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Cropley TC, Liu FC, Chai M, Bush MF, Bleiholder C. Metastability of Protein Solution Structures in the Absence of a Solvent: Rugged Energy Landscape and Glass-like Behavior. J Am Chem Soc 2024. [PMID: 38598661 DOI: 10.1021/jacs.3c12892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Native ion mobility/mass spectrometry is well-poised to structurally screen proteomes but characterizes protein structures in the absence of a solvent. This raises long-standing unanswered questions about the biological significance of protein structures identified through ion mobility/mass spectrometry. Using newly developed computational and experimental ion mobility/ion mobility/mass spectrometry methods, we investigate the unfolding of the protein ubiquitin in a solvent-free environment. Our data suggest that the folded, solvent-free ubiquitin observed by ion mobility/mass spectrometry exists in a largely native fold with an intact β-grasp motif and α-helix. The ensemble of folded, solvent-free ubiquitin ions can be partitioned into kinetically stable subpopulations that appear to correspond to the structural heterogeneity of ubiquitin in solution. Time-resolved ion mobility/ion mobility/mass spectrometry measurements show that folded, solvent-free ubiquitin exhibits a strongly stretched-exponential time dependence, which simulations trace to a rugged energy landscape with kinetic traps. Unfolding rate constants are estimated to be approximately 800 to 20,000 times smaller than in the presence of water, effectively quenching the unfolding process on the time scale of typical ion mobility/mass spectrometry measurements. Our proposed unfolding pathway of solvent-free ubiquitin shares substantial characteristics with that established for the presence of solvent, including a polarized transition state with significant native content in the N-terminal β-hairpin and α-helix. Our experimental and computational data suggest that (1) the energy landscape governing the motions of folded, solvent-free proteins is rugged in analogy to that of glassy systems; (2) large-scale protein motions may at least partially be determined by the amino acid sequence of a polypeptide chain; and (3) solvent facilitates, rather than controls, protein motions.
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Affiliation(s)
- Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
| | - Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
| | - Mengqi Chai
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32304, United States
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32304, United States
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2
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Liu FC, Cropley TC, Bleiholder C. Elucidating Structures of Protein Complexes by Collision-Induced Dissociation at Elevated Gas Pressures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2247-2258. [PMID: 37729591 PMCID: PMC11162217 DOI: 10.1021/jasms.3c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Ion activation methods carried out at gas pressures compatible with ion mobility separations are not yet widely established. This limits the analytical utility of emerging tandem-ion mobility spectrometers that conduct multiple ion mobility separations in series. The present work investigates the applicability of collision-induced dissociation (CID) at 1 to 3 mbar in a tandem-trapped ion mobility spectrometer (tandem-TIMS) to study the architecture of protein complexes. We show that CID of the homotetrameric protein complexes streptavidin (53 kDa), neutravidin (60 kDa), and concanavalin A (110 kDa) provides access to all subunits of the investigated protein complexes, including structurally informative dimers. We report on an "atypical" dissociation pathway, which for concanavalin A proceeds via symmetric partitioning of the precursor charges and produces dimers with the same charge states that were previously reported from surface induced dissociation. Our data suggest a correlation between the formation of subunits by CID in tandem-TIMS/MS, their binding strengths in the native tetramer structures, and the applied activation voltage. Ion mobility spectra of in situ-generated subunits reveal a marked structural heterogeneity inconsistent with annealing into their most stable gas phase structures. Structural transitions are observed for in situ-generated subunits that resemble the transitions reported from collision-induced unfolding of natively folded proteins. These observations indicate that some aspects of the native precursor structure is preserved in the subunits generated from disassembly of the precursor complex. We rationalize our observations by an approximately 100-fold shorter activation time scale in comparison to traditional CID in a collision cell. Finally, the approach discussed here to conduct CID at elevated pressures appears generally applicable also for other types of tandem-ion mobility spectrometers.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Tyler C. Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
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3
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Cropley TC, Liu FC, Pedrete T, Hossain MA, Agar JN, Bleiholder C. Structure Relaxation Approximation (SRA) for Elucidation of Protein Structures from Ion Mobility Measurements (II). Protein Complexes. J Phys Chem B 2023. [PMID: 37311097 DOI: 10.1021/acs.jpcb.3c01024] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Characterizing structures of protein complexes and their disease-related aberrations is essential to understanding molecular mechanisms of many biological processes. Electrospray ionization coupled with hybrid ion mobility/mass spectrometry (ESI-IM/MS) methods offer sufficient sensitivity, sample throughput, and dynamic range to enable systematic structural characterization of proteomes. However, because ESI-IM/MS characterizes ionized protein systems in the gas phase, it generally remains unclear to what extent the protein ions characterized by IM/MS have retained their solution structures. Here, we discuss the first application of our computational structure relaxation approximation [Bleiholder, C.; et al. J. Phys. Chem. B 2019, 123 (13), 2756-2769] to assign structures of protein complexes in the range from ∼16 to ∼60 kDa from their "native" IM/MS spectra. Our analysis shows that the computed IM/MS spectra agree with the experimental spectra within the errors of the methods. The structure relaxation approximation (SRA) indicates that native backbone contacts appear largely retained in the absence of solvent for the investigated protein complexes and charge states. Native contacts between polypeptide chains of the protein complex appear to be retained to a comparable extent as contacts within a folded polypeptide chain. Our computations also indicate that the hallmark "compaction" often observed for protein systems in native IM/MS measurements appears to be a poor indicator of the extent to which native residue-residue interactions are lost in the absence of solvent. Further, the SRA indicates that structural reorganization of the protein systems in IM/MS measurements appears driven largely by remodeling of the protein surface that increases its hydrophobic content by approximately 10%. For the systems studied here, this remodeling of the protein surface appears to occur mainly by structural reorganization of surface-associated hydrophilic amino acid residues not associated with β-strand secondary structure elements. Properties related to the internal protein structure, as assessed by void volume or packing density, appear unaffected by remodeling of the surface. Taken together, the structural reorganization of the protein surface appears to be generic in nature and to sufficiently stabilize protein structures to render them metastable on the time scale of IM/MS measurements.
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Affiliation(s)
- Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Thais Pedrete
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
| | - Md Amin Hossain
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
- Barnett Institute of Chemical and Biological Analysis, 140 The Fenway, Boston, Massachusetts 02115, United States
| | - Jeffrey N Agar
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
- Barnett Institute of Chemical and Biological Analysis, 140 The Fenway, Boston, Massachusetts 02115, United States
- Department of Pharmaceutical Sciences, Northeastern University, 10 Leon St, Boston, Massachusetts 02115, United States
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32306, United States
- Institute of Molecular Biophysics, Florida State University, 91 Chieftain Way, Tallahassee, Florida 32306, United States
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4
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Cropley TC, Chai M, Liu FC, Bleiholder C. Perspective on the potential of tandem-ion mobility /mass spectrometry methods for structural proteomics applications. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1106752. [PMID: 37333518 PMCID: PMC10273136 DOI: 10.3389/frans.2023.1106752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Cellular processes are usually carried out collectively by the entirety of all proteins present in a biological cell, i.e. the proteome. Mass spectrometry-based methods have proven particularly successful in identifying and quantifying the constituent proteins of proteomes, including different molecular forms of a protein. Nevertheless, protein sequences alone do not reveal the function or dysfunction of the identified proteins. A straightforward way to assign function or dysfunction to proteins is characterization of their structures and dynamics. However, a method capable to characterize detailed structures of proteins and protein complexes in a large-scale, systematic manner within the context of cellular processes does not yet exist. Here, we discuss the potential of tandem-ion mobility / mass spectrometry (tandem-IM/MS) methods to provide such ability. We highlight the capability of these methods using two case studies on the protein systems ubiquitin and avidin using the tandem-TIMS/MS technology developed in our laboratory and discuss these results in the context of other developments in the broader field of tandem-IM/MS.
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Affiliation(s)
- Tyler C. Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Mengqi Chai
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Department of Chemistry, Washington University in St. Louis, Saint-Louis, Missouri, USA
| | - Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, USA
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, USA
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5
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Changes within the central stalk of E. coli F 1F o ATP synthase observed after addition of ATP. Commun Biol 2023; 6:26. [PMID: 36631659 PMCID: PMC9834311 DOI: 10.1038/s42003-023-04414-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/03/2023] [Indexed: 01/13/2023] Open
Abstract
F1Fo ATP synthase functions as a biological generator and makes a major contribution to cellular energy production. Proton flow generates rotation in the Fo motor that is transferred to the F1 motor to catalyze ATP production, with flexible F1/Fo coupling required for efficient catalysis. F1Fo ATP synthase can also operate in reverse, hydrolyzing ATP and pumping protons, and in bacteria this function can be regulated by an inhibitory ε subunit. Here we present cryo-EM data showing E. coli F1Fo ATP synthase in different rotational and inhibited sub-states, observed following incubation with 10 mM MgATP. Our structures demonstrate how structural transitions within the inhibitory ε subunit induce torsional movement in the central stalk, thereby enabling its rotation within the Fο motor. This highlights the importance of the central rotor for flexible coupling of the F1 and Fo motors and provides further insight into the regulatory mechanism mediated by subunit ε.
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6
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Liu FC, Ridgeway ME, Park MA, Bleiholder C. Tandem-trapped ion mobility spectrometry/mass spectrometry ( tTIMS/MS): a promising analytical method for investigating heterogenous samples. Analyst 2022; 147:2317-2337. [PMID: 35521797 PMCID: PMC9914546 DOI: 10.1039/d2an00335j] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ion mobility spectrometry/mass spectrometry (IMS/MS) is widely used to study various levels of protein structure. Here, we review the current state of affairs in tandem-trapped ion mobility spectrometry/mass spectrometry (tTIMS/MS). Two different tTIMS/MS instruments are discussed in detail: the first tTIMS/MS instrument, constructed from coaxially aligning two TIMS devices; and an orthogonal tTIMS/MS configuration that comprises an ion trap for irradiation of ions with UV photons. We discuss the various workflows the two tTIMS/MS setups offer and how these can be used to study primary, tertiary, and quaternary structures of protein systems. We also discuss, from a more fundamental perspective, the processes that lead to denaturation of protein systems in tTIMS/MS and how to soften the measurement so that biologically meaningful structures can be characterised with tTIMS/MS. We emphasize the concepts underlying tTIMS/MS to underscore the opportunities tandem-ion mobility spectrometry methods offer for investigating heterogeneous samples.
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | | | | | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA. .,Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306-4390, USA
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7
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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.
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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
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8
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Wittig S, Ganzella M, Barth M, Kostmann S, Riedel D, Pérez-Lara Á, Jahn R, Schmidt C. Cross-linking mass spectrometry uncovers protein interactions and functional assemblies in synaptic vesicle membranes. Nat Commun 2021; 12:858. [PMID: 33558502 PMCID: PMC7870876 DOI: 10.1038/s41467-021-21102-w] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/18/2020] [Indexed: 02/08/2023] Open
Abstract
Synaptic vesicles are storage organelles for neurotransmitters. They pass through a trafficking cycle and fuse with the pre-synaptic membrane when an action potential arrives at the nerve terminal. While molecular components and biophysical parameters of synaptic vesicles have been determined, our knowledge on the protein interactions in their membranes is limited. Here, we apply cross-linking mass spectrometry to study interactions of synaptic vesicle proteins in an unbiased approach without the need for specific antibodies or detergent-solubilisation. Our large-scale analysis delivers a protein network of vesicle sub-populations and functional assemblies including an active and an inactive conformation of the vesicular ATPase complex as well as non-conventional arrangements of the luminal loops of SV2A, Synaptophysin and structurally related proteins. Based on this network, we specifically target Synaptobrevin-2, which connects with many proteins, in different approaches. Our results allow distinction of interactions caused by 'crowding' in the vesicle membrane from stable interaction modules.
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Affiliation(s)
- Sabine Wittig
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Marcelo Ganzella
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Marie Barth
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Susann Kostmann
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dietmar Riedel
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ángel Pérez-Lara
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Physical Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Reinhard Jahn
- Department for Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carla Schmidt
- Interdisciplinary Research Centre HALOmem, Charles Tanford Protein Centre, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany.
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9
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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: 4] [Impact Index Per Article: 1.3] [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.
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Affiliation(s)
- Andy M Lau
- Department of Chemistry, King's College London, London, UK
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10
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Structural predictions of the functions of membrane proteins from HDX-MS. Biochem Soc Trans 2020; 48:971-979. [PMID: 32597490 PMCID: PMC7329338 DOI: 10.1042/bst20190880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/02/2020] [Accepted: 06/04/2020] [Indexed: 11/17/2022]
Abstract
HDX-MS has emerged as a powerful tool to interrogate the structure and dynamics of proteins and their complexes. Recent advances in the methodology and instrumentation have enabled the application of HDX-MS to membrane proteins. Such targets are challenging to investigate with conventional strategies. Developing new tools are therefore pertinent for improving our fundamental knowledge of how membrane proteins function in the cell. Importantly, investigating this central class of biomolecules within their native lipid environment remains a challenge but also a key goal ahead. In this short review, we outline recent progresses in dissecting the conformational mechanisms of membrane proteins using HDX-MS. We further describe how the use of computational strategies can aid the interpretation of experimental data and enable visualisation of otherwise intractable membrane protein states. This unique integration of experiments with computations holds significant potential for future applications.
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11
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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]
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12
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Petroff JT, Tong A, Chen LJ, Dekoster GT, Khan F, Abramson J, Frieden C, Cheng WWL. Charge Reduction of Membrane Proteins in Native Mass Spectrometry Using Alkali Metal Acetate Salts. Anal Chem 2020; 92:6622-6630. [PMID: 32250604 DOI: 10.1021/acs.analchem.0c00454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Native mass spectrometry (MS) provides the capacity to monitor membrane protein complexes and noncovalent binding of ligands and lipids to membrane proteins. The charge states produced by native MS of membrane proteins often result in gas-phase protein unfolding or loss of noncovalent interactions. In an effort to reduce the charge of membrane proteins, we examined the utility of alkali metal salts as a charge-reducing agent. Low concentrations of alkali metal salts caused marked charge reduction in the membrane protein, Erwinia ligand-gated ion channel (ELIC). The charge-reducing effect only occurred for membrane proteins and was detergent-dependent, being most pronounced in long polyethylene glycol (PEG)-based detergents such as C10E5 and C12E8. On the basis of these results, we propose a mechanism for alkali metal charge reduction of membrane proteins. Addition of low concentrations of alkali metals may provide an advantageous approach for charge reduction of detergent-solubilized membrane proteins by native MS.
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Affiliation(s)
| | | | | | | | - Farha Khan
- Department of Physiology, David Geffen School of Medicine at UCLA, 310833 Le Conte Avenue, Los Angeles, California 90095, United States
| | - Jeff Abramson
- Department of Physiology, David Geffen School of Medicine at UCLA, 310833 Le Conte Avenue, Los Angeles, California 90095, United States
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13
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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.
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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,
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14
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Liu FC, Cropley TC, Ridgeway ME, Park MA, Bleiholder C. Structural Analysis of the Glycoprotein Complex Avidin by Tandem-Trapped Ion Mobility Spectrometry-Mass Spectrometry (Tandem-TIMS/MS). Anal Chem 2020; 92:4459-4467. [PMID: 32083467 DOI: 10.1021/acs.analchem.9b05481] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Glycoproteins play a central role in many biological processes including disease mechanisms. Nevertheless, because glycoproteins are heterogeneous entities, it remains unclear how glycosylation modulates the protein structure and function. Here, we assess the ability of tandem-trapped ion mobility spectrometry-mass spectrometry (tandem-TIMS/MS) to characterize the structure and sequence of the homotetrameric glycoprotein avidin. We show that (1) tandem-TIMS/MS retains native-like avidin tetramers with deeply buried solvent particles; (2) applying high activation voltages in the interface of tandem-TIMS results in collision-induced dissociation (CID) of avidin tetramers into compact monomers, dimers, and trimers with cross sections consistent with X-ray structures and reports from surface-induced dissociation (SID); (3) avidin oligomers are best described as heterogeneous ensembles with (essentially) random combinations of monomer glycoforms; (4) native top-down sequence analysis of the avidin tetramer is possible by CID in tandem-TIMS. Overall, our results demonstrate that tandem-TIMS/MS has the potential to correlate individual proteoforms to variations in protein structure.
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Affiliation(s)
- Fanny C Liu
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Tyler C Cropley
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - Mark E Ridgeway
- Bruker Daltonics Inc., 40 Manning Road, Billerica, Massachusetts 01821, United States
| | - Melvin A Park
- Bruker Daltonics Inc., 40 Manning Road, Billerica, Massachusetts 01821, United States
| | - Christian Bleiholder
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States.,Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306-4390, United States
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15
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Xiong C, Liu H, Liu C, Xue J, Zhan L, Nie Z. Mass, Size, and Density Measurements of Microparticles in a Quadrupole Ion Trap. Anal Chem 2019; 91:13508-13513. [PMID: 31608618 DOI: 10.1021/acs.analchem.9b02574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The physical properties of microparticles, such as mass, size, and density, are critical for their functions. The comprehensive characterization of these physical parameters, however, remains a fundamental challenge. Here, we developed a particle mass spectrometry (PMS) methodology for determining the mass, size, and density of microparticles simultaneously. The collisional cross-section (CCS) and mass spectrometry (MS) measurements were performed in a single quadrupole ion trap (QIT), and the two modes can be switched easily by tuning the electric and gas hydrodynamic fields of the QIT. The feasibility of the method was demonstrated through a series of monodispersed polystyrene (PS) and silica (SiO2) particle standards. The SiO2/polypyrrole core-shell particles were also successfully characterized, and the measured results were verified by using conventional methods.
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Affiliation(s)
- Caiqiao Xiong
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Huihui Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Chaozi Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Jinjuan Xue
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Lingpeng Zhan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zongxiu Nie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry , Chinese Academy of Sciences , Beijing 100190 China.,University of Chinese Academy of Sciences , Beijing 100049 , China
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16
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Martens C, Shekhar M, Lau AM, Tajkhorshid E, Politis A. Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. Nat Protoc 2019; 14:3183-3204. [PMID: 31605097 PMCID: PMC7058097 DOI: 10.1038/s41596-019-0219-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022]
Abstract
Biological membranes define the boundaries of cells and are composed primarily of phospholipids and membrane proteins. It has become increasingly evident that direct interactions of membrane proteins with their surrounding lipids play key roles in regulating both protein conformations and function. However, the exact nature and structural consequences of these interactions remain difficult to track at the molecular level. Here, we present a protocol that specifically addresses this challenge. First, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of membrane proteins incorporated into nanodiscs of controlled lipid composition is used to obtain information on the lipid species that are involved in modulating the conformational changes in the membrane protein. Then molecular dynamics (MD) simulations in lipid bilayers are used to pinpoint likely lipid-protein interactions, which can be tested experimentally using HDX-MS. By bringing together the MD predictions with the conformational readouts from HDX-MS, we have uncovered key lipid-protein interactions implicated in stabilizing important functional conformations. This protocol can be applied to virtually any integral membrane protein amenable to classic biophysical studies and for which a near-atomic-resolution structure or homology model is available. This protocol takes ~4 d to complete, excluding the time for data analysis and MD simulations, which depends on the size of the protein under investigation.
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Affiliation(s)
- Chloe Martens
- Department of Chemistry, King's College London, London, UK
- Department of Chemistry, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Mrinal Shekhar
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy M Lau
- Department of Chemistry, King's College London, London, UK
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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17
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Beckett D, El-Baba TJ, Gilbert K, Clemmer DE, Raghavachari K. Untangling Hydrogen Bond Networks with Ion Mobility Spectrometry and Quantum Chemical Calculations: A Case Study on H +XPGG. J Phys Chem B 2019; 123:5730-5741. [PMID: 31241336 DOI: 10.1021/acs.jpcb.9b03803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ion mobility spectrometry-mass spectrometry and quantum chemical calculations are used to determine the structures and stabilities of singly protonated XaaProGlyGly peptides: H+DPGG, H+NPGG, H+EPGG, and H+QPGG. The IMS distributions are similar, suggesting the peptides adopt closely related structures in the gas phase. Quantum chemical calculations show that all conformers seen in the experimental spectrum correspond to the cis configuration about the Xaa-Pro peptide bond, significantly different from the behavior seen previously for H+GPGG. Density functional theory and quantum theory of atoms in molecules (QTAIM) investigations uncover a silent drama as a minor conformer not observed in the H+DPGG spectrum becomes the preferred conformer in H+QPGG, with both conformers being coincident in collision cross section. Investigation of the highly coupled hydrogen bond network, replete with CH···O interactions and bifurcated hydrogen bonds, reveals the cause of this effect as well as the absence of trans conformers from the spectra. A series of generalized observations are provided to aid in enzyme and ligand design using these coupled hydrogen bond motifs.
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Affiliation(s)
- Daniel Beckett
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - Tarick J El-Baba
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - Kevin Gilbert
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
| | - Krishnan Raghavachari
- Department of Chemistry , Indiana University , Bloomington Indiana 47401 , United States
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18
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19
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Polasky DA, Dixit SM, Fantin SM, Ruotolo BT. CIUSuite 2: Next-Generation Software for the Analysis of Gas-Phase Protein Unfolding Data. Anal Chem 2019; 91:3147-3155. [DOI: 10.1021/acs.analchem.8b05762] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daniel A. Polasky
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sugyan M. Dixit
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Sarah M. Fantin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T. Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Calabrese AN, Radford SE. Mass spectrometry-enabled structural biology of membrane proteins. Methods 2018; 147:187-205. [DOI: 10.1016/j.ymeth.2018.02.020] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/30/2018] [Accepted: 02/21/2018] [Indexed: 01/01/2023] Open
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21
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Wongkongkathep P, Han JY, Choi TS, Yin S, Kim HI, Loo JA. Native Top-Down Mass Spectrometry and Ion Mobility MS for Characterizing the Cobalt and Manganese Metal Binding of α-Synuclein Protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1870-1880. [PMID: 29951842 PMCID: PMC6087494 DOI: 10.1007/s13361-018-2002-2] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/27/2018] [Accepted: 05/29/2018] [Indexed: 05/22/2023]
Abstract
Structural characterization of intrinsically disordered proteins (IDPs) has been a major challenge in the field of protein science due to limited capabilities to obtain full-length high-resolution structures. Native ESI-MS with top-down MS was utilized to obtain structural features of protein-ligand binding for the Parkinson's disease-related protein, α-synuclein (αSyn), which is natively unstructured. Binding of heavy metals has been implicated in the accelerated formation of αSyn aggregation. Using high-resolution Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry, native top-down MS with various fragmentation methods, including electron capture dissociation (ECD), collisional activated dissociation (CAD), and multistage tandem MS (MS3), deduced the binding sites of cobalt and manganese to the C-terminal region of the protein. Ion mobility MS (IM-MS) revealed a collapse toward compacted states of αSyn upon metal binding. The combination of native top-down MS and IM-MS provides structural information of protein-ligand interactions for intrinsically disordered proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- Piriya Wongkongkathep
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jong Yoon Han
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - Tae Su Choi
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - Sheng Yin
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Hugh I Kim
- Department of Chemistry, Korea University, Seoul, Republic of Korea
| | - 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, UCLA Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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22
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Kulesza A, Marklund EG, MacAleese L, Chirot F, Dugourd P. Bringing Molecular Dynamics and Ion-Mobility Spectrometry Closer Together: Shape Correlations, Structure-Based Predictors, and Dissociation. J Phys Chem B 2018; 122:8317-8329. [DOI: 10.1021/acs.jpcb.8b03825] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Kulesza
- Université de Lyon, F-69622, Lyon, France
- CNRS et
Université
Lyon 1, UMR5306, Institut Lumière Matière, France
| | - Erik G. Marklund
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Luke MacAleese
- Université de Lyon, F-69622, Lyon, France
- CNRS et
Université
Lyon 1, UMR5306, Institut Lumière Matière, France
| | - Fabien Chirot
- Université
Lyon, Université Claude Bernard Lyon 1, Ens de Lyon, CNRS,
Institut des Sciences Analytiques UMR 5280, F-69100, Villeurbanne, France
| | - Philippe Dugourd
- Université de Lyon, F-69622, Lyon, France
- CNRS et
Université
Lyon 1, UMR5306, Institut Lumière Matière, France
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23
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Sharma S, Oot RA, Wilkens S. MgATP hydrolysis destabilizes the interaction between subunit H and yeast V 1-ATPase, highlighting H's role in V-ATPase regulation by reversible disassembly. J Biol Chem 2018; 293:10718-10730. [PMID: 29754144 DOI: 10.1074/jbc.ra118.002951] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 04/22/2018] [Indexed: 01/01/2023] Open
Abstract
Vacuolar H+-ATPases (V-ATPases; V1Vo-ATPases) are rotary-motor proton pumps that acidify intracellular compartments and, in some tissues, the extracellular space. V-ATPase is regulated by reversible disassembly into autoinhibited V1-ATPase and Vo proton channel sectors. An important player in V-ATPase regulation is subunit H, which binds at the interface of V1 and Vo H is required for MgATPase activity in holo-V-ATPase but also for stabilizing the MgADP-inhibited state in membrane-detached V1 However, how H fulfills these two functions is poorly understood. To characterize the H-V1 interaction and its role in reversible disassembly, we determined binding affinities of full-length H and its N-terminal domain (HNT) for an isolated heterodimer of subunits E and G (EG), the N-terminal domain of subunit a (aNT), and V1 lacking subunit H (V1ΔH). Using isothermal titration calorimetry (ITC) and biolayer interferometry (BLI), we show that HNT binds EG with moderate affinity, that full-length H binds aNT weakly, and that both H and HNT bind V1ΔH with high affinity. We also found that only one molecule of HNT binds V1ΔH with high affinity, suggesting conformational asymmetry of the three EG heterodimers in V1ΔH. Moreover, MgATP hydrolysis-driven conformational changes in V1 destabilized the interaction of H or HNT with V1ΔH, suggesting an interplay between MgADP inhibition and subunit H. Our observation that H binding is affected by MgATP hydrolysis in V1 points to H's role in the mechanism of reversible disassembly.
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Affiliation(s)
- Stuti Sharma
- From the Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210
| | - Rebecca A Oot
- From the Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210
| | - Stephan Wilkens
- From the Department of Biochemistry and Molecular Biology, State University of New York (SUNY) Upstate Medical University, Syracuse, New York 13210
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24
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Re S, Watabe S, Nishima W, Muneyuki E, Yamaguchi Y, MacKerell AD, Sugita Y. Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase. Sci Rep 2018; 8:1644. [PMID: 29374210 PMCID: PMC5786100 DOI: 10.1038/s41598-018-20012-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 01/10/2018] [Indexed: 12/18/2022] Open
Abstract
Ion mobility mass spectrometry (IM-MS) is a technique capable of investigating structural changes of biomolecules based on their collision cross section (CCS). Recent advances in IM-MS allow us to separate carbohydrate isomers with subtle conformational differences, but the relationship between CCS and atomic structure remains elusive. Here, we characterize conformational ensembles of gas-phase N-glycans under the electrospray ionization condition using molecular dynamics simulations with enhanced sampling. We show that the separation of CCSs between isomers reflects folding features of N-glycans, which are determined both by chemical compositions and protonation states. Providing a physicochemical basis of CCS for N-glycans helps not only to interpret IM-MS measurements but also to estimate CCSs of complex glycans.
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Affiliation(s)
- Suyong Re
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Shigehisa Watabe
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Wataru Nishima
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Eiro Muneyuki
- Graduate School of Science and Engineering, Chuo University, 1-13-27, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Yoshiki Yamaguchi
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, 21201, USA
| | - Yuji Sugita
- RIKEN Theoretical Molecular Science Laboratory, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. .,RIKEN iTHES, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
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25
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Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase. Cell Chem Biol 2018; 25:309-317.e4. [PMID: 29358052 PMCID: PMC5856493 DOI: 10.1016/j.chembiol.2017.12.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/21/2017] [Accepted: 12/20/2017] [Indexed: 11/23/2022]
Abstract
The interactions between proteins and biological membranes are important for drug development, but remain notoriously refractory to structural investigation. We combine non-denaturing mass spectrometry (MS) with molecular dynamics (MD) simulations to unravel the connections among co-factor, lipid, and inhibitor binding in the peripheral membrane protein dihydroorotate dehydrogenase (DHODH), a key anticancer target. Interrogation of intact DHODH complexes by MS reveals that phospholipids bind via their charged head groups at a limited number of sites, while binding of the inhibitor brequinar involves simultaneous association with detergent molecules. MD simulations show that lipids support flexible segments in the membrane-binding domain and position the inhibitor and electron acceptor-binding site away from the membrane surface, similar to the electron acceptor-binding site in respiratory chain complex I. By complementing MS with MD simulations, we demonstrate how a peripheral membrane protein uses lipids to modulate its structure in a similar manner as integral membrane proteins. Mass spectrometry captures intact complexes of the peripheral membrane protein DHODH Detergent removal in the gas phase reveals lipid and co-factor binding DHODH attaches to the membrane by binding charged phospholipids Lipids stabilize the flexible substrate- and drug-binding site
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26
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Liu FC, Ridgeway ME, Park MA, Bleiholder C. Tandem trapped ion mobility spectrometry. Analyst 2018; 143:2249-2258. [DOI: 10.1039/c7an02054f] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Design, characteristics, and application of tandem trapped ion mobility spectrometry (TIMS-TIMS).
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Affiliation(s)
- Fanny C. Liu
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
| | | | | | - Christian Bleiholder
- Department of Chemistry and Biochemistry
- Florida State University
- Tallahassee
- USA
- Institute of Molecular Biophysics
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27
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Rowland EA, Snowden CK, Cristea IM. Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease. Curr Opin Chem Biol 2017; 42:76-85. [PMID: 29169048 DOI: 10.1016/j.cbpa.2017.11.003] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 02/07/2023]
Abstract
Lipoylation is a rare, but highly conserved lysine posttranslational modification. To date, it is known to occur on only four multimeric metabolic enzymes in mammals, yet these proteins are staples in the core metabolic landscape. The dysregulation of these mitochondrial proteins is linked to a range of human metabolic disorders. Perhaps most striking is that lipoylation itself, the proteins that add or remove the modification, as well as the proteins it decorates are all evolutionarily conserved from bacteria to humans, highlighting the importance of this essential cofactor. Here, we discuss the biological significance of protein lipoylation, the importance of understanding its regulation in health and disease states, and the advances in mass spectrometry-based proteomic technologies that can aid these studies.
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Affiliation(s)
- Elizabeth A Rowland
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States
| | - Caroline K Snowden
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, United States.
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28
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Eschweiler JD, Frank AT, Ruotolo BT. Coming to Grips with Ambiguity: Ion Mobility-Mass Spectrometry for Protein Quaternary Structure Assignment. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1991-2000. [PMID: 28752478 PMCID: PMC5693686 DOI: 10.1007/s13361-017-1757-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 07/04/2017] [Accepted: 07/05/2017] [Indexed: 05/21/2023]
Abstract
Multiprotein complexes are central to our understanding of cellular biology, as they play critical roles in nearly every biological process. Despite many impressive advances associated with structural characterization techniques, large and highly-dynamic protein complexes are too often refractory to analysis by conventional, high-resolution approaches. To fill this gap, ion mobility-mass spectrometry (IM-MS) methods have emerged as a promising approach for characterizing the structures of challenging assemblies due in large part to the ability of these methods to characterize the composition, connectivity, and topology of large, labile complexes. In this Critical Insight, we present a series of bioinformatics studies aimed at assessing the information content of IM-MS datasets for building models of multiprotein structure. Our computational data highlights the limits of current coarse-graining approaches, and compelled us to develop an improved workflow for multiprotein topology modeling, which we benchmark against a subset of the multiprotein complexes within the PDB. This improved workflow has allowed us to ascertain both the minimal experimental restraint sets required for generation of high-confidence multiprotein topologies, and quantify the ambiguity in models where insufficient IM-MS information is available. We conclude by projecting the future of IM-MS in the context of protein quaternary structure assignment, where we predict that a more complete knowledge of the ultimate information content and ambiguity within such models will undoubtedly lead to applications for a broader array of challenging biomolecular assemblies. Graphical Abstract ᅟ.
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Affiliation(s)
| | - Aaron T Frank
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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29
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Ishii K, Zhou M, Uchiyama S. Native mass spectrometry for understanding dynamic protein complex. Biochim Biophys Acta Gen Subj 2017; 1862:275-286. [PMID: 28965879 DOI: 10.1016/j.bbagen.2017.09.019] [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: 07/20/2017] [Revised: 09/17/2017] [Accepted: 09/19/2017] [Indexed: 12/13/2022]
Abstract
Biomolecules have evolved to perform specific and sophisticated activities in a highly coordinated manner organizing into multi-component complexes consisting of proteins, nucleic acids, cofactors or ligands. Understanding such complexes represents a task in earnest for modern bioscience. Traditional structural techniques when extrapolating to macromolecules of ever increasing sizes are confronted with limitations posed by the difficulty in enrichment, solubility, stability as well as lack of homogeneity of these complexes. Alternative approaches are therefore prompted to bridge the gap, one of which is native mass spectrometry. Here we demonstrate the strength of native mass spectrometry, used alone or in combination with other biophysical methods such as analytical ultracentrifugation, small-angle neutron scattering, and small-angle X-ray scattering etc., in addressing dynamic aspects of protein complexes including structural reorganization, subunit exchange, as well as the assembly/disassembly processes in solution that are dictated by transient non-covalent interactions. We review recent studies from our laboratories and others applying native mass spectrometry to both soluble and membrane-embedded assemblies. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.
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Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan
| | - Min Zhou
- Institute of Bio-analytical Chemistry, School of Chemical Engineering, Nanjing University of Science and Technology, No. 200 Xiaolingwei Street, Nanjing 210094, China.
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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30
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Laszlo KJ, Bush MF. Effects of Charge State, Charge Distribution, and Structure on the Ion Mobility of Protein Ions in Helium Gas: Results from Trajectory Method Calculations. J Phys Chem A 2017; 121:7768-7777. [PMID: 28910102 DOI: 10.1021/acs.jpca.7b08154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Collision cross section (Ω) values of gas-phase ions of proteins and protein complexes are used to probe the structures of the corresponding species in solution. Ions of many proteins exhibit increasing Ω-values with increasing charge state but most Ω-values calculated for protein ions have used simple collision models that do not explicitly account for charge. Here we use a combination of ion mobility mass spectrometry experiments with helium gas and trajectory method calculations to characterize the extents to which increases in experimental Ω-values with increasing charge state may be attributed to increased momentum transfer concomitant with enhanced long-range interactions between the protein ion and helium atoms. Ubiquitin and C-to-N terminally linked diubiquitin ions generated from different solution conditions exhibit more than a 2-fold increase in Ω with increasing charge state. For native and energy-relaxed models of the proteins and most methods for distributing charge, Ω-values calculated using the trajectory method increase by less than 1% over the range of charge states observed from typical solution conditions used for native mass spectrometry. However, the calculated Ω-values increase by 10% to 15% over the full range of charge states observed from all solution conditions. Therefore, contributions from enhanced ion-induced dipole interactions with increasing charge state are significant but without additional structural changes can account for only a fraction of the increase in Ω observed experimentally. On the basis of these results, we suggest guidelines for calculating Ω-values in the context of applications in biophysics and structural biology.
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Affiliation(s)
- Kenneth J Laszlo
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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31
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Calabrese AN, Jackson SM, Jones LN, Beckstein O, Heinkel F, Gsponer J, Sharples D, Sans M, Kokkinidou M, Pearson AR, Radford SE, Ashcroft AE, Henderson PJF. Topological Dissection of the Membrane Transport Protein Mhp1 Derived from Cysteine Accessibility and Mass Spectrometry. Anal Chem 2017; 89:8844-8852. [PMID: 28726379 PMCID: PMC5588088 DOI: 10.1021/acs.analchem.7b01310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/20/2017] [Indexed: 01/01/2023]
Abstract
Cys accessibility and quantitative intact mass spectrometry (MS) analyses have been devised to study the topological transitions of Mhp1, the membrane protein for sodium-linked transport of hydantoins from Microbacterium liquefaciens. Mhp1 has been crystallized in three forms (outward-facing open, outward-facing occluded with substrate bound, and inward-facing open). We show that one natural cysteine residue, Cys327, out of three, has an enhanced solvent accessibility in the inward-facing (relative to the outward-facing) form. Reaction of the purified protein, in detergent, with the thiol-reactive N-ethylmalemide (NEM), results in modification of Cys327, suggesting that Mhp1 adopts predominantly inward-facing conformations. Addition of either sodium ions or the substrate 5-benzyl-l-hydantoin (L-BH) does not shift this conformational equilibrium, but systematic co-addition of the two results in an attenuation of labeling, indicating a shift toward outward-facing conformations that can be interpreted using conventional enzyme kinetic analyses. Such measurements can afford the Km for each ligand as well as the stoichiometry of ion-substrate-coupled conformational changes. Mutations that perturb the substrate binding site either result in the protein being unable to adopt outward-facing conformations or in a global destabilization of structure. The methodology combines covalent labeling, mass spectrometry, and kinetic analyses in a straightforward workflow applicable to a range of systems, enabling the interrogation of changes in a protein's conformation required for function at varied concentrations of substrates, and the consequences of mutations on these conformational transitions.
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Affiliation(s)
| | | | | | - Oliver Beckstein
- Department of Physics, Arizona State University , Tempe, Arizona 85287-1504, United States
| | - Florian Heinkel
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | - Joerg Gsponer
- Centre for High-Throughput Biology, University of British Columbia , Vancouver, British Columbia, Canada V6T 1Z4
| | | | - Marta Sans
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Maria Kokkinidou
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
| | - Arwen R Pearson
- Hamburg Centre for Ultrafast Imaging, Institute for Nanostructure and Solid State Physics, Universität Hamburg , Hamburg 22761, Germany
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Devine PWA, Fisher HC, Calabrese AN, Whelan F, Higazi DR, Potts JR, Lowe DC, Radford SE, Ashcroft AE. Investigating the Structural Compaction of Biomolecules Upon Transition to the Gas-Phase Using ESI-TWIMS-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1855-1862. [PMID: 28484973 PMCID: PMC5556138 DOI: 10.1007/s13361-017-1689-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/07/2017] [Accepted: 04/13/2017] [Indexed: 05/11/2023]
Abstract
Collision cross-section (CCS) measurements obtained from ion mobility spectrometry-mass spectrometry (IMS-MS) analyses often provide useful information concerning a protein's size and shape and can be complemented by modeling procedures. However, there have been some concerns about the extent to which certain proteins maintain a native-like conformation during the gas-phase analysis, especially proteins with dynamic or extended regions. Here we have measured the CCSs of a range of biomolecules including non-globular proteins and RNAs of different sequence, size, and stability. Using traveling wave IMS-MS, we show that for the proteins studied, the measured CCS deviates significantly from predicted CCS values based upon currently available structures. The results presented indicate that these proteins collapse to different extents varying on their elongated structures upon transition into the gas-phase. Comparing two RNAs of similar mass but different solution structures, we show that these biomolecules may also be susceptible to gas-phase compaction. Together, the results suggest that caution is needed when predicting structural models based on CCS data for RNAs as well as proteins with non-globular folds. Graphical Abstract ᅟ.
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Affiliation(s)
- Paul W A Devine
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Henry C Fisher
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Antonio N Calabrese
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Fiona Whelan
- Department of Biology, University of York, York, YO10 5DD, UK
| | - Daniel R Higazi
- Ipsen Ltd. UK, Wrexham Industrial Estate, 9 Ash Road North, Wrexham, LL13 9UF, UK
| | | | - David C Lowe
- MedImmune, Sir Aaron Klug Building, Granta Science Park, Cambridge, CB21 6GH, UK
| | - Sheena E Radford
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Alison E Ashcroft
- Astbury Center for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK.
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33
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Hybrid Mass Spectrometry: Towards Characterization of Protein Conformational States. Trends Biochem Sci 2017; 41:650-653. [PMID: 27211036 DOI: 10.1016/j.tibs.2016.04.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/17/2016] [Accepted: 04/26/2016] [Indexed: 01/14/2023]
Abstract
A current challenge in structural biology is to unravel the conformational states of protein complexes. Hybrid mass spectrometry (MS) has emerged as a key tool to study the structural dynamics of large protein complexes unattainable by traditional methods. Here, we discuss recent advances in hybrid MS allowing characterization of challenging biological systems.
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34
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Laszlo KJ, Bush MF. Interpreting the Collision Cross Sections of Native-like Protein Ions: Insights from Cation-to-Anion Proton-Transfer Reactions. Anal Chem 2017. [PMID: 28636334 DOI: 10.1021/acs.analchem.7b01474] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of charge state on structures of native-like cations of serum albumin, streptavidin, avidin, and alcohol dehydrogenase were probed using cation-to-anion proton-transfer reactions (CAPTR), ion mobility, mass spectrometry, and complementary energy-dependent experiments. The CAPTR products all have collision cross-section (Ω) values that are within 5.5% of the original precursor cations. The first CAPTR event for each precursor yields products that have smaller Ω values and frequently exhibit the greatest magnitude of change in Ω resulting from a single CAPTR event. To investigate how the structures of the precursors affect the structures of the products, ions were activated as a function of energy prior to CAPTR. In each case, the Ω values of the activated precursors increase with increasing energy, but the Ω values of the CAPTR products are smaller than the activated precursors. To investigate the stabilities of the CAPTR products, the products were activated immediately prior to ion mobility. These results show that additional structures with smaller or larger Ω values can be populated and that the structures and stabilities of these ions depend most strongly on the identity of the protein and the charge state of the product, rather than the charge state of the precursor or the number of CAPTR events. Together, these results indicate that the excess charges initially present on native-like ions have a modest, but sometimes statistically significant, effect on their Ω values. Therefore, potential contributions from charge state should be considered when using experimental Ω values to elucidate structures in solution.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- Department of Chemistry, University of Washington , Box 351700, Seattle, Washington 98195-1700, United States
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35
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Allen SJ, Eaton RM, Bush MF. Structural Dynamics of Native-Like Ions in the Gas Phase: Results from Tandem Ion Mobility of Cytochrome c. Anal Chem 2017. [PMID: 28636328 DOI: 10.1021/acs.analchem.7b01234] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ion mobility (IM) is a gas-phase separation technique that is used to determine the collision cross sections of native-like ions of proteins and protein complexes, which are in turn used as restraints for modeling the structures of those analytes in solution. Here, we evaluate the stability of native-like ions using tandem IM experiments implemented using structures for lossless ion manipulations (SLIM). In this implementation of tandem IM, ions undergo a first dimension of IM up to a switch that is used to selectively transmit ions of a desired mobility. Selected ions are accumulated in a trap and then released after a delay to initiate the second dimension of IM. For delays ranging from 16 to 33 231 ms, the collision cross sections of native-like, 7+ cytochrome c ions increase monotonically from 15.1 to 17.1 nm2. The largest products formed in these experiments at near-ambient temperature are still far smaller than those formed in energy-dependent experiments (∼21 nm2). However, the collision cross section increases by ∼2% between delay times of 16 and 211 ms, which may have implications for other IM experiments on these time scales. Finally, two subpopulations from the full population were each mobility selected and analyzed as a function of delay time, showing that the three populations can be differentiated for at least 1 s. Together, these results suggest that elements of native-like structure can have long lifetimes at near-ambient temperature in the gas phase but that gas-phase dynamics should be considered when interpreting results from IM.
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Affiliation(s)
- Samuel J Allen
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Rachel M Eaton
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F Bush
- University of Washington , Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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36
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Laszlo KJ, Buckner JH, Munger EB, Bush MF. Native-Like and Denatured Cytochrome c Ions Yield Cation-to-Anion Proton Transfer Reaction Products with Similar Collision Cross-Sections. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1382-1391. [PMID: 28224394 PMCID: PMC5555649 DOI: 10.1007/s13361-017-1620-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 05/04/2023]
Abstract
The relationship between structures of protein ions, their charge states, and their original structures prior to ionization remains challenging to decouple. Here, we use cation-to-anion proton transfer reactions (CAPTR) to reduce the charge states of cytochrome c ions in the gas phase, and ion mobility to probe their structures. Ions were formed using a new temperature-controlled nanoelectrospray ionization source at 25 °C. Characterization of this source demonstrates that the temperature of the liquid sample is decoupled from that of the atmospheric pressure interface, which is heated during CAPTR experiments. Ionization from denaturing conditions yields 18+ to 8+ ions, which were each isolated and reacted with monoanions to generate all CAPTR products with charge states of at least 3+. The highest, intermediate, and lowest charge-state products exhibit collision cross-section distributions that are unimodal, multimodal, and unimodal, respectively. These distributions depend strongly on the charge state of the product, although those for the intermediate charge-state products also depend on that of the precursor. The distributions of the 3+ products are all similar, with averages that are less than half that of the 18+ precursor ions. Ionization of cytochrome c from native-like conditions yields 7+ and 6+ ions. The 3+ CAPTR products from these precursors have slightly more compact collision cross-section distributions that are indistinguishable from those for the 3+ CAPTR products from denaturing conditions. More broadly, these results indicate that the collision cross-sections of ions of this single domain protein depend strongly on charge state for charge states greater than ~4. Graphical Abstract ᅟ.
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Affiliation(s)
- Kenneth J Laszlo
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - John H Buckner
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
- Department of Chemistry, Carleton College, One North College Street, Northfield, MN, 55057, USA
| | - Eleanor B Munger
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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37
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Yen HY, Hopper JTS, Liko I, Allison TM, Zhu Y, Wang D, Stegmann M, Mohammed S, Wu B, Robinson CV. Ligand binding to a G protein-coupled receptor captured in a mass spectrometer. SCIENCE ADVANCES 2017; 3:e1701016. [PMID: 28630934 PMCID: PMC5473672 DOI: 10.1126/sciadv.1701016] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/27/2017] [Indexed: 05/08/2023]
Abstract
G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors belong to the largest family of membrane-embedded cell surface proteins and are involved in a diverse array of physiological processes. Despite progress in the mass spectrometry of membrane protein complexes, G protein-coupled receptors have remained intractable because of their low yield and instability after extraction from cell membranes. We established conditions in the mass spectrometer that preserve noncovalent ligand binding to the human purinergic receptor P2Y1. Results established differing affinities for nucleotides and the drug MRS2500 and link antagonist binding with the absence of receptor phosphorylation. Overall, therefore, our results are consistent with drug binding, preventing the conformational changes that facilitate downstream signaling. More generally, we highlight opportunities for mass spectrometry to probe effects of ligand binding on G protein-coupled receptors.
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Affiliation(s)
- Hsin-Yung Yen
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Jonathan T. S. Hopper
- OMass Technologies Ltd., Centre for Innovation and Enterprise, Begbroke Science Park, Woodstock Road, Oxford OX5 1PF, UK
| | - Idlir Liko
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
- OMass Technologies Ltd., Centre for Innovation and Enterprise, Begbroke Science Park, Woodstock Road, Oxford OX5 1PF, UK
| | - Timothy M. Allison
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
| | - Ya Zhu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
| | - Dejian Wang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai 201203, China
| | - Monika Stegmann
- Departments of Chemistry and Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Shabaz Mohammed
- Departments of Chemistry and Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, 99 Haike Road, Pudong, Shanghai 201203, China
| | - Carol V. Robinson
- Chemistry Research Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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38
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Lai AL, Clerico EM, Blackburn ME, Patel NA, Robinson CV, Borbat PP, Freed JH, Gierasch LM. Key features of an Hsp70 chaperone allosteric landscape revealed by ion-mobility native mass spectrometry and double electron-electron resonance. J Biol Chem 2017; 292:8773-8785. [PMID: 28428246 PMCID: PMC5448104 DOI: 10.1074/jbc.m116.770404] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/12/2017] [Indexed: 11/06/2022] Open
Abstract
Proteins are dynamic entities that populate conformational ensembles, and most functions of proteins depend on their dynamic character. Allostery, in particular, relies on ligand-modulated shifts in these conformational ensembles. Hsp70s are allosteric molecular chaperones with conformational landscapes that involve large rearrangements of their two domains (viz. the nucleotide-binding domain and substrate-binding domain) in response to adenine nucleotides and substrates. However, it remains unclear how the Hsp70 conformational ensemble is populated at each point of the allosteric cycle and how ligands control these populations. We have mapped the conformational species present under different ligand-binding conditions throughout the allosteric cycle of the Escherichia coli Hsp70 DnaK by two complementary methods, ion-mobility mass spectrometry and double electron-electron resonance. Our results obtained under biologically relevant ligand-bound conditions confirm the current picture derived from NMR and crystallographic data of domain docking upon ATP binding and undocking in response to ADP and substrate. Additionally, we find that the helical lid of DnaK is a highly dynamic unit of the structure in all ligand-bound states. Importantly, we demonstrate that DnaK populates a partially docked state in the presence of ATP and substrate and that this state represents an energy minimum on the DnaK allosteric landscape. Because Hsp70s are emerging as potential drug targets for many diseases, fully mapping an allosteric landscape of a molecular chaperone like DnaK will facilitate the development of small molecules that modulate Hsp70 function via allosteric mechanisms.
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Affiliation(s)
- Alex L Lai
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-2703
| | | | - Mandy E Blackburn
- the School of Environmental, Physical, and Applied Sciences, University of Central Missouri, Warrensburg, Missouri 64093, and
| | - Nisha A Patel
- the Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Carol V Robinson
- the Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Peter P Borbat
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-2703
| | - Jack H Freed
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-2703
| | - Lila M Gierasch
- the Departments of Biochemistry and Molecular Biology and .,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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39
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Schmidt C, Macpherson JA, Lau AM, Tan KW, Fraternali F, Politis A. Surface Accessibility and Dynamics of Macromolecular Assemblies Probed by Covalent Labeling Mass Spectrometry and Integrative Modeling. Anal Chem 2017; 89:1459-1468. [PMID: 28208298 PMCID: PMC5299547 DOI: 10.1021/acs.analchem.6b02875] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 01/04/2017] [Indexed: 12/22/2022]
Abstract
Mass spectrometry (MS) has become an indispensable tool for investigating the architectures and dynamics of macromolecular assemblies. Here we show that covalent labeling of solvent accessible residues followed by their MS-based identification yields modeling restraints that allow mapping the location and orientation of subunits within protein assemblies. Together with complementary restraints derived from cross-linking and native MS, we built native-like models of four heterocomplexes with known subunit structures and compared them with available X-ray crystal structures. The results demonstrated that covalent labeling followed by MS markedly increased the predictive power of the integrative modeling strategy enabling more accurate protein assembly models. We applied this strategy to the F-type ATP synthase from spinach chloroplasts (cATPase) providing a structural basis for its function as a nanomotor. By subjecting the models generated by our restraint-based strategy to molecular dynamics (MD) simulations, we revealed the conformational states of the peripheral stalk and assigned flexible regions in the enzyme. Our strategy can readily incorporate complementary chemical labeling strategies and we anticipate that it will be applicable to many other systems providing new insights into the structure and function of protein complexes.
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Affiliation(s)
- Carla Schmidt
- Interdisciplinary
Research Center HALOmem, Martin Luther University
Halle-Wittenberg, Kurt-Mothes-Strasse 3, 06120 Halle/Saale, Germany
| | - Jamie A. Macpherson
- Division
of Cell & Molecular Biophysics, King’s
College London, New Hunt’s
House, SE1 1UL, London, United Kingdom
| | - Andy M. Lau
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB, London, United Kingdom
| | - Ken Wei Tan
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB, London, United Kingdom
| | - Franca Fraternali
- Division
of Cell & Molecular Biophysics, King’s
College London, New Hunt’s
House, SE1 1UL, London, United Kingdom
| | - Argyris Politis
- Department
of Chemistry, King’s College London, 7 Trinity Street, SE1 1DB, London, United Kingdom
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40
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Davies RB, Smits C, Wong ASW, Stock D, Christie M, Sandin S, Stewart AG. Cryo-EM analysis of a domain antibody bound rotary ATPase complex. J Struct Biol 2017; 197:350-353. [PMID: 28115258 DOI: 10.1016/j.jsb.2017.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 01/11/2023]
Abstract
The bacterial A/V-type ATPase/synthase rotary motor couples ATP hydrolysis/synthesis with proton translocation across biological membranes. The A/V-type ATPase/synthase from Thermus thermophilus has been extensively studied both structurally and functionally for many years. Here we provide an 8.7Å resolution cryo-electron microscopy 3D reconstruction of this complex bound to single-domain antibody fragments, small monomeric antibodies containing just the variable heavy domain. Docking of known structures into the density revealed the molecular orientation of the domain antibodies, suggesting that structure determination of co-domain antibody:protein complexes could be a useful avenue for unstable or smaller proteins. Although previous studies suggested that the presence of fluoroaluminate in this complex could change the rotary state of this enzyme, we observed no gross structural rearrangements under these conditions.
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Affiliation(s)
- Roberta B Davies
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Callum Smits
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia
| | - Andrew S W Wong
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore
| | - Daniela Stock
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Mary Christie
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Sara Sandin
- NTU Institute of Structural Biology, Nanyang Technological University, 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Alastair G Stewart
- Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; Faculty of Medicine, The University of New South Wales, Sydney, NSW 2052, Australia.
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41
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Allen SJ, Bush MF. Radio-Frequency (rf) Confinement in Ion Mobility Spectrometry: Apparent Mobilities and Effective Temperatures. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2054-2063. [PMID: 27582119 DOI: 10.1007/s13361-016-1479-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/08/2016] [Accepted: 08/11/2016] [Indexed: 06/06/2023]
Abstract
Ion mobility is a powerful tool for separating and characterizing the structures of ions. Here, a radio-frequency (rf) confining drift cell is used to evaluate the drift times of ions over a broad range of drift field strengths (E/P, V cm-1 Torr-1). The presence of rf potentials radially confines ions and results in excellent ion transmission at low E/P (less than 1 V cm-1 Torr-1), thereby reducing the dependence of ion transmission on the applied drift voltage. Non-linear responses between drift time and reciprocal drift voltages are observed for extremely low E/P and high rf amplitudes. Under these conditions, pseudopotential wells generated by the rf potentials dampen the mobility of ions. The effective potential approximation is used to characterize this mobility dampening behavior, which can be mitigated by adjusting rf amplitudes and electrode dimensions. Using SIMION trajectories and statistical arguments, the effective temperatures of ions in an rf-confining drift cell are evaluated. Results for the doubly charged peptide GRGDS suggest that applied rf potentials can result in a subtle increase (2 K) in effective temperature compared to an electrostatic drift tube. Additionally, simulations of native-like ions of the protein complex avidin suggest that rf potentials have a negligible effect on the effective temperature of these ions. In general, the results of this study suggest that applied rf potentials enable the measurement of drift times at extremely low E/P and that these potentials have negligible effects on ion effective temperature. Graphical Abstract ᅟ.
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Affiliation(s)
- Samuel J Allen
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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42
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Allen SJ, Eaton RM, Bush MF. Analysis of Native-Like Ions Using Structures for Lossless Ion Manipulations. Anal Chem 2016; 88:9118-26. [DOI: 10.1021/acs.analchem.6b02089] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Samuel J. Allen
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Rachel M. Eaton
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
| | - Matthew F. Bush
- University of Washington, Department of Chemistry, Box 351700, Seattle, Washington 98195-1700, United States
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43
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Palamini M, Canciani A, Forneris F. Identifying and Visualizing Macromolecular Flexibility in Structural Biology. Front Mol Biosci 2016; 3:47. [PMID: 27668215 PMCID: PMC5016524 DOI: 10.3389/fmolb.2016.00047] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/22/2016] [Indexed: 12/29/2022] Open
Abstract
Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.
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Affiliation(s)
| | | | - Federico Forneris
- The Armenise-Harvard Laboratory of Structural Biology, Department of Biology and Biotechnology, University of PaviaPavia, Italy
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44
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Benigni P, Marin R, Molano-Arevalo JC, Garabedian A, Wolff JJ, Ridgeway ME, Park MA, Fernandez-Lima F. Towards the Analysis of High Molecular Weight Proteins and Protein complexes using TIMS-MS. INTERNATIONAL JOURNAL FOR ION MOBILITY SPECTROMETRY : OFFICIAL PUBLICATION OF THE INTERNATIONAL SOCIETY FOR ION MOBILITY SPECTROMETRY 2016; 19:95-104. [PMID: 27818614 PMCID: PMC5091298 DOI: 10.1007/s12127-016-0201-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 05/26/2016] [Accepted: 05/29/2016] [Indexed: 01/02/2023]
Abstract
In the present work, we demonstrate the potential and versatility of TIMS for the analysis of proteins, DNA-protein complexes and protein-protein complexes in their native and denatured states. In addition, we show that accurate CCS measurement are possible and in good agreement with previously reported CCS values using other IMS analyzers (<5% difference). The main challenges for the analysis of high mass proteins and protein complexes in the mobility and m/z domain are described. That is, the analysis of high molecular weight systems in their native state may require the use of higher electric fields or a compromise in the TIMS mobility resolution by reducing the bath gas velocity in order to effectively trap at lower electric fields. This is the first report of CCS measurements of high molecular weight biomolecules and biomolecular complexes (~ 150 kDa) using TIMS-MS.
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Affiliation(s)
- Paolo Benigni
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | - Rebecca Marin
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | - Alyssa Garabedian
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
| | | | | | - Melvin A. Park
- Bruker Daltonics, Inc., Billerica, Massachusetts 01821, USA
| | - Francisco Fernandez-Lima
- Department of Chemistry & Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Science Institute, Florida International University, Miami, FL 33199, USA
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45
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Native Mass Spectrometry in Fragment-Based Drug Discovery. Molecules 2016; 21:molecules21080984. [PMID: 27483215 PMCID: PMC6274484 DOI: 10.3390/molecules21080984] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/14/2016] [Accepted: 07/23/2016] [Indexed: 11/17/2022] Open
Abstract
The advent of native mass spectrometry (MS) in 1990 led to the development of new mass spectrometry instrumentation and methodologies for the analysis of noncovalent protein-ligand complexes. Native MS has matured to become a fast, simple, highly sensitive and automatable technique with well-established utility for fragment-based drug discovery (FBDD). Native MS has the capability to directly detect weak ligand binding to proteins, to determine stoichiometry, relative or absolute binding affinities and specificities. Native MS can be used to delineate ligand-binding sites, to elucidate mechanisms of cooperativity and to study the thermodynamics of binding. This review highlights key attributes of native MS for FBDD campaigns.
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Mikhailov VA, Liko I, Mize TH, Bush MF, Benesch JLP, Robinson CV. Infrared Laser Activation of Soluble and Membrane Protein Assemblies in the Gas Phase. Anal Chem 2016; 88:7060-7. [PMID: 27328020 DOI: 10.1021/acs.analchem.6b00645] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Collision-induced dissociation (CID) is the dominant method for probing intact macromolecular complexes in the gas phase by means of mass spectrometry (MS). The energy obtained from collisional activation is dependent on the charge state of the ion and the pressures and potentials within the instrument: these factors limit CID capability. Activation by infrared (IR) laser radiation offers an attractive alternative as the radiation energy absorbed by the ions is charge-state-independent and the intensity and time scale of activation is controlled by a laser source external to the mass spectrometer. Here we implement and apply IR activation, in different irradiation regimes, to study both soluble and membrane protein assemblies. We show that IR activation using high-intensity pulsed lasers is faster than collisional and radiative cooling and requires much lower energy than continuous IR irradiation. We demonstrate that IR activation is an effective means for studying membrane protein assemblies, and liberate an intact V-type ATPase complex from detergent micelles, a result that cannot be achieved by means of CID using standard collision energies. Notably, we find that IR activation can be sufficiently soft to retain specific lipids bound to the complex. We further demonstrate that, by applying a combination of collisional activation, mass selection, and IR activation of the liberated complex, we can elucidate subunit stoichiometry and the masses of specifically bound lipids in a single MS experiment.
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Affiliation(s)
- Victor A Mikhailov
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Idlir Liko
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Todd H Mize
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Matthew F Bush
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, OX1 3QZ, United Kingdom
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Mazhab-Jafari MT, Rubinstein JL. Cryo-EM studies of the structure and dynamics of vacuolar-type ATPases. SCIENCE ADVANCES 2016; 2:e1600725. [PMID: 27532044 PMCID: PMC4985227 DOI: 10.1126/sciadv.1600725] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/15/2016] [Indexed: 06/06/2023]
Abstract
Electron cryomicroscopy (cryo-EM) has significantly advanced our understanding of molecular structure in biology. Recent innovations in both hardware and software have made cryo-EM a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. Cryo-EM has even become the method of choice in some situations where x-ray crystallography and NMR spectroscopy are possible but where cryo-EM can determine structures at higher resolution or with less time or effort. Rotary adenosine triphosphatases (ATPases) are crucial to the maintenance of cellular homeostasis. These enzymes couple the synthesis or hydrolysis of adenosine triphosphate to the use or production of a transmembrane electrochemical ion gradient, respectively. However, the membrane-embedded nature and conformational heterogeneity of intact rotary ATPases have prevented their high-resolution structural analysis to date. Recent application of cryo-EM methods to the different types of rotary ATPase has led to sudden advances in understanding the structure and function of these enzymes, revealing significant conformational heterogeneity and characteristic transmembrane α helices that are highly tilted with respect to the membrane. In this Review, we will discuss what has been learned recently about rotary ATPase structure and function, with a particular focus on the vacuolar-type ATPases.
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Affiliation(s)
- Mohammad T. Mazhab-Jafari
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - John L. Rubinstein
- Molecular Structure and Function Program, The Hospital for Sick Children Research Institute, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
- Department of Biochemistry, The University of Toronto, 1 King’s College Circle, Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, The University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
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48
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Papachristos K, Muench SP, Paci E. Characterization of the flexibility of the peripheral stalk of prokaryotic rotary A-ATPases by atomistic simulations. Proteins 2016; 84:1203-12. [PMID: 27177595 PMCID: PMC4988496 DOI: 10.1002/prot.25066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/03/2016] [Accepted: 05/09/2016] [Indexed: 12/31/2022]
Abstract
Rotary ATPases are involved in numerous physiological processes, with the three distinct types (F/A/V‐ATPases) sharing functional properties and structural features. The basic mechanism involves the counter rotation of two motors, a soluble ATP hydrolyzing/synthesizing domain and a membrane‐embedded ion pump connected through a central rotor axle and a stator complex. Within the A/V‐ATPase family conformational flexibility of the EG stators has been shown to accommodate catalytic cycling and is considered to be important to function. For the A‐ATPase three EG structures have been reported, thought to represent conformational states of the stator during different stages of rotary catalysis. Here we use long, detailed atomistic simulations to show that those structures are conformers explored through thermal fluctuations, but do not represent highly populated states of the EG stator in solution. We show that the coiled coil tail domain has a high persistence length (∼100 nm), but retains the ability to adapt to different conformational states through the presence of two hinge regions. Moreover, the stator network of the related V‐ATPase has been suggested to adapt to subunit interactions in the collar region in addition to the nucleotide occupancy of the catalytic domain. The MD simulations reported here, reinforce this observation showing that the EG stators have enough flexibility to adapt to significantly different structural re‐arrangements and accommodate structural changes in the catalytic domain whilst resisting the large torque generated by catalytic cycling. These results are important to understand the role the stators play in the rotary‐ATPase mechanism. Proteins 2016; 84:1203–1212. © 2016 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Kostas Papachristos
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.,School of Molecular and Cellular Biology, University of Leeds, Leeds, England
| | - Stephen P Muench
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.,School of Biomedical Sciences, University of Leeds, Leeds, England
| | - Emanuele Paci
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, England.,School of Molecular and Cellular Biology, University of Leeds, Leeds, England
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Loo RRO, Loo JA. Salt Bridge Rearrangement (SaBRe) Explains the Dissociation Behavior of Noncovalent Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:975-90. [PMID: 27052739 PMCID: PMC4865452 DOI: 10.1007/s13361-016-1375-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/28/2016] [Accepted: 03/01/2016] [Indexed: 05/11/2023]
Abstract
Native electrospray ionization-mass spectrometry, with gas-phase activation and solution compositions that partially release subcomplexes, can elucidate topologies of macromolecular assemblies. That so much complexity can be preserved in gas-phase assemblies is remarkable, although a long-standing conundrum has been the differences between their gas- and solution-phase decompositions. Collision-induced dissociation of multimeric noncovalent complexes typically distributes products asymmetrically (i.e., by ejecting a single subunit bearing a large percentage of the excess charge). That unexpected behavior has been rationalized as one subunit "unfolding" to depart with more charge. We present an alternative explanation based on heterolytic ion-pair scission and rearrangement, a mechanism that inherently partitions charge asymmetrically. Excessive barriers to dissociation are circumvented in this manner, when local charge rearrangements access a lower-barrier surface. An implication of this ion pair consideration is that stability differences between high- and low-charge state ions usually attributed to Coulomb repulsion may, alternatively, be conveyed by attractive forces from ion pairs (salt bridges) stabilizing low-charge state ions. Should the number of ion pairs be roughly inversely related to charge, symmetric dissociations would be favored from highly charged complexes, as observed. Correlations between a gas-phase protein's size and charge reflect the quantity of restraining ion pairs. Collisionally-facilitated salt bridge rearrangement (SaBRe) may explain unusual size "contractions" seen for some activated, low charge state complexes. That some low-charged multimers preferentially cleave covalent bonds or shed small ions to disrupting noncovalent associations is also explained by greater ion pairing in low charge state complexes. Graphical Abstract ᅟ.
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Affiliation(s)
- Rachel R Ogorzalek Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA.
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50
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Hu B, Yao ZP. Mobility of Proteins in Porous Substrates under Electrospray Ionization Conditions. Anal Chem 2016; 88:5585-9. [DOI: 10.1021/acs.analchem.6b00894] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Bin Hu
- State
Key Laboratory for Chirosciences, Food Safety and Technology Research
Centre and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong
Kong SAR, China
- State
Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation)
and Shenzhen Key Laboratory
of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, 518057, China
| | - Zhong-Ping Yao
- State
Key Laboratory for Chirosciences, Food Safety and Technology Research
Centre and Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong
Kong SAR, China
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules (Yanbian University), Ministry of Education, Yanji, 133002, China
- State
Key Laboratory of Chinese Medicine and Molecular Pharmacology (Incubation)
and Shenzhen Key Laboratory
of Food Biological Safety Control, Shenzhen Research Institute of The Hong Kong Polytechnic University, Shenzhen, 518057, China
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