945320 PMCID: PMC7086155 DOI: 10.1016/j.bbamem.2020.183192] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/06/2019] [Accepted: 01/10/2020] [Indexed: 12/24/2022]
Abstract
Membrane proteins are traditionally extracted and purified in detergent for biochemical and structural characterisation. This process is often costly and laborious, and the stripping away of potentially stabilising lipids from the membrane protein of interest can have detrimental effects on protein integrity. Recently, styrene-maleic acid (SMA) co-polymers have offered a solution to this problem by extracting membrane proteins directly from their native membrane, while retaining their naturally associated lipids in the form of stable SMA lipid particles (SMALPs). However, the inherent nature and heterogeneity of the polymer renders their use challenging for some downstream applications – particularly mass spectrometry (MS). While advances in cryo-electron microscopy (cryo-EM) have enhanced our understanding of membrane protein:lipid interactions in both SMALPs and detergent, the resolution obtained with this technique is often insufficient to accurately identify closely associated lipids within the transmembrane annulus. Native-MS has the power to fill this knowledge gap, but the SMA polymer itself remains largely incompatible with this technique. To increase sample homogeneity and allow characterisation of membrane protein:lipid complexes by native-MS, we have developed a novel SMA-exchange method; whereby the membrane protein of interest is first solubilised and purified in SMA, then transferred into amphipols or detergents. This allows the membrane protein and endogenously associated lipids extracted by SMA co-polymer to be identified and examined by MS, thereby complementing results obtained by cryo-EM and creating a better understanding of how the lipid bilayer directly affects membrane protein structure and function. First reported exchange protocol for transferring membrane proteins solubilised in SMALPs, into detergent or amphipols. Purification of protein:lipid complexes without detergent for mass spectrometry and subsequent lipid identification. Cost effective membrane protein purification requiring only minimal amounts of detergents in the exchange process.
Collapse
|
39
|
Sipe SN, Patrick JW, Laganowsky A, Brodbelt JS. Enhanced Characterization of Membrane Protein Complexes by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2019; 92:899-907. [PMID: 31765130 DOI: 10.1021/acs.analchem.9b03689] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Development of chemical chaperones to solubilize membrane protein complexes in aqueous solutions has allowed for gas-phase analysis of their native-like assemblies, including rapid evaluation of stability and interacting partners. Characterization of protein primary sequence, however, has thus far been limited. Ultraviolet photodissociation (UVPD) generates a multitude of sequence ions for the E. coli ammonia channel (AmtB), provides improved localization of a possible post-translational modification of aquaporin Z (AqpZ), and surpasses previous reports of sequence coverage for mechanosensitive channel of large conductance (MscL). Variations in UVPD sequence ion abundance have been shown to correspond to structural changes induced upon some perturbation. Preliminary results are reported here for elucidating increased rigidity or flexibility of MscL when bound to various phospholipids.
Collapse
Affiliation(s)
- Sarah N Sipe
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - John W Patrick
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - Arthur Laganowsky
- Department of Chemistry , Texas A&M University , College Station , Texas 77842 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| |
Collapse
|
40
|
Szymkowicz L, Lento C, Wilson DJ. Impact of Cardiolipin and Phosphatidylcholine Interactions on the Conformational Ensemble of Cytochrome c. Biochemistry 2019; 58:3617-3626. [DOI: 10.1021/acs.biochem.9b00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lisa Szymkowicz
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
- Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada M3J 1P3
| |
Collapse
|
41
|
Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1416-1425. [PMID: 30972726 PMCID: PMC6675625 DOI: 10.1007/s13361-019-02174-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/12/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
Collapse
Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
| |
Collapse
|
42
|
Kostelic MM, Ryan AM, Reid DJ, Noun JM, Marty MT. Expanding the Types of Lipids Amenable to Native Mass Spectrometry of Lipoprotein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1416-1425. [PMID: 30972726 DOI: 10.1007/s13361-13019-02174-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 05/26/2023]
Abstract
Native mass spectrometry (MS) has become an important tool for the analysis of membrane proteins. Although detergent micelles are the most commonly used method for solubilizing membrane proteins for native MS, nanoscale lipoprotein complexes such as nanodiscs are emerging as a promising complementary approach because they solubilize membrane proteins in a lipid bilayer environment. However, prior native MS studies of intact nanodiscs have employed only a limited set of phospholipids that are similar in mass. Here, we extend the range of lipids that are amenable to native MS of nanodiscs by combining lipids with masses that are simple integer multiples of each other. Although these lipid combinations create complex distributions, overlap between resonant peak series allows interpretation of nanodisc spectra containing glycolipids, sterols, and cardiolipin. We also investigate the gas-phase stability of nanodiscs with these new lipids towards collisional activation. We observe that negative ionization mode or charge reduction stabilizes nanodiscs and is essential to preserving labile lipids such as sterols. These new approaches to native MS of nanodiscs will enable future studies of membrane proteins embedded in model membranes that more accurately mimic natural bilayers. Graphical Abstract.
Collapse
Affiliation(s)
- Marius M Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Alex M Ryan
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Deseree J Reid
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Jibriel M Noun
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA
| | - Michael T Marty
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E University Blvd, Tucson, AZ, 85721, USA.
| |
Collapse
|
43
|
Schachner LF, Ives AN, McGee JP, Melani RD, Kafader JO, Compton PD, Patrie SM, Kelleher NL. Standard Proteoforms and Their Complexes for Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1190-1198. [PMID: 30963455 PMCID: PMC6592724 DOI: 10.1007/s13361-019-02191-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/04/2019] [Accepted: 03/11/2019] [Indexed: 05/09/2023]
Abstract
Native mass spectrometry (nMS) is a technique growing at the interface of analytical chemistry, structural biology, and proteomics that enables the detection and partial characterization of non-covalent protein assemblies. Currently, the standardization and dissemination of nMS is hampered by technical challenges associated with instrument operation, benchmarking, and optimization over time. Here, we provide a standard operating procedure for acquiring high-quality native mass spectra of 30-300 kDa proteins using an Orbitrap mass spectrometer. By describing reproducible sample preparation, loading, ionization, and nMS analysis, we forward two proteoforms and three complexes as possible standards to advance training and longitudinal assessment of instrument performance. Spectral data for five standards can guide assessment of instrument parameters, data production, and data analysis. By introducing this set of standards and protocols, we aim to help normalize native mass spectrometry practices across labs and provide benchmarks for reproducibility and high-quality data production in the years ahead. Graphical abstract.
Collapse
Affiliation(s)
- Luis F Schachner
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Ashley N Ives
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - John P McGee
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Rafael D Melani
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Jared O Kafader
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Philip D Compton
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Steven M Patrie
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- Departments of Chemistry and Molecular Biosciences, the Chemistry of Life Processes Institute, and the Proteomics Center of Excellence, Northwestern University, 2170 Tech Dr., Silverman Hall, Evanston, IL, 60208, USA.
| |
Collapse
|
44
|
Frick M, Schmidt C. Mass spectrometry—A versatile tool for characterising the lipid environment of membrane protein assemblies. Chem Phys Lipids 2019; 221:145-157. [DOI: 10.1016/j.chemphyslip.2019.04.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 01/02/2023]
|
45
|
Native top-down mass spectrometry provides insights into the copper centers of membrane-bound methane monooxygenase. Nat Commun 2019; 10:2675. [PMID: 31209220 PMCID: PMC6572826 DOI: 10.1038/s41467-019-10590-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/15/2019] [Indexed: 01/12/2023] Open
Abstract
Aerobic methane oxidation is catalyzed by particulate methane monooxygenase (pMMO), a copper-dependent, membrane metalloenzyme composed of subunits PmoA, PmoB, and PmoC. Characterization of the copper active site has been limited by challenges in spectroscopic analysis stemming from the presence of multiple copper binding sites, effects of detergent solubilization on activity and crystal structures, and the lack of a heterologous expression system. Here we utilize nanodiscs coupled with native top-down mass spectrometry (nTDMS) to determine the copper stoichiometry in each pMMO subunit and to detect post-translational modifications (PTMs). These results indicate the presence of a mononuclear copper center in both PmoB and PmoC. pMMO-nanodisc complexes with a higher stoichiometry of copper-bound PmoC exhibit increased activity, suggesting that the PmoC copper site plays a role in methane oxidation activity. These results provide key insights into the pMMO copper centers and demonstrate the ability of nTDMS to characterize complex membrane-bound metalloenzymes.
Collapse
|
46
|
Anderson NS, Barlowe C. Conserved juxtamembrane domains in the yeast golgin Coy1 drive assembly of a megadalton-sized complex and mediate binding to tethering and SNARE proteins. J Biol Chem 2019; 294:9690-9705. [PMID: 31073031 DOI: 10.1074/jbc.ra119.008107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
The architecture and organization of the Golgi complex depend on a family of coiled-coil proteins called golgins. Golgins are thought to form extended homodimers that are C-terminally anchored to Golgi membranes, whereas their N termini extend into the cytoplasm to initiate vesicle capture. Previously, we reported that the Saccharomyces cerevisiae golgin Coy1 contributes to intra-Golgi retrograde transport and binds to the conserved oligomeric Golgi (COG) complex and multiple retrograde Golgi Q-SNAREs (where SNARE is soluble NSF-attachment protein receptor). Here, using various engineered yeast strains, membrane protein extraction and fractionation methods, and in vitro binding assays, we mapped the Coy1 regions responsible for these activities. We also report that Coy1 assembles into a megadalton-size complex and that assembly of this complex depends on the most C-terminal coiled-coil and a conserved region between this coiled-coil and the transmembrane domain of Coy1. We found that this conserved region is necessary and sufficient for binding the SNARE protein Sed5 and the COG complex. Mutagenesis of conserved arginine residues within the C-terminal coiled-coil disrupted oligomerization, binding, and function of Coy1. Our findings indicate that the stable incorporation of Coy1 into a higher-order oligomer is required for its interactions and role in maintaining Golgi homeostasis. We propose that Coy1 assembles into a docking platform that directs COG-bound vesicles toward cognate SNAREs on the Golgi membrane.
Collapse
Affiliation(s)
- Nadine S Anderson
- From the Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - Charles Barlowe
- From the Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| |
Collapse
|
47
|
Österlund N, Luo J, Wärmländer SK, Gräslund A. Membrane-mimetic systems for biophysical studies of the amyloid-β peptide. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:492-501. [DOI: 10.1016/j.bbapap.2018.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/18/2018] [Accepted: 11/17/2018] [Indexed: 10/27/2022]
|
48
|
Native Nanodiscs and the Convergence of Lipidomics, Metabolomics, Interactomics and Proteomics. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9061230] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The omics disciplines remain largely distinct sciences due to the necessity of separating molecular classes for different assays. For example, water-soluble and lipid bilayer-bound proteins and metabolites are usually studied separately. Nonetheless, it is at the interface between these sciences where biology happens. That is, lipid-interacting proteins typically recognize and transduce signals and regulate the flow of metabolites in the cell. Technologies are emerging to converge the omics. It is now possible to separate intact membrane:protein assemblies (memteins) directly from intact cells or cell membranes. Such complexes mediate complete metabolon, receptor, channel, and transporter functions. The use of poly(styrene-co-maleic acid) (SMA) copolymers has allowed their separation in a single step without any exposure to synthetic detergents or artificial lipids. This is a critical development as these agents typically strip away biological lipids, signals, and metabolites from their physiologically-relevant positions on proteins. The resulting SMA lipid particles (SMALPs) represent native nanodiscs that are suitable for elucidation of structures and interactions that occur in vivo. Compatible tools for resolving the contained memteins include X-ray diffraction (XRD), cryo-electron microscopy (cryoEM), mass spectrometry (MS), and nuclear magnetic resonance (NMR) spectroscopy. Recent progress shows that memteins are more representative than naked membrane proteins devoid of natural lipid and is driving the development of next generation polymers.
Collapse
|
49
|
Bolla JR, Agasid MT, Mehmood S, Robinson CV. Membrane Protein-Lipid Interactions Probed Using Mass Spectrometry. Annu Rev Biochem 2019; 88:85-111. [PMID: 30901263 DOI: 10.1146/annurev-biochem-013118-111508] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Membrane proteins that exist in lipid bilayers are not isolated molecular entities. The lipid molecules that surround them play crucial roles in maintaining their full structural and functional integrity. Research directed at investigating these critical lipid-protein interactions is developing rapidly. Advancements in both instrumentation and software, as well as in key biophysical and biochemical techniques, are accelerating the field. In this review, we provide a brief outline of structural techniques used to probe protein-lipid interactions and focus on the molecular aspects of these interactions obtained from native mass spectrometry (native MS). We highlight examples in which lipids have been shown to modulate membrane protein structure and show how native MS has emerged as a complementary technique to X-ray crystallography and cryo-electron microscopy. We conclude with a short perspective on future developments that aim to better understand protein-lipid interactions in the native environment.
Collapse
Affiliation(s)
- Jani Reddy Bolla
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Mark T Agasid
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Shahid Mehmood
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom;
| |
Collapse
|
50
|
Cleary SP, Prell JS. Liberating Native Mass Spectrometry from Dependence on Volatile Salt Buffers by Use of Gábor Transform. Chemphyschem 2019; 20:519-523. [DOI: 10.1002/cphc.201900022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 11/07/2022]
Affiliation(s)
- Sean P. Cleary
- Department of Chemistry and Biochemistry 1253 University of Oregon Eugene OR 97403-1253 USA
| | - James S. Prell
- Department of Chemistry and Biochemistry 1253 University of Oregon Eugene OR 97403-1253 USA
- Materials Science Institute 1252 University of Oregon Eugene OR 97403-1252 USA
| |
Collapse
|