1
|
Du C, Cleary SP, Kostelic MM, Jones BJ, Kafader JO, Wysocki VH. Combining Surface-Induced Dissociation and Charge Detection Mass Spectrometry to Reveal the Native Topology of Heterogeneous Protein Complexes. Anal Chem 2023; 95:13889-13896. [PMID: 37672632 PMCID: PMC10874503 DOI: 10.1021/acs.analchem.3c02185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Charge detection mass spectrometry (CDMS) enables the direct mass measurement of heterogeneous samples on the megadalton scale, as the charge state for a single ion is determined simultaneously with the mass-to-charge ratio (m/z). Surface-induced dissociation (SID) is an effective activation method to dissociate non-intertwined, non-covalent protein complexes without extensive gas-phase restructuring, producing various subcomplexes reflective of the native protein topology. Here, we demonstrate that using CDMS after SID on an Orbitrap platform offers subunit connectivity, topology, proteoform information, and relative interfacial strengths of the intact macromolecular assemblies. SID dissects the capsids (∼3.7 MDa) of adeno-associated viruses (AAVs) into trimer-containing fragments (3mer, 6mer, 9mer, 15mer, etc.) that can be detected by the individual ion mass spectrometry (I2MS) approach on Orbitrap instruments. SID coupled to CDMS provides unique structural insights into heterogeneous assemblies that are not readily obtained by traditional MS measurements.
Collapse
Affiliation(s)
- Chen Du
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sean P Cleary
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Marius M Kostelic
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Benjamin J Jones
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jared O Kafader
- Departments of Chemistry, Molecular Biosciences, The Chemistry of Life Processes Institute, The Proteomics Center of Excellence at Northwestern University, Evanston, Illinois 60208, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Resource for Native MS Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
2
|
Zhu Y, Peng BJ, Kumar S, Stover L, Chang JY, Lyu J, Zhang T, Schrecke S, Azizov D, Russell DH, Fang L, Laganowsky A. Polyamine detergents tailored for native mass spectrometry studies of membrane proteins. Nat Commun 2023; 14:5676. [PMID: 37709761 PMCID: PMC10502129 DOI: 10.1038/s41467-023-41429-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/28/2023] [Indexed: 09/16/2023] Open
Abstract
Native mass spectrometry (MS) is a powerful technique for interrogating membrane protein complexes and their interactions with other molecules. A key aspect of the technique is the ability to preserve native-like structures and noncovalent interactions, which can be challenging depending on the choice of detergent. Different strategies have been employed to reduce charge on protein complexes to minimize activation and preserve non-covalent interactions. Here, we report the synthesis of a class of polyamine detergents tailored for native MS studies of membrane proteins. These detergents, a series of spermine covalently attached to various alkyl tails, are exceptional charge-reducing molecules, exhibiting a ten-fold enhanced potency over spermine. Addition of polyamine detergents to proteins solubilized in maltoside detergents results in improved, charge-reduced native mass spectra and reduced dissociation of subunits. Polyamine detergents open new opportunities to investigate membrane proteins in different detergent environments that have thwarted previous native MS studies.
Collapse
Affiliation(s)
- Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Bo-Ji Peng
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Smriti Kumar
- 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
| | - Jing-Yuan Chang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Jixing Lyu
- 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
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Djavdat Azizov
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Lei Fang
- 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
|
Harvey SR, VanAernum ZL, Wysocki VH. Surface-Induced Dissociation of Anionic vs Cationic Native-Like Protein Complexes. J Am Chem Soc 2021; 143:7698-7706. [PMID: 33983719 DOI: 10.1021/jacs.1c00855] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Characterizing protein-protein interactions, stoichiometries, and subunit connectivity is key to understanding how subunits assemble into biologically relevant, multisubunit protein complexes. Native mass spectrometry (nMS) has emerged as a powerful tool to study protein complexes due to its low sample consumption and tolerance for heterogeneity. In nMS, positive mode ionization is routinely used and charge reduction, through the addition of solution additives, is often used, as the resulting lower charge states are often considered more native-like. When fragmented by surface-induced dissociation (SID), charge reduced complexes often give increased structural information over their "normal-charged" counterparts. A disadvantage of solution phase charge reduction is that increased adduction, and hence peak broadening, is often observed. Previous studies have shown that protein complexes ionized using negative mode generally form lower charge states relative to positive mode. Here we demonstrate that the lower charged protein complex anions activated by surface collisions fragment in a manner consistent with their solved structures, hence providing substructural information. Negative mode ionization in ammonium acetate offers the advantage of charge reduction without the peak broadening associated with solution phase charge reduction additives and provides direct structural information when coupled with SID. SID of 20S human proteasome (a 28-mer comprised of four stacked heptamer rings in an αββα formation), for example, provides information on both substructure (e.g., splitting into a 7α ring and the corresponding ββα 21-mer, and into α dimers and trimers to provide connectivity around the 7 α ring) and proteoform information on monomers.
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, Ohio 43210, United States
| | - Zachary L VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
4
|
Donor MT, Shepherd SO, Prell JS. Rapid Determination of Activation Energies for Gas-Phase Protein Unfolding and Dissociation in a Q-IM-ToF Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:602-610. [PMID: 32126776 PMCID: PMC8063716 DOI: 10.1021/jasms.9b00055] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Ion mobility-mass spectrometry has emerged as a powerful tool for interrogating a wide variety of chemical systems. Collision-induced unfolding (CIU), typically performed in time-of-flight instruments, has been utilized to obtain valuable qualitative insight into protein structure and illuminate subtle differences between related species. CIU experiments can be performed relatively quickly, but unfolding energy information obtained from them has not yet been interpreted quantitatively. While several methods can determine quantitative dissociation energetics for small molecules, clusters, and peptides, these methods have rarely been applied to proteins, and never to study unfolding. Here, we present a method to rapidly determine activation energies for protein unfolding and dissociation, built on a model for energy deposition during collisional activation. The method is validated by comparing activation energies for dissociation of three complexes with those obtained using blackbody infrared radiative dissociation (BIRD); values from the two methods are in agreement. Several protein monomers were unfolded using CIU, including multiple charge states of both cations and anions, and activation energies determined. ΔH⧧ and ΔS⧧ values are found to be correlated, leading to ΔG⧧ values that lie within a narrow range (∼70-80 kJ/mol) and vary more with charge state than with protein identity. ΔG⧧ is anticorrelated with charge density, highlighting the key role of Coulombic repulsion in gas-phase unfolding. Measured ΔG⧧ values are similar to those computed for proton transfer within small peptides, suggesting that proton transfer is the rate-limiting step in gas-phase unfolding and providing evidence of a link between the Mobile Proton model and CIU.
Collapse
Affiliation(s)
- Micah T. Donor
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - Samantha O. Shepherd
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University of Oregon, Eugene OR 97403-1253
- Materials Science Institute, University of Oregon, 1252 University of Oregon, Eugene, OR 97403-1252
- Address reprint requests to James S. Prell, 1253 University of Oregon, Eugene, OR 97405, Tel: +1 (541) 346-2597,
| |
Collapse
|
5
|
McAlary L, Harrison JA, Aquilina JA, Fitzgerald SP, Kelso C, Benesch JL, Yerbury JJ. Trajectory Taken by Dimeric Cu/Zn Superoxide Dismutase through the Protein Unfolding and Dissociation Landscape Is Modulated by Salt Bridge Formation. Anal Chem 2019; 92:1702-1711. [DOI: 10.1021/acs.analchem.9b01699] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Luke McAlary
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Julian A. Harrison
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - J. Andrew Aquilina
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | | | - Celine Kelso
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Justin L.P. Benesch
- Department of Chemistry, Physical and Theoretical Chemistry Department, University of Oxford, Oxford OX1 3QZ, U.K
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, New South Wales 2522, Australia
- Molecular Horizons and School of Chemistry and Molecular Bioscience, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, New South Wales 2522, Australia
| |
Collapse
|
6
|
Leney AC. Subunit pI Can Influence Protein Complex Dissociation Characteristics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1389-1395. [PMID: 31077092 PMCID: PMC6669198 DOI: 10.1007/s13361-019-02198-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 05/05/2023]
Abstract
Mass spectrometry is frequently used to determine protein complex topology. By combining in-solution and gas-phase dissociation measurements, information can be indirectly inferred about the original composition of the protein complex. Although the mechanisms behind gas-phase complex dissociation are becoming more established, protein complex dissociation is not always predictable. Here, we looked into the effect of the protein subunits pI on complex dissociation. We chose two structurally similar, hexameric protein complexes that consist of a ring of alternating alpha and beta subunits. For one complex, allophycocyanin, the alpha and beta subunits are structurally similar, almost identical in mass, but have distinct pIs. In contrast, the other complex, phycoerythrin, is structural similar to allophycocyanin, yet the subunits have identical pIs. As predicted based on the structural arrangement, dissociation of phycoerythrin resulted in the observation of both the alpha and beta monomeric subunits in the mass spectrometer. However, for allophycocyanin, the results differed dramatically, with only the alpha monomeric subunit being detected upon gas-phase dissociation. Together, the results highlighted the importance of considering the isoelectric points of individual subunits within a protein complex when using tandem mass spectrometry data to elucidate protein complex topology.
Collapse
Affiliation(s)
- Aneika C Leney
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
7
|
Dyachenko A, Tamara S, Heck AJR. Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:7-15. [PMID: 29736602 PMCID: PMC6318259 DOI: 10.1007/s13361-018-1910-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. Graphical Abstract.
Collapse
Affiliation(s)
- Andrey Dyachenko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, 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, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| |
Collapse
|
8
|
Mistarz UH, Chandler SA, Brown JM, Benesch JLP, Rand KD. Probing the Dissociation of Protein Complexes by Means of Gas-Phase H/D Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:45-57. [PMID: 30460642 DOI: 10.1007/s13361-018-2064-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 05/16/2023]
Abstract
Gas-phase hydrogen/deuterium exchange measured by mass spectrometry (gas-phase HDX-MS) is a fast method to probe the conformation of protein ions. The use of gas-phase HDX-MS to investigate the structure and interactions of protein complexes is however mostly unharnessed. Ionizing proteins under conditions that maximize preservation of their native structure (native MS) enables the study of solution-like conformation for milliseconds after electrospray ionization (ESI), which enables the use of ND3-gas inside the mass spectrometer to rapidly deuterate heteroatom-bound non-amide hydrogens. Here, we explored the utility of gas-phase HDX-MS to examine protein-protein complexes and inform on their binding surface and the structural consequences of gas-phase dissociation. Protein complexes ranging from 24 kDa dimers to 395 kDa 24mers were analyzed by gas-phase HDX-MS with subsequent collision-induced dissociation (CID). The number of exchangeable sites involved in complex formation could, therefore, be estimated. For instance, dimers of cytochrome c or α-lactalbumin incorporated less deuterium/subunit than their unbound monomer counterparts, providing a measure of the number of heteroatom-bound side-chain hydrogens involved in complex formation. We furthermore studied if asymmetric charge-partitioning upon dissociation of protein complexes caused intermolecular H/D migration. In larger multimeric protein complexes, the dissociated monomer showed a significant increase in deuterium. This indicates that intermolecular H/D migration occurs as part of the asymmetric partitioning of charge during CID. We discuss several models that may explain this increase deuterium content and find that a model where only deuterium involved in migrating charge can account for most of the deuterium enrichment observed on the ejected monomer. In summary, the deuterium content of the ejected subunit can be used to estimate that of the intact complex with deviations observed for large complexes accounted for by charge migration. Graphical abstract ᅟ.
Collapse
Affiliation(s)
- Ulrik H Mistarz
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Shane A Chandler
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
| |
Collapse
|
9
|
Yefremova Y, Melder FTI, Danquah BD, Opuni KFM, Koy C, Ehrens A, Frommholz D, Illges H, Koelbel K, Sobott F, Glocker MO. Apparent activation energies of protein-protein complex dissociation in the gas-phase determined by electrospray mass spectrometry. Anal Bioanal Chem 2017; 409:6549-6558. [PMID: 28900708 DOI: 10.1007/s00216-017-0603-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 08/09/2017] [Accepted: 08/23/2017] [Indexed: 11/30/2022]
Abstract
We have developed a method to determine apparent activation energies of dissociation for ionized protein-protein complexes in the gas phase using electrospray ionization mass spectrometry following the Rice-Ramsperger-Kassel-Marcus quasi-equilibrium theory. Protein-protein complexes were formed in solution, transferred into the gas phase, and separated from excess free protein by ion mobility filtering. Afterwards, complex disassembly was initiated by collision-induced dissociation with step-wise increasing energies. Relative intensities of ion signals were used to calculate apparent activation energies of dissociation in the gas phase by applying linear free energy relations. The method was developed using streptavidin tetramers. Experimentally determined apparent gas-phase activation energies for dissociation ([Formula: see text]) of complexes consisting of Fc parts from immunoglobulins (IgG-Fc) and three closely related protein G' variants (IgG-Fc•protein G'e, IgG-Fc•protein G'f, and IgG-Fc•protein G'g) show the same order of stabilities as can be inferred from their in-solution binding constants. Differences in stabilities between the protein-protein complexes correspond to single amino acid residue exchanges in the IgG-binding regions of the protein G' variants. Graphical abstract Electrospray mass spectrometry and collision-induced dissociation delivers apparent activation energies and supramolecular bond force constants of protein-protein complexes in the gas phase.
Collapse
Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - F Teresa I Melder
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - Bright D Danquah
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - Kwabena F M Opuni
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany.,School of Pharmacy, University of Ghana, P.O. Box LG43, Legon Accra, Ghana
| | - Cornelia Koy
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany
| | - Alexandra Ehrens
- University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359, Rheinbach, Germany.,University Hospital of Bonn, Sigmung-Freud-Str. 25, 53105, Bonn, Germany
| | - David Frommholz
- University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359, Rheinbach, Germany
| | - Harald Illges
- University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359, Rheinbach, Germany
| | - Knut Koelbel
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium.,Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Michael O Glocker
- Proteome Center Rostock, University Rostock Medical Center, Schillingallee 69, 18059, Rostock, Germany.
| |
Collapse
|
10
|
Harvey SR, Liu Y, Liu W, Wysocki VH, Laganowsky A. Surface induced dissociation as a tool to study membrane protein complexes. Chem Commun (Camb) 2017; 53:3106-3109. [PMID: 28243658 PMCID: PMC5445643 DOI: 10.1039/c6cc09606a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Native ion mobility mass spectrometry (MS) and surface induced dissociation (SID) are applied to study the integral membrane protein complexes AmtB and AqpZ. Fragments produced from SID are consistent with the solved structures of these complexes. SID is, therefore, a promising tool for characterization of membrane protein complexes.
Collapse
Affiliation(s)
- Sophie R Harvey
- The Department of Chemistry and Biochemistry, The Ohio State University, 460 W 12th Avenue, Columbus, Ohio 43210, USA. and School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Yang Liu
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030, USA.
| | - Wen Liu
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030, USA.
| | - Vicki H Wysocki
- The Department of Chemistry and Biochemistry, The Ohio State University, 460 W 12th Avenue, Columbus, Ohio 43210, USA.
| | - Arthur Laganowsky
- Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas 77030, USA. and Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA
| |
Collapse
|
11
|
Tamara S, Dyachenko A, Fort KL, Makarov AA, Scheltema RA, Heck AJR. Symmetry of Charge Partitioning in Collisional and UV Photon-Induced Dissociation of Protein Assemblies. J Am Chem Soc 2016; 138:10860-8. [PMID: 27480281 PMCID: PMC6392339 DOI: 10.1021/jacs.6b05147] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Indexed: 01/08/2023]
Abstract
Tandem mass spectrometry can provide structural information on intact protein assemblies, generating mass fingerprints indicative of the stoichiometry and quaternary arrangement of the subunits. However, in such experiments, collision-induced dissociation yields restricted information due to simultaneous subunit unfolding, charge rearrangement, and subsequent ejection of a highly charged unfolded single subunit. Alternative fragmentation strategies can potentially overcome this and supply a deeper level of structural detail. Here, we implemented ultraviolet photodissociation (UVPD) on an Orbitrap mass spectrometer optimized for native MS and benchmark its performance to HCD fragmentation using various protein oligomers. We investigated dimeric β-lactoglobulin, dimeric superoxide dismutase, dimeric and tetrameric concanavalin A, and heptameric GroES and Gp31; ranging in molecular weight from 32 to 102 kDa. We find that, for the investigated systems, UVPD produces more symmetric charge partitioning than HCD. While HCD spectra show sporadic fragmentation over the full protein backbone sequence of the subunits with a bias toward fragmenting labile bonds, UVPD spectra provided higher sequence coverage. Taken together, we conclude that UVPD is a strong addition to the toolbox of fragmentation methods for top-down proteomics experiments, especially for native protein assemblies.
Collapse
Affiliation(s)
- Sem Tamara
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Andrey Dyachenko
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Kyle L. Fort
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Alexander A. Makarov
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
- Thermo
Fisher Scientific (Bremen), 28199 Bremen, Germany
| | - Richard A. Scheltema
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, and Netherlands
Proteomics Center, Utrecht University, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
12
|
Thachuk M, Fegan SK, Raheem N. Description and control of dissociation channels in gas-phase protein complexes. J Chem Phys 2016. [DOI: 10.1063/1.4960615] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark Thachuk
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Sarah K. Fegan
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Nigare Raheem
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| |
Collapse
|
13
|
Popa V, Trecroce DA, McAllister RG, Konermann L. Collision-Induced Dissociation of Electrosprayed Protein Complexes: An All-Atom Molecular Dynamics Model with Mobile Protons. J Phys Chem B 2016; 120:5114-24. [DOI: 10.1021/acs.jpcb.6b03035] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Vlad Popa
- Department
of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
| | - Danielle A. Trecroce
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Robert G. McAllister
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Lars Konermann
- Department
of Biochemistry, The University of Western Ontario, London, ON N6A 5C1, Canada
- Department
of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| |
Collapse
|
14
|
Pacholarz KJ, Barran PE. Distinguishing Loss of Structure from Subunit Dissociation for Protein Complexes with Variable Temperature Ion Mobility Mass Spectrometry. Anal Chem 2015; 87:6271-9. [DOI: 10.1021/acs.analchem.5b01063] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Kamila J. Pacholarz
- University of Edinburgh, School of Chemistry, West Mains Road, Edinburgh EH9 3JJ, United Kingdom
- University of Manchester, School of Chemistry, Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, 131
Princess Street, Manchester M1 7DN, United Kingdom
| | - Perdita E. Barran
- University of Manchester, School of Chemistry, Manchester
Institute of Biotechnology, Michael Barber Centre for Collaborative
Mass Spectrometry, 131
Princess Street, Manchester M1 7DN, United Kingdom
| |
Collapse
|
15
|
Fegan SK, Thachuk M. Controlling dissociation channels of gas-phase protein complexes using charge manipulation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:722-728. [PMID: 24526466 DOI: 10.1007/s13361-014-0831-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 12/20/2013] [Accepted: 01/18/2014] [Indexed: 06/03/2023]
Abstract
Coarse-grained simulations with charge hopping were performed for a positively charged tetrameric transthyretin (TTR) protein complex with a total charge of +20. Charges were allowed to move among basic amino acid sites as well as N-termini. Charge distributions and radii of gyration were calculated for complexes simulated at two temperatures, 300 and 600 K, under different scenarios. One scenario treated the complex in its normal state allowing charge to move to any basic site. Another scenario blocked protonation of all the N-termini except one. A final scenario used the complex in its normal state but added a basic-site containing tether (charge tag) near the N-terminus of one chain. The differences in monomer unfolding and charging were monitored in all three scenarios and compared. The simulation results show the importance of the N-terminus in leading the unfolding of the monomer units; a process that follows a zipper-like mechanism. Overall, experimentally modifying the complex by adding a tether or blocking the protonation of N-termini may give the potential for controlling the unraveling and subsequent dissociation of protein complexes.
Collapse
Affiliation(s)
- Sarah K Fegan
- Department of Chemistry, University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | | |
Collapse
|
16
|
Liu J, Konermann L. Cation-induced stabilization of protein complexes in the gas phase: mechanistic insights from hemoglobin dissociation studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:595-603. [PMID: 24452299 DOI: 10.1007/s13361-013-0814-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 12/13/2013] [Accepted: 12/14/2013] [Indexed: 06/03/2023]
Abstract
Collision-induced dissociation (CID) of electrosprayed protein complexes usually involves asymmetric charge partitioning, where a single unfolded chain gets ejected that carries a disproportionately large fraction of charge. Using hemoglobin (Hb) tetramers as model system, we confirm earlier reports that bound metal ions can stabilize protein complexes under CID conditions. We examine the mechanism underlying this effect. Nonvolatile salts cause extensive adduct formation. Significant stabilization was observed for Mg(2+) and Ca(2+), whereas K(+), Rb(+), and Cs(+) had no effect. Precursor ion selection was used to examine Hb subpopulations with well-defined metal binding levels. K(+), Rb(+), and Cs(+)-adducted tetramers eject monomers that carry roughly one-quarter of the metal ions that were bound to the precursor. This demonstrates that charge migration during CID is exclusively due to proton transfer, not metal ion transfer. Also, replacement of highly mobile charge carriers (protons) with less mobile species (metal ions) does not exert a stabilizing influence under the conditions used here. Interestingly, Hb carrying stabilizing ions (Mg(2+) and Ca(2+)) generates monomeric CID products that are metal depleted. This effect is attributed to a combination of two factors: (1) Me(2+) binding stabilizes Hb via formation of chelation bridges (e.g., R-COO(-) Me(2+) (-)OOC-R); the more Me(2+) a subunit contains the more stable it is. (2) More than ~90% of the tetramers contain at least one subunit with a below-average number of Me(2+). The prevalence of monomeric CID products with depleted Me(2+) levels is caused by the tendency of these low metal-containing subunits to undergo preferential unfolding/ejection.
Collapse
Affiliation(s)
- JiangJiang Liu
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | | |
Collapse
|
17
|
Zhang Y, Deng L, Kitova EN, Klassen JS. Dissociation of multisubunit protein-ligand complexes in the gas phase. Evidence for ligand migration. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1573-1583. [PMID: 23943432 DOI: 10.1007/s13361-013-0712-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Revised: 06/19/2013] [Accepted: 06/27/2013] [Indexed: 06/02/2023]
Abstract
The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp (GM1)) and corresponding glycosphingolipid (β-D-Galp-(1→3)-β-D-GalpNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Galp-(1→4)-β-D-Glcp-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S4) with biotin (B) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)(n+) ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)(n-) ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S4 + 4B)(n+/-) ions, as well as for deprotonated (S4 + 4Btl)(n-) ions, was loss of the ligand. However, subunit loss from the (S4 + 4B)(n+) ions was observed as a minor pathway. The (S4 + 4Btl)(n+) ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)(15+) ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.
Collapse
Affiliation(s)
- Yixuan Zhang
- Department of Chemistry and Alberta Glycomics Centre, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | | | | | | |
Collapse
|
18
|
Zhou M, Jones CM, Wysocki VH. Dissecting the Large Noncovalent Protein Complex GroEL with Surface-Induced Dissociation and Ion Mobility–Mass Spectrometry. Anal Chem 2013; 85:8262-7. [DOI: 10.1021/ac401497c] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mowei Zhou
- Department of Chemistry
and Biochemistry, Ohio State University, 484 W. 12th Ave., Columbus, Ohio 43210, United States
- Department of Chemistry
and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, United States
| | - Christopher M. Jones
- Department of Chemistry
and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, United States
| | - Vicki H. Wysocki
- Department of Chemistry
and Biochemistry, Ohio State University, 484 W. 12th Ave., Columbus, Ohio 43210, United States
- Department of Chemistry
and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, Arizona 85721, United States
| |
Collapse
|
19
|
Hall Z, Hernández H, Marsh J, Teichmann S, Robinson C. The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes. Structure 2013; 21:1325-37. [PMID: 23850452 PMCID: PMC3737473 DOI: 10.1016/j.str.2013.06.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 05/16/2013] [Accepted: 06/05/2013] [Indexed: 01/07/2023]
Abstract
Mass spectrometry can be used to characterize multiprotein complexes, defining their subunit stoichiometry and composition following solution disruption and collision-induced dissociation (CID). While CID of protein complexes in the gas phase typically results in the dissociation of unfolded subunits, a second atypical route is possible wherein compact subunits or subcomplexes are ejected without unfolding. Because tertiary structure and subunit interactions may be retained, this is the preferred route for structural investigations. How can we influence which pathway is adopted? By studying properties of a series of homomeric and heteromeric protein complexes and varying their overall charge in solution, we found that low subunit flexibility, higher charge densities, fewer salt bridges, and smaller interfaces are likely to be involved in promoting dissociation routes without unfolding. Manipulating the charge on a protein complex therefore enables us to direct dissociation through structurally informative pathways that mimic those followed in solution.
Collapse
Affiliation(s)
- Zoe Hall
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Helena Hernández
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Joseph A. Marsh
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sarah A. Teichmann
- EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Carol V. Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| |
Collapse
|
20
|
Fegan SK, Thachuk M. A Charge Moving Algorithm for Molecular Dynamics Simulations of Gas-Phase Proteins. J Chem Theory Comput 2013; 9:2531-9. [DOI: 10.1021/ct300906a] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah K. Fegan
- Department of Chemistry, University
of British Columbia,
2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Mark Thachuk
- Department of Chemistry, University
of British Columbia,
2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| |
Collapse
|
21
|
Kinetic Stability of the Streptavidin–Biotin Interaction Enhanced in the Gas Phase. J Am Chem Soc 2012; 134:16586-96. [DOI: 10.1021/ja305213z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
22
|
Zhou M, Huang C, Wysocki VH. Surface-induced dissociation of ion mobility-separated noncovalent complexes in a quadrupole/time-of-flight mass spectrometer. Anal Chem 2012; 84:6016-23. [PMID: 22747517 DOI: 10.1021/ac300810u] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A custom in-line surface-induced dissociation (SID) device has been incorporated into a commercial ion mobility quadrupole/time-of-flight mass spectrometer in order to provide an alternative and potentially more informative activation method than the commonly used collision-induced dissociation (CID). Complicated sample mixtures can be fractionated by ion mobility (IM) and then dissociated by CID or SID for further structural analysis. Interpretation of SID spectra for cesium iodide clusters was greatly simplified with IM prior to dissociation because products originating from different precursors and overlapping in m/z but separated in drift time can be examined individually. Multiple conformations of two protein complexes, source-activated transthyretin tetramer and nativelike serum amyloid P decamer, were separated in ion mobility and subjected to CID and SID. CID spectra of the mobility separated conformations are similar. However, drastic differences can be observed for SID spectra of different conformations, implying different structures in the gas phase. This work highlights the potential of utilizing IM-SID to study quaternary structures of protein complexes and provides information that is complementary to our recently reported SID-IM approach.
Collapse
Affiliation(s)
- Mowei Zhou
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0041, United States
| | | | | |
Collapse
|
23
|
Zhou M, Dagan S, Wysocki VH. Protein Subunits Released by Surface Collisions of Noncovalent Complexes: Nativelike Compact Structures Revealed by Ion Mobility Mass Spectrometry. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
24
|
Zhou M, Dagan S, Wysocki VH. Protein subunits released by surface collisions of noncovalent complexes: nativelike compact structures revealed by ion mobility mass spectrometry. Angew Chem Int Ed Engl 2012; 51:4336-9. [PMID: 22438323 DOI: 10.1002/anie.201108700] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 02/10/2012] [Indexed: 12/20/2022]
Affiliation(s)
- Mowei Zhou
- Department of Chemistry and Biochemistry, University of Arizona, 1306 E. University Blvd., Tucson, AZ, USA
| | | | | |
Collapse
|
25
|
Fegan SK, Thachuk M. Suitability of the MARTINI Force Field for Use with Gas-Phase Protein Complexes. J Chem Theory Comput 2012; 8:1304-13. [DOI: 10.1021/ct200739s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah K. Fegan
- Department of Chemistry, University of British Columbia, 2036
Main Mall, Vancouver,
BC, V6T 1Z1, Canada
| | - Mark Thachuk
- Department of Chemistry, University of British Columbia, 2036
Main Mall, Vancouver,
BC, V6T 1Z1, Canada
| |
Collapse
|
26
|
Sciuto SV, Liu J, Konermann L. An electrostatic charge partitioning model for the dissociation of protein complexes in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1679-1689. [PMID: 21952881 DOI: 10.1007/s13361-011-0205-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2011] [Revised: 06/27/2011] [Accepted: 06/28/2011] [Indexed: 05/31/2023]
Abstract
Electrosprayed multi-protein complexes can be dissociated by collisional activation in the gas phase. Typically, these processes follow a mechanism whereby a single subunit gets ejected with a disproportionately high amount of charge relative to its mass. This asymmetric behavior suggests that the departing subunit undergoes some degree of unfolding prior to being separated from the residual complex. These structural changes occur concomitantly with charge (proton) transfer towards the subunit that is being unraveled. Charge accumulation takes place up to the point where the subunit loses physical contact with the residual complex. This work develops a simple electrostatic model for studying the relationship between conformational changes and charge enrichment during collisional activation. Folded subunits are described as spheres that carry continuum surface charge. The unfolded chain is envisioned as random coil bead string. Simulations are guided by the principle that the system will adopt the charge configuration with the lowest potential energy for any backbone conformation. A finite-difference gradient algorithm is used to determine the charge on each subunit throughout the dissociation process. Both dimeric and tetrameric protein complexes are investigated. The model reproduces the occurrence of asymmetric charge partitioning for dissociation events that are preceded by subunit unfolding. Quantitative comparisons of experimental MS/MS data with model predictions yield estimates of the structural changes that occur during collisional activation. Our findings suggest that subunit separation can occur over a wide range of scission point structures that correspond to different degrees of unfolding.
Collapse
Affiliation(s)
- Stephen V Sciuto
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | | | | |
Collapse
|
27
|
Pukala TL. Mass Spectrometry for Structural Biology: Determining the Composition and Architecture of Protein Complexes. Aust J Chem 2011. [DOI: 10.1071/ch11025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Knowledge of protein structure and protein–protein interactions is vital for appreciating the elaborate biochemical pathways that underlie cellular function. While many techniques exist to probe the structure and complex interplay between functional proteins, none currently offer a complete picture. Mass spectrometry and associated methods provide complementary information to established structural biology tools, and with rapidly evolving technological advances, can in some cases even exceed other techniques by its diversity in application and information content. This is primarily because of the ability of mass spectrometry to precisely identify protein complex stoichiometry, detect individual species present in a mixture, and concomitantly offer conformational information. This review describes the attributes of mass spectrometry for the structural investigation of multiprotein assemblies in the context of recent developments and highlights in the field.
Collapse
|
28
|
Erba EB, Ruotolo BT, Barsky D, Robinson CV. Ion Mobility-Mass Spectrometry Reveals the Influence of Subunit Packing and Charge on the Dissociation of Multiprotein Complexes. Anal Chem 2010; 82:9702-10. [DOI: 10.1021/ac101778e] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elisabetta Boeri Erba
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Brandon T. Ruotolo
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Daniel Barsky
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Carol V. Robinson
- University Chemistry Department, University of Cambridge, Cambridge, United Kingdom, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, Lawrence Livermore National Laboratory, Livermore, California, and Department of Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
29
|
Wanasundara SN, Thachuk M. Toward an Improved Understanding of the Dissociation Mechanism of Gas Phase Protein Complexes. J Phys Chem B 2010; 114:11646-53. [DOI: 10.1021/jp103576b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Surajith N. Wanasundara
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Mark Thachuk
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| |
Collapse
|
30
|
Pagel K, Hyung SJ, Ruotolo BT, Robinson CV. Alternate Dissociation Pathways Identified in Charge-Reduced Protein Complex Ions. Anal Chem 2010; 82:5363-72. [DOI: 10.1021/ac101121r] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kevin Pagel
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Suk-Joon Hyung
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Brandon T. Ruotolo
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| | - Carol V. Robinson
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, U.K
| |
Collapse
|
31
|
Feketeová L, O'Hair RAJ. Electron-induced dissociation of doubly protonated betaine clusters: controlling fragmentation chemistry through electron energy. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3259-3263. [PMID: 19764074 DOI: 10.1002/rcm.4239] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The [M21+2H]2+ cluster of the zwitterion betaine, M = (CH3)3NCH2CO2, formed via electrospray ionisation (ESI), has been allowed to interact with electrons with energies ranging from >0 to 50 eV in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer. The types of gas-phase electron-induced dissociation (EID) reactions observed are dependent on the energy of the electrons. In the low-energy region up to 10 eV, electrons are mainly captured, forming the charge-reduced species, {[M21+2H]+*}*, in an excited state, which stabilises via the ejection of an H atom and one or more neutral betaines. In the higher energy region, above 12 eV, a Coulomb explosion of the multiply charged clusters is observed in highly asymmetric fission with singly charged fragments carrying away more than 70% of the parent mass. Neutral betaine evaporation is also observed in this energy region. In addition, a series of singly charged fragments appears which arise from C-X bond cleavage reactions, including decarboxylation and CH3 group transfer. These latter reactions may arise from access of electronic excited states of the precursor ions.
Collapse
Affiliation(s)
- Linda Feketeová
- School of Chemistry, University of Melbourne, Victoria 3010, Australia.
| | | |
Collapse
|
32
|
Konermann L. A simple model for the disintegration of highly charged solvent droplets during electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:496-506. [PMID: 19110444 DOI: 10.1016/j.jasms.2008.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Revised: 11/12/2008] [Accepted: 11/14/2008] [Indexed: 05/27/2023]
Abstract
This work uses a minimalist model for deciphering the opposing effects of Coulomb repulsion and surface tension on the stability of electrosprayed droplets. Guided by previous observations, it is assumed that progeny droplets are ejected from the tip of liquid filaments that are formed as protrusions of an initially spherical parent. Nonspherical shapes are approximated as assemblies of multiple closely spaced beads. This strategy greatly facilitates the calculation of electrostatic and surface energies. For a droplet at the Rayleigh limit the model predicts that growth of a very thin filament is a spontaneous process with a negligible activation barrier. In contrast, significant barriers are encountered for the formation of larger diameter filaments. These different barrier heights favor highly asymmetric droplet fission because the dimensions of the filament determine those of the ejected droplet(s). Substantial charge accumulation occurs at the filament termini. This allows each progeny droplet to carry a significant fraction of charge, despite its very small volume. In the absence of a long connecting filament, relieving electrostatic stress through progeny droplet emission would be ineffective. The model predicts the prevalence of fission events leading to the formation of several progeny droplets, instead of just a single one. Ejection bursts are followed by collapse back to a spherical shape. The resulting charge depleted system is incapable of producing additional progeny droplets until solvent evaporation returns it to the Rayleigh limit. Despite the very simple nature of the model used here, all of these predictions agree with experimental data.
Collapse
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada.
| |
Collapse
|
33
|
Benesch JLP. Collisional activation of protein complexes: picking up the pieces. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:341-8. [PMID: 19110440 DOI: 10.1016/j.jasms.2008.11.014] [Citation(s) in RCA: 132] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2008] [Revised: 11/19/2008] [Accepted: 11/19/2008] [Indexed: 05/12/2023]
Abstract
Mass spectrometry is fast becoming a vital approach not only for the identification and quantification of proteins, but also for the study of the noncovalent assemblies they form. Approaches for ionizing, transmitting, and detecting protein complexes intact in the mass spectrometer are now well established. The challenge has therefore shifted to developing and applying mass spectrometry approaches to elucidate the structure of such species. A crucial aspect to this goal is inducing their disassembly in the gas phase to mine information as to their composition and organization. Here the consequences of collisionally activating protein complexes are illustrated through ion mobility mass spectrometry measurements and discussed in the context of the current literature. Although a consensus view of the mechanism of dissociation is starting to emerge, it is also clear that a number of aspects remain unresolved. These outstanding questions and frontier challenges must be addressed if gas-phase dissociative approaches are to reach their full potential in the study of protein assemblies.
Collapse
Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
34
|
Wanasundara SN, Thachuk M. Free Energy Barrier Estimation for the Dissociation of Charged Protein Complexes in the Gas Phase. J Phys Chem A 2009; 113:3814-21. [DOI: 10.1021/jp8094227] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Surajith N. Wanasundara
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Mark Thachuk
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
| |
Collapse
|
35
|
Macdonald BI, Thachuk M. Gas-phase proton-transfer pathways in protonated histidylglycine. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2008; 22:2946-2954. [PMID: 18729239 DOI: 10.1002/rcm.3697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Pathways for proton transfer in the histidylglycine cation are examined in the gas-phase environment with the goal of understanding the mechanism by which protons may become mobile in proteins with basic amino acid residues. An extensive search of the potential energy surface is performed using density functional theory (DFT) methods. After corrections for zero-point energy are included, it is found that all the lowest energy barriers for proton transfer between the N-terminus and the imidazole ring have heights of only a few kcal/mol, while those between the imidazole ring and the backbone amide oxygen have heights of approximately 15 kcal/mol when the proton is moving from the ring to the backbone and only a few kcal/mol when moving from the backbone to the imidazole ring. In mass spectrometric techniques employing collision-induced dissociation to dissociate protein complex ions or to fragment peptides, these barriers can be overcome, and the protons mobilized.
Collapse
|
36
|
Wanasundara SN, Thachuk M. Theoretical investigations of the dissociation of charged protein complexes in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:2242-2253. [PMID: 17977010 DOI: 10.1016/j.jasms.2007.09.022] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 06/21/2007] [Accepted: 09/17/2007] [Indexed: 05/25/2023]
Abstract
A series of calculations, varying from simple electrostatic to more detailed semi-empirical based molecular dynamics ones, were carried out on charged gas phase ions of the cytochrome c(') dimer. The energetics of differing charge states, charge partitionings, and charge configurations were examined in both the low and high charge regimes. As well, preliminary free energy calculations of dissociation barriers are presented. It is shown that one must always consider distributions of charge configurations, once protein relaxation effects are taken into account, and that no single configuration dominates. All these results also indicate that in the high charge limit, the dissociation of protein complex ions is governed by electrostatic repulsion from the net charges, the consequences of which are enumerated and discussed. There are two main trends deriving from this, namely that charges will move so as to approximately maintain constant surface charge density, and that the lowest barrier to dissociation is the one that produces fragment ions with equal charges. In particular, it is shown that the charge-to-mass ratio of a fragment ion is not the key physical parameter in predicting dissociation products. In fact, from the perspective of the division of total charge, many dissociation pathways reported to be "asymmetric" in the literature should be more properly labelled as "symmetric" or "near-symmetric". The Coulomb repulsion model assumes that the timescale for charge transfer is faster than that for protein structural changes, which in turn is faster than that for complex dissociation.
Collapse
|
37
|
Benesch JLP, Ruotolo BT, Simmons DA, Robinson CV. Protein complexes in the gas phase: technology for structural genomics and proteomics. Chem Rev 2007; 107:3544-67. [PMID: 17649985 DOI: 10.1021/cr068289b] [Citation(s) in RCA: 344] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Justin L P Benesch
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | | | | | | |
Collapse
|
38
|
Perham M, Wittung-Stafshede P. Folding and assembly of co-chaperonin heptamer probed by forster resonance energy transfer. Arch Biochem Biophys 2007; 464:306-13. [PMID: 17521602 DOI: 10.1016/j.abb.2007.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2007] [Accepted: 04/17/2007] [Indexed: 10/23/2022]
Abstract
The ring-shaped heptameric co-chaperonin protein 10 (cpn10) is one of few oligomeric beta-sheet proteins that unfold and disassemble reversibly in vitro. Here, we labeled human mitochondrial cpn10 with donor and acceptor dyes to obtain FRET signals. Cpn10 mixed in a 1:1:5 ratio of donor:acceptor:unlabeled monomers form heptamers that are active in an in vitro functional assay. Monomer-monomer affinity, as well as thermal and chemical stability, of the labeled cpn10 is similar to the unlabeled protein, demonstrating that the labels do not perturb the system. Using changes in FRET, we then probed for the first time cpn10 heptamer-monomer assembly/disassembly kinetics. Heptamer dissociation is very slow (1/k(diss) approximately 3h; 20 degrees C, pH 7) corresponding to an activation energy of approximately 50kJ/mol. Ring-ring mixing experiments reveal that cpn10 heptamer dissociation is rate limiting; subsequent associations events are faster. Kinetic inertness explains how cpn10 cycles on and off cpn60 as an intact heptamer in vivo.
Collapse
Affiliation(s)
- Michael Perham
- Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77251, United States
| | | |
Collapse
|