1
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Fu L, Eakins GS, Carlsen MS, McLuckey SA. Single-Frequency Ion Parking in a Digital 3D Quadrupole Ion Trap. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 503:117282. [PMID: 39006163 PMCID: PMC11238766 DOI: 10.1016/j.ijms.2024.117282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Single-frequency ion parking, a useful technique in electrospray mass spectrometry (ESI-MS), involves gas-phase charge-reduction ion/ion reactions in an electrodynamic ion trap in conjunction with the application of a supplementary oscillatory voltage to selectively inhibit the reaction rate of an ion of interest. The ion parking process provides a means for limiting the extent of charge reduction in a controlled fashion and allows for ions distributed over a range of charge states to be concentrated into fewer charge states (a single charge state under optimal conditions). As charge reduction inherently leads to an increase in the mass-to-charge (m/z) ratio of the ions, it is important that the means for storing and analyzing ions be able to accommodate ions of high m/z ratios. The so-called 'digital ion trap' (DIT), which uses a digital waveform as the trapping RF, has been demonstrated to be well-suited for the analysis of high m/z ions by taking advantage of its ability to manipulate the waveform frequency. In this study, the feasibility of ion parking in a 3D quadrupole ion trap operated as a DIT using a slow-amplitude single-frequency sine-wave for selective inhibition of an ion/ion reaction is demonstrated. A recently described model that describes ion parking has been adjusted for the DIT case and is used to interpret experimental data for proteins ranging in mass from 8600 Da to 467,000 Da.
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Affiliation(s)
- Liangxuan Fu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
| | - Gregory S Eakins
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
| | - Mark S Carlsen
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, USA 47907-2084
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2
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Kumar S, Stover L, Wang L, Bahramimoghaddam H, Zhou M, Russell DH, Laganowsky A. Native mass spectrometry of membrane protein-lipid interactions in different detergent environments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601044. [PMID: 38979331 PMCID: PMC11230385 DOI: 10.1101/2024.06.27.601044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Native mass spectrometry (MS) is revealing the role of specific lipids in modulating membrane protein structure and function. Membrane proteins solubilized in detergents are often introduced into the mass spectrometer; however, commonly used detergents for structural studies, such as dodecylmaltoside, tend to generate highly charged ions, leading to protein unfolding, thereby diminishing their utility for characterizing protein-lipid interactions. Thus, there is a critical need to develop approaches to investigate protein-lipid interactions in different detergents. Here, we demonstrate how charge-reducing molecules, such as spermine and trimethylamine-N-oxide, enable characterization of lipid binding to the bacterial water channel (AqpZ) and ammonia channel (AmtB) in complex with regulatory protein GlnK in different detergent environments. We find protein-lipid interactions are not only protein-dependent but can also be influenced by the detergent and type of charge-reducing molecule. AqpZ-lipid interactions are enhanced in LDAO (n-dodecyl-N,N-dimethylamine-N-oxide), whereas the interaction of AmtB-GlnK with lipids is comparable among different detergents. A fluorescent lipid binding assay also shows detergent dependence for AqpZ-lipid interactions, consistent with results from native MS. Taken together, native MS will play a pivotal role in establishing optimal experimental parameters that will be invaluable for various applications, such as drug discovery, as well as biochemical and structural investigations.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lie Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | | | - Ming Zhou
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David H. Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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3
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Pizzala NJ, Bhanot JS, Carrick IJ, Dziekonski ET, McLuckey SA. Ion parking in native mass spectrometry. Analyst 2024; 149:2966-2977. [PMID: 38600834 PMCID: PMC11089522 DOI: 10.1039/d4an00242c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
A forced, damped harmonic oscillator model for gas-phase ion parking using single-frequency resonance excitation is described and applied to high-mass ions of relevance to native mass spectrometry. Experimental data are provided to illustrate key findings revealed by the modelling. These include: (i) ion secular frequency spacings between adjacent charge states of a given protein are essentially constant and decrease with the mass of the protein (ii) the mechanism for ion parking of high mass ions is the separation of the ion clouds of the oppositely-charged ions with much less influence from an increase in the relative ion velocity due to resonance excitation, (iii) the size of the parked ion cloud ultimately limits ion parking at high m/z ratio, and (iv) the extent of ion parking of off-target ions is highly sensitive to the bath gas pressure in the ion trap. The model is applied to ions of 17 kDa, 467 kDa, and 2 MDa while experimental data are also provided for ions of horse skeletal muscle myoglobin (≈17 kDa) and β-galactosidase (≈467 kDa). The model predicts and data show that it is possible to effect ion parking on a 17 kDa protein to the 1+ charge state under trapping conditions that are readily accessible with commercially available ion traps. It is also possible to park β-galactosidase efficiently to a roughly equivalent m/z ratio (i.e., the 26+ charge state) under the same trapping conditions. However, as charge states decrease, analyte ion cloud sizes become too large to allow for efficient ion trapping. The model allows for a semi-quantitative prediction of ion trapping performance as a function of ion trapping, resonance excitation, and pressure conditions.
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Affiliation(s)
- Nicolas J Pizzala
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Jay S Bhanot
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Ian J Carrick
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Eric T Dziekonski
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, USA.
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4
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Stutzman JR, Hutchins PD, Bain RM. Online Bipolar Dual Spray for the Charge State Reduction and Characterization of Complex Synthetic Polymers. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2840-2848. [PMID: 38053368 DOI: 10.1021/jasms.3c00333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Charge reduction mass spectrometry (CR/MS) hyphenated to liquid chromatography (LC) couples liquid-phase compound separation and mass spectral decompression to resolve and characterize multicomponent systems. LC/CR/MS has proven to be effective for complex mixture analysis, particularly synthetic polymers. A newer charge manipulation approach called bipolar dual spray has previously been demonstrated to reduce the observed charge state distribution of ammoniated polyethene glycol. In this approach, two electrospray emitters, in close proximity and of opposite polarity, fuse droplets from their electrospray plumes, which allows the subsequent chemistry. In this work, we investigate the ability of bipolar dual spray to reduce the charge of synthetic polyols, thereby simplifying complex mixture analysis and generating new compositional information only available through the coupling of charge reduction with LC/MS analysis. This work also represents the first demonstration of online charge reduction via dual spray. Polyethylene glycol (PEG) 7.2K subjected to LC/MS with dual spray reduced the average charge state from 8.2+ to 4.4+. LC/MS with dual spray was also applied to the characterization of an end-group-modified PEG 10K (i.e., aminated) containing several reaction impurities. This approach allowed for the identification of low-level starting material, tosylated PEG, and PEG mono(amine), where both LC/MS and direct infusion dual spray did not detect the impurities. Overall, the results demonstrated that bipolar dual spray can be incorporated into an LC/MS analysis and affords the ability to reduce the charge state distribution of PEG cations, decompress the m/z axis, lower spectra complexity, and enable/simplify data interpretation.
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Affiliation(s)
- John R Stutzman
- Analytical Sciences, Dow Inc., Midland, Michigan 48640, United States
| | - Paul D Hutchins
- Analytical Sciences, Dow Inc., Midland, Michigan 48640, United States
| | - Ryan M Bain
- Analytical Sciences, Dow Inc., Midland, Michigan 48640, United States
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5
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van Schaick G, Wuhrer M, Domínguez-Vega E. Dopant-enriched nitrogen gas to boost ionization of glycoproteins analyzed with native liquid chromatography coupled to nano-electrospray ionization. Anal Chim Acta 2023; 1265:341271. [PMID: 37230565 DOI: 10.1016/j.aca.2023.341271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/27/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Proteins carry a plethora of post-translational modifications (PTMs), such as glycosylation or phosphorylation, which may affect stability and activity. Analytical strategies are needed to investigate these PTMs in their native state to determine the link between structure and function. The coupling of native separation techniques with mass spectrometry (MS) has emerged as a powerful tool for in-depth protein characterization. Yet obtaining high ionization efficiency still can be challenging. Here, we explored the potential of dopant-enriched nitrogen (DEN) gas to improve nano-electrospray ionization (nano-ESI)-MS of native proteins after anion exchange chromatography. The dopant gas was enriched with different dopants (acetonitrile, methanol, and isopropanol) and the effects were compared with the use of solely nitrogen gas for six proteins covering a wide range of physicochemical properties. The use of DEN gas resulted generally in lower charge states, independent of the selected dopant. Moreover, less adduct formation was observed, particularly for the acetonitrile-enriched nitrogen gas. Importantly, striking differences in MS signal intensity and spectral quality were observed for extensively glycosylated proteins, where isopropanol- and methanol-enriched nitrogen appeared to be most beneficial. Altogether, the use of DEN gas improved nano-ESI of native glycoproteins and increased spectral quality for highly glycosylated proteins that normally suffer from low ionization efficiency.
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Affiliation(s)
- Guusje van Schaick
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Manfred Wuhrer
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands
| | - Elena Domínguez-Vega
- Leiden University Medical Center, Center for Proteomics and Metabolomics, Leiden, the Netherlands.
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6
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Lin CW, Oney-Hawthorne SD, Kuo ST, Barondeau DP, Russell DH. Mechanistic Insights into IscU Conformation Regulation for Fe-S Cluster Biogenesis Revealed by Variable Temperature Electrospray Ionization Native Ion Mobility Mass Spectrometry. Biochemistry 2022; 61:2733-2741. [PMID: 36351081 PMCID: PMC10009881 DOI: 10.1021/acs.biochem.2c00429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Iron-sulfur (Fe-S) cluster (ISC) cofactors are required for the function of many critical cellular processes. In the ISC Fe-S cluster biosynthetic pathway, IscU assembles Fe-S cluster intermediates from iron, electrons, and inorganic sulfur, which is provided by the cysteine desulfurase enzyme IscS. IscU also binds to Zn, which mimics and competes for binding with the Fe-S cluster. Crystallographic and nuclear magnetic resonance spectroscopic studies reveal that IscU is a metamorphic protein that exists in multiple conformational states, which include at least a structured form and a disordered form. The structured form of IscU is favored by metal binding and is stable in a narrow temperature range, undergoing both cold and hot denaturation. Interestingly, the form of IscU that binds IscS and functions in Fe-S cluster assembly remains controversial. Here, results from variable temperature electrospray ionization (vT-ESI) native ion mobility mass spectrometry (nIM-MS) establish that IscU exists in structured, intermediate, and disordered forms that rearrange to more extended conformations at higher temperatures. A comparison of Zn-IscU and apo-IscU reveals that Zn(II) binding attenuates the cold/heat denaturation of IscU, promotes refolding of IscU, favors the structured and intermediate conformations, and inhibits the disordered high charge states. Overall, these findings provide a structural rationalization for the role of Zn(II) in stabilizing IscU conformations and IscS in altering the IscU active site to prepare for Zn(II) release and cluster synthesis. This work highlights how vT-ESI-nIM-MS can be applied as a powerful tool in mechanistic enzymology by providing details of relationships among temperature, protein conformations, and ligand/protein binding.
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Affiliation(s)
- Cheng-Wei Lin
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Shelby D Oney-Hawthorne
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - Syuan-Ting Kuo
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David P Barondeau
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A & M University, College Station, Texas 77843, United States
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7
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Marty MT. Fundamentals: How Do We Calculate Mass, Error, and Uncertainty in Native Mass Spectrometry? JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1807-1812. [PMID: 36130030 DOI: 10.1021/jasms.2c00218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry (MS) is uniquely powerful for measuring the mass of intact proteins and other biomolecules. New applications have expanded intact protein analysis into biopharmaceuticals, native MS, and top-down proteomics, all of which have driven the need for more automated data-processing pipelines. However, key metrics in the field are often not precisely defined. For example, there are different views on how to calculate uncertainty from spectra. This Critical Insight will explore the different definitions of mass, error, and uncertainty. It will discuss situations where different definitions may be more suitable and provide recommendations for best practices. Targeting both beginners and experts, the goal of the discussion is to provide a common foundation of terminology, enhance statistical rigor, and improve automation of data analysis.
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Affiliation(s)
- Michael T Marty
- Department of Chemistry and Biochemistry and Bio5 Institute, University of Arizona, Tucson, Arizona 85721, United States
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8
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Kumar S, Zhu Y, Stover L, Laganowsky A. Step toward Probing the Nonannular Belt of Membrane Proteins. Anal Chem 2022; 94:13906-13912. [PMID: 36170465 DOI: 10.1021/acs.analchem.2c02811] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Integral membrane proteins are embedded in the biological membrane, where they carry out numerous biological processes. Although lipids present in the membrane are crucial for membrane protein function, it remains difficult to characterize many lipid binding events to membrane proteins, such as those that form the annular belt. Here, we use native mass spectrometry along with the charge-reducing properties of trimethylamine N-oxide (TMAO) to characterize a large number of lipid binding events to the bacterial ammonia channel (AmtB). In the absence of TMAO, significant peak overlap between neighboring charge states is observed, resulting in erroneous abundances for different molecular species. With the addition of TMAO, the weighted average charge state (Zavg) was decreased. In addition, the increased spacing between nearby charge states enabled a higher number of lipid binding species to be observed while minimizing mass spectral peak overlap. These conditions helped us to determine the equilibrium binding constants (Kd) for up to 16 lipid binding events. The binding constants for the first few lipid binding events display the highest affinity, whereas the binding constants for higher lipid binding events converge to a similar value. These findings suggest a transition from nonannular to annular lipid binding to AmtB.
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Affiliation(s)
- Smriti Kumar
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yun Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lauren Stover
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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9
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Snyder DT, Harvey SR, Wysocki VH. Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool. Chem Rev 2022; 122:7442-7487. [PMID: 34726898 PMCID: PMC9282826 DOI: 10.1021/acs.chemrev.1c00309] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Native mass spectrometry (nMS) is evolving into a workhorse for structural biology. The plethora of online and offline preparation, separation, and purification methods as well as numerous ionization techniques combined with powerful new hybrid ion mobility and mass spectrometry systems has illustrated the great potential of nMS for structural biology. Fundamental to the progression of nMS has been the development of novel activation methods for dissociating proteins and protein complexes to deduce primary, secondary, tertiary, and quaternary structure through the combined use of multiple MS/MS technologies. This review highlights the key features and advantages of surface collisions (surface-induced dissociation, SID) for probing the connectivity of subunits within protein and nucleoprotein complexes and, in particular, for solving protein structure in conjunction with complementary techniques such as cryo-EM and computational modeling. Several case studies highlight the significant role SID, and more generally nMS, will play in structural elucidation of biological assemblies in the future as the technology becomes more widely adopted. Cases are presented where SID agrees with solved crystal or cryoEM structures or provides connectivity maps that are otherwise inaccessible by "gold standard" structural biology techniques.
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Affiliation(s)
- Dalton T. Snyder
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210,Corresponding author:
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10
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Studying protein structure and function by native separation–mass spectrometry. Nat Rev Chem 2022; 6:215-231. [PMID: 37117432 DOI: 10.1038/s41570-021-00353-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 12/13/2022]
Abstract
Alterations in protein structure may have profound effects on biological function. Analytical techniques that permit characterization of proteins while maintaining their conformational and functional state are crucial for studying changes in the higher order structure of proteins and for establishing structure-function relationships. Coupling of native protein separations with mass spectrometry is emerging rapidly as a powerful approach to study these aspects in a reliable, fast and straightforward way. This Review presents the available native separation modes for proteins, covers practical considerations on the hyphenation of these separations with mass spectrometry and highlights the involvement of affinity-based separations to simultaneously obtain structural and functional information of proteins. The impact of these approaches is emphasized by selected applications addressing biomedical and biopharmaceutical research questions.
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11
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Newsome GA, Cleland TP. In-Line Dopant Generation for Atmospheric Pressure Ionization Mass Spectrometry. Anal Chem 2021; 93:13527-13533. [PMID: 34590816 DOI: 10.1021/acs.analchem.1c02400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A concentric trace gas permeation tube that diffuses chemical reagents to a central carrier gas stream is used to drive chemical reaction pathways and influence gas-phase chemistry for a variety of atmospheric pressure ionization sources for mass spectrometry. Tunable permeation through the reservoir-jacketed polymer membrane is triggered by the heated gas moving through the tube, evaporating the dopant into a sheath dry gas or into a sample stream in room air without diluting the analyte concentration. The permeator is used to add dopants to an electrospray plume for analyte ion charge reduction and to perform hydrogen-deuterium exchange on biomolecules in different spray conditions. Dopants are also added to atmospheric pressure chemical ionization to favor the ionization of select components of diesel fuel. Atmospheric pressure photoionization is performed with the permeation tube in line with tubing transporting sample headspace to an enclosed discharge lamp. Toluene dopant from the permeator increases the proton transfer and charge exchange signal from clove oil and mothballs many times without exposing the laboratory to reagent fumes. Water permeation is also used to humidify the sample gas stream.
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Affiliation(s)
- G Asher Newsome
- Smithsonian Museum Conservation Institute, Suitland, Maryland 20746, United States
| | - Timothy P Cleland
- Smithsonian Museum Conservation Institute, Suitland, Maryland 20746, United States
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12
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Affiliation(s)
- James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Guozhi Zhang
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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13
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Kosuge H, Nakakido M, Nagatoishi S, Fukuda T, Bando Y, Ohnuma SI, Tsumoto K. Proteomic identification and validation of novel interactions of the putative tumor suppressor PRELP with membrane proteins including IGFI-R and p75NTR. J Biol Chem 2021; 296:100278. [PMID: 33428936 PMCID: PMC7948961 DOI: 10.1016/j.jbc.2021.100278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 01/19/2023] Open
Abstract
Proline and arginine-rich end leucine-rich repeat protein (PRELP) is a member of the small leucine-rich repeat proteoglycans (SLRPs) family. Levels of PRELP mRNA are downregulated in many types of cancer, and PRELP has been reported to have suppressive effects on tumor cell growth, although the molecular mechanism has yet to be fully elucidated. Given that other SLRPs regulate signaling pathways through interactions with various membrane proteins, we reasoned that PRELP likely interacts with membrane proteins to maintain cellular homeostasis. To identify membrane proteins that interact with PRELP, we carried out coimmunoprecipitation coupled with mass spectrometry (CoIP-MS). We prepared membrane fractions from Expi293 cells transfected to overexpress FLAG-tagged PRELP or control cells and analyzed samples precipitated with anti-FLAG antibody by mass spectrometry. Comparison of membrane proteins in each sample identified several that seem to interact with PRELP; among them, we noted two growth factor receptors, insulin-like growth factor I receptor (IGFI-R) and low-affinity nerve growth factor receptor (p75NTR), interactions with which might help to explain PRELP's links to cancer. We demonstrated that PRELP directly binds to extracellular domains of these two growth factor receptors with low micromolar affinities by surface plasmon resonance analysis using recombinant proteins. Furthermore, cell-based analysis using recombinant PRELP protein showed that PRELP suppressed cell growth and affected cell morphology of A549 lung carcinoma cells, also at micromolar concentration. These results suggest that PRELP regulates cellular functions through interactions with IGFI-R and p75NTR and provide a broader set of candidate partners for further exploration.
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Affiliation(s)
- Hirofumi Kosuge
- School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Makoto Nakakido
- School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Satoru Nagatoishi
- The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | | | - Shin-Ichi Ohnuma
- The Institute of Ophthalmology, University College London, London, United Kingdom
| | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, Tokyo, Japan; The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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14
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Yan Y, Xing T, Wang S, Li N. Versatile, Sensitive, and Robust Native LC-MS Platform for Intact Mass Analysis of Protein Drugs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:2171-2179. [PMID: 32865416 DOI: 10.1021/jasms.0c00277] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Over the past several years, hyphenation of native (nondenaturing) liquid chromatography (nLC) methods, such as size exclusion chromatography (SEC), ion exchange chromatography (IEX), and hydrophobic interaction chromatography (HIC) with mass spectrometry (MS) have become increasingly popular to study the size, charge, and structural heterogeneity of protein drug products. Despite the availability of a wide variety of nLC-MS methods, an integrated platform that can accommodate different applications is still lacking. In this study, we described the development of a versatile, sensitive, and robust nLC-MS platform that can support various nLC-MS applications. In particular, the developed platform can tolerate a wide range of LC flow rates and high salt concentrations, which are critical for accommodating different nLC methods. In addition, a dopant-modified desolvation gas can be readily applied on this platform to achieve online charge-reduction native MS, which improves the characterization of both heterogeneous and labile biomolecules. Finally, we demonstrated that this nLC-MS platform is highly sensitive and robust and can be routinely applied in protein drug characterization.
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Affiliation(s)
- Yuetian Yan
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Tao Xing
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Shunhai Wang
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry Group, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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15
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Yin Z, Huang J, Miao H, Hu O, Li H. High-Pressure Electrospray Ionization Yields Supercharged Protein Complexes from Native Solutions While Preserving Noncovalent Interactions. Anal Chem 2020; 92:12312-12321. [DOI: 10.1021/acs.analchem.0c01965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Zhibin Yin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hui Miao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ou Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Huilin Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China
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16
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Lyu J, Liu Y, McCabe JW, Schrecke S, Fang L, Russell DH, Laganowsky A. Discovery of Potent Charge-Reducing Molecules for Native Ion Mobility Mass Spectrometry Studies. Anal Chem 2020; 92:11242-11249. [PMID: 32672445 DOI: 10.1021/acs.analchem.0c01826] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
There is growing interest in the characterization of protein complexes and their interactions with ligands using native ion mobility mass spectrometry. A particular challenge, especially for membrane proteins, is preserving noncovalent interactions and maintaining native-like structures. Different approaches have been developed to minimize activation of protein complexes by manipulating charge on protein complexes in solution and the gas-phase. Here, we report the utility of polyamines that have exceptionally high charge-reducing potencies with some molecules requiring 5-fold less than trimethylamine oxide to elicit the same effect. The charge-reducing molecules do not adduct to membrane protein complexes and are also compatible with ion-mobility mass spectrometry, paving the way for improved methods of charge reduction.
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Affiliation(s)
- Jixing Lyu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Yang Liu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jacob W McCabe
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Samantha Schrecke
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Lei Fang
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - David H Russell
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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17
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Thinius M, Polaczek C, Langner M, Bräkling S, Haack A, Kersten H, Benter T. Charge Retention/Charge Depletion in ESI-MS: Experimental Evidence. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:773-784. [PMID: 32150403 DOI: 10.1021/jasms.9b00044] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The effects of liquid and gas phase additives (chemical modifiers) on the ion signal distribution for Substance P (SP), recorded with a nanoelectrospray setup, are evaluated. Depletion of the higher charge state of Substance P ([SP+3H]3+) is observed with polar protic gas phase modifiers. This is attributed to their ability to form larger hydrogen-bonded clusters, whose proton affinity increases with cluster size. These clusters are able to deprotonate the higher charge state. "Supercharging agents" (SCAs) as well as aprotic polar gas phase modifiers, which promote the retention of the higher charge state of Substance P, do not form such large clusters under the given conditions and are therefore not able to deprotonate Substance P. Both SCAs and aprotic modifiers form clusters with the higher charge state, leading to stabilization of the charge. Whereas supercharging agents have low vapor pressures and are therefore enriched in late-stage electrospray droplets, the gas phase modifiers are volatile organic solvents. Collision induced dissociation experiments revealed that the addition of a modifier significantly delays the droplet evaporation and ion release process. This indicates that the droplet takes up the gas phase modifier to a certain extent (accommodation). Depending on the modifier's properties either charge depletion or retention may eventually be promoted.
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Affiliation(s)
- Marco Thinius
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
| | - Christine Polaczek
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
| | - Markus Langner
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
| | - Steffen Bräkling
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
| | - Alexander Haack
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
| | - Hendrik Kersten
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
| | - Thorsten Benter
- Department of Physical and Theoretical Chemistry, University of Wuppertal, Gauss Str. 20, 42119 Wuppertal, Germany
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18
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Stiving AQ, Jones BJ, Ujma J, Giles K, Wysocki VH. Collision Cross Sections of Charge-Reduced Proteins and Protein Complexes: A Database for Collision Cross Section Calibration. Anal Chem 2020; 92:4475-4483. [PMID: 32048834 PMCID: PMC7170229 DOI: 10.1021/acs.analchem.9b05519] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The use of charge-reducing reagents to generate lower-charge ions has gained popularity in the field of native mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS). This is because the lower number of charged sites decreases the propensity for Coulombic repulsions and unfolding/restructuring, helping to preserve the native-like structure. Furthermore, lowering the charge state consequently increases the mass-to-charge values (m/z), effectively increasing spacing between signals originating from small mass differences, such as different proteoforms or protein-drug complexes. IM-MS yields collision cross section (CCS, Ω) values that provide information about the three-dimensional structure of the ion. Traveling wave IM (TWIM) is an established and expanding technique within the native MS field. TWIM measurements require CCS calibration, which is achieved via the use of standard species of known CCS. Current databases for native-like proteins and protein complexes provide CCS values obtained using normal (i.e., non-charge-reducing) conditions. Herein, we explored the validity of using "normal" charge calibrants to calibrate for charge-reduced proteins and show cases where it is not appropriate. Using a custom linear field drift cell that enables the determination of ion mobilities from "first principles", we directly determined CCS values for 19 protein calibrant species under three solution conditions (yielding a broad range of charge states) and two drift gases. This has established a database of CCS and reduced-mobility (K0) values, along with their associated uncertainties, for proteins and protein complexes over a large m/z range. TWIM validation of this database shows improved accuracy over existing methods in calibrating CCS values for charge-reduced proteins.
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Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Benjamin J. Jones
- Department of Chemistry and Biochemistry
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
| | - Jakub Ujma
- Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Kevin Giles
- Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry
- Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH, USA
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19
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Martin LM, Konermann L. Enhancing Protein Electrospray Charge States by Multivalent Metal Ions: Mechanistic Insights from MD Simulations and Mass Spectrometry Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:25-33. [PMID: 32881517 DOI: 10.1021/jasms.9b00027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The structure and reactivity of electrosprayed protein ions is governed by their net charge. Native proteins in non-denaturing aqueous solutions produce low charge states. More highly charged ions are formed when electrospraying proteins that are unfolded and/or exposed to organic supercharging agents. Numerous studies have explored the electrospray process under these various conditions. One phenomenon that has received surprisingly little attention is the charge enhancement caused by multivalent metal ions such as La3+ when electrospraying proteins out of non-denaturing solutions. Here, we conducted mass spectrometry and ion mobility spectrometry experiments, in combination with molecular dynamics (MD) simulations, to uncover the mechanistic basis of this charge enhancement. MD simulations of aqueous ESI droplets reproduced the experimental observation that La3+ boosts protein charge states relative to monovalent metals (e.g., Na+). The simulations showed that gaseous proteins were released by solvent evaporation to dryness, consistent with the charged residue model. Metal ion ejection kept the shrinking droplets close to the Rayleigh limit until ∼99% of the solvent had left. For droplets charged with Na+, metal adduction during the final stage of solvent evaporation produced low protein charge states. Droplets containing La3+ showed a very different behavior. The trivalent nature of La3+ favored adduction to the protein at a very early stage, when most of the solvent had not evaporated yet. This irreversible binding via multidentate contacts suppressed La3+ ejection from the vanishing droplets, such that the resulting gaseous proteins carried significantly more charge. Our results illustrate that MD simulations are suitable for uncovering intricate aspects of electrospray mechanisms, paving the way toward an atomistic understanding of mass spectrometry based analytical workflows.
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Affiliation(s)
- Leanne M Martin
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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20
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Javanshad R, Maser TL, Honarvar E, Venter AR. The Addition of Polar Organic Solvent Vapors During the Analysis of Proteins by DESI-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2571-2575. [PMID: 31758521 DOI: 10.1007/s13361-019-02345-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 06/10/2023]
Abstract
Exposure of electrospray droplets to organic vapors was shown to dramatically reduce alkali-metal adduction on protein ions and shift protein charge states. Since DESI-MS is affected by similar adduct species as ESI-MS and shares similar ionization mechanisms, polar organic vapor additives should likewise also improve the DESI-MS analysis of proteins. Here the DESI spray was exposed to a variety of polar organic vapor additives. Head space vapors of polar organic solvents were entrained in nitrogen gas and delivered to the atmosphere inside a semi-enclosed plastic enclosure surrounding the spray plume. The vapors of acetone, acetonitrile, ethyl acetate, methanol, and water were investigated. Vapor dependent effects were observed with respect to changes in protein charge state distributions and signal intensities. With ethyl acetate vapor addition, the signal intensities of all proteins investigated were significantly increased, including proteins larger than 25 kDa such as carbonic anhydrase II and bovine serum albumin.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Tara L Maser
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Elahe Honarvar
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, 49008-5413, USA.
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21
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Patrick JW, Laganowsky A. Generation of Charge-Reduced Ions of Membrane Protein Complexes for Native Ion Mobility Mass Spectrometry Studies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:886-892. [PMID: 30887461 PMCID: PMC6504596 DOI: 10.1007/s13361-019-02187-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/27/2019] [Accepted: 03/05/2019] [Indexed: 05/15/2023]
Abstract
Recent advances in native mass spectrometry (MS) have enabled the elucidation of how small molecule binding to membrane proteins modulates their structure and function. The protein-stabilizing osmolyte, trimethylamine oxide (TMAO), exhibits attractive properties for native MS studies. Here, we report significant charge reduction, nearly threefold, for three membrane protein complexes in the presence of this osmolyte without compromising mass spectral resolution. TMAO improves the ability to resolve individual lipid-binding events to the ammonia channel (AmtB) by over 200% compared to typical native conditions. The generation of ions with compact structure and access to a larger number of lipid-binding events through the incorporation of TMAO increases the utility of IM-MS for structural biology studies. Graphical Abstract.
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Affiliation(s)
- John W Patrick
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA
- Janssen Research & Development, 1400 Mckean Road, Spring House, PA, 19477, USA
| | - Arthur Laganowsky
- Department of Chemistry, Texas A&M University, College Station, TX, 77842, USA.
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22
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Abou-Elwafa Abdallah M, Nguyen KH, Ebele AJ, Atia NN, Ali HRH, Harrad S. A single run, rapid polarity switching method for determination of 30 pharmaceuticals and personal care products in waste water using Q-Exactive Orbitrap high resolution accurate mass spectrometry. J Chromatogr A 2019; 1588:68-76. [DOI: 10.1016/j.chroma.2018.12.033] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 08/09/2018] [Accepted: 12/16/2018] [Indexed: 11/26/2022]
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23
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Gavriilidou AFM, Hunziker H, Mayer D, Vuckovic Z, Veprintsev DB, Zenobi R. Insights into the Basal Activity and Activation Mechanism of the β1 Adrenergic Receptor Using Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:529-537. [PMID: 30511235 DOI: 10.1007/s13361-018-2110-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/01/2018] [Accepted: 11/08/2018] [Indexed: 06/09/2023]
Abstract
In the absence of orthosteric ligands, most G protein-coupled receptors (GPCRs) exist in an equilibrium of different conformational states. This equilibrium is shifted by an agonist towards the active state or by an inverse agonist towards the inactive state. The basal activity of the receptor, and its ability to activate intracellular signaling pathways, is defined by the probability that a fraction of the receptor adopts the active state in the absence of ligand. Despite breakthroughs in native MS of membrane proteins, GPCR-transducing complexes have not been studied by this approach until very recently. Here, we investigated different conformational states of the turkey β1 adrenergic receptor (tβ1AR) in complex with two transducing partners: a G protein mimicking nanobody, Nb80, and an engineered truncated Gs protein (miniGs), in the presence of the full agonist isoprenaline by native MS. Interestingly, complex formation with both transducing partners was also observed in the absence of agonist, and allowed us to quantify basal activity of tβ1AR. We followed the stepwise disassembly of the transducing complexes by increasing the concentration of the inverse agonist S32212 in the presence of a constant concentration of isoprenaline. This allowed us to determine the relative binding affinity of S32212 in comparison to isoprenaline by native MS. Our approach provides a fast and sensitive way to detect complexes, study their stability in the presence of different ligands, and determine relative ligand affinities. Native mass spectrometry thus has the potential to become a useful tool to screen for orthosteric and allosteric GPCR drugs. Graphical Abstract.
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Affiliation(s)
- Agni F M Gavriilidou
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
- OMass Technologies Ltd The Schrodinger Building, Heatly Road, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Hanna Hunziker
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Daniel Mayer
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Ziva Vuckovic
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.
- Department of Biology, ETH Zurich, Zurich, Switzerland.
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
- School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
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24
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Wang S, Xing T, Liu AP, He Z, Yan Y, Daly TJ, Li N. Simple Approach for Improved LC-MS Analysis of Protein Biopharmaceuticals via Modification of Desolvation Gas. Anal Chem 2019; 91:3156-3162. [PMID: 30682238 DOI: 10.1021/acs.analchem.8b05846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
LC-MS based analysis of protein biopharmaceuticals could benefit from improved data quality, which can subsequently lead to improved drug characterization with higher confidence and less ambiguity. In this study, we created a simple device to modify the desolvation gas on a Q-Exactive mass spectrometer and to demonstrate the utility in improving both peptide mapping analysis and intact mass analysis, the two most routinely and widely applied LC-MS techniques in protein biopharmaceutical characterization. By modifying the desolvation gas with acid vapor from propionic acid (PA) and isopropanol (IPA), the ion suppression effects from trifluoroacetic acid (TFA) in a typical peptide mapping method can be effectively mitigated, thus leading to improved MS sensitivity. By modifying the desolvation gas with base vapor from triethylamine (TEA), the charge reduction effect can be achieved and utilized to improve the spectral quality from intact mass analysis of protein biopharmaceuticals. The approach and device described in this work suggests a low-cost and practical solution to improve the LC-MS characterization of protein biopharmaceuticals, which has the potential to be widely implemented in biopharmaceutical analytical laboratories.
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Affiliation(s)
- Shunhai Wang
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Tao Xing
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Anita P Liu
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Zehong He
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Yuetian Yan
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Thomas J Daly
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
| | - Ning Li
- Analytical Chemistry Group , Regeneron Pharmaceuticals Inc. , 777 Old Saw Mill River Road , Tarrytown , New York 10591-6707 , United States
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25
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Gault J, Lianoudaki D, Kaldmäe M, Kronqvist N, Rising A, Johansson J, Lohkamp B, Laín S, Allison TM, Lane DP, Marklund EG, Landreh M. Mass Spectrometry Reveals the Direct Action of a Chemical Chaperone. J Phys Chem Lett 2018; 9:4082-4086. [PMID: 29975538 DOI: 10.1021/acs.jpclett.8b01817] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Despite their fundamental biological importance and therapeutic potential, the interactions between chemical chaperones and proteins remain difficult to capture due to their transient and nonspecific nature. Using a simple mass spectrometric assay, we are able to follow the interactions between proteins and the chemical chaperone trimethylamine- N-oxide (TMAO). In this manner, we directly observe that the counteraction of TMAO and the denaturant urea is driven by the exclusion of TMAO from the protein surface, whereas the surfactant lauryl dimethylamine- N-oxide cannot be displaced. Our results clearly demonstrate a direct chaperoning mechanism for TMAO, corroborating extensive computational studies, and pave the way for the use of nondenaturing mass spectrometry and related techniques to study chemical chaperones in molecular detail.
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Affiliation(s)
- Joseph Gault
- Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
| | - Danai Lianoudaki
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , Tomtebodavägen 23A , 171 65 Stockholm , Sweden
| | - Margit Kaldmäe
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , Tomtebodavägen 23A , 171 65 Stockholm , Sweden
| | - Nina Kronqvist
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society (NVS) , Karolinska Institutet , 141 83 Huddinge , Sweden
| | - Anna Rising
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society (NVS) , Karolinska Institutet , 141 83 Huddinge , Sweden
- Swedish University of Agricultural Sciences, Dept of Anatomy, Physiology and Biochemistry, Box 7011 , 750 07 Uppsala , Sweden
| | - Jan Johansson
- Division for Neurogeriatrics, Department of Neurobiology, Care Sciences and Society (NVS) , Karolinska Institutet , 141 83 Huddinge , Sweden
| | - Bernhard Lohkamp
- Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Solnavägen 9 , 171 77 Stockholm , Sweden
| | - Sonia Laín
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , Tomtebodavägen 23A , 171 65 Stockholm , Sweden
| | - Timothy M Allison
- Biomolecular Interaction Centre and School of Physical and Chemical Sciences , University of Canterbury , Christchurch 8140 , New Zealand
| | - David P Lane
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , Tomtebodavägen 23A , 171 65 Stockholm , Sweden
| | - Erik G Marklund
- Department of Chemistry - BMC , Uppsala University , Box 576, 751 23 Uppsala , Sweden
| | - Michael Landreh
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , Tomtebodavägen 23A , 171 65 Stockholm , Sweden
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26
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De P, McNeil M, Xia M, Boot CM, Hesser DC, Denef K, Rithner C, Sours T, Dobos KM, Hoft D, Chatterjee D. Structural determinants in a glucose-containing lipopolysaccharide from Mycobacterium tuberculosis critical for inducing a subset of protective T cells. J Biol Chem 2018; 293:9706-9717. [PMID: 29716995 PMCID: PMC6016469 DOI: 10.1074/jbc.ra118.002582] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/30/2018] [Indexed: 12/22/2022] Open
Abstract
Mycobacteria synthesize intracellular, 6-O-methylglucose–containing lipopolysaccharides (mGLPs) proposed to modulate bacterial fatty acid metabolism. Recently, it has been shown that Mycobacterium tuberculosis mGLP specifically induces a specific subset of protective γ9δ2 T cells. Mild base treatment, which removes all the base-labile groups, reduces the specific activity of mGLP required for induction of these T cells, suggesting that acylation of the saccharide moieties is required for γ9δ2 T-cell activation. On the basis of this premise, we used analytical LC/MS and NMR methods to identify and locate the acyl functions on the mGLP saccharides. We found that mGLP is heterogeneous with respect to acyl functions and contains acetyl, isobutyryl, succinyl, and octanoyl groups and that all acylations in mGLP, except for succinyl and octanoyl residues, reside on the glucosyl residues immediately following the terminal 3-O-methylglucose. Our analyses also indicated that the octanoyl residue resides at position 2 of an internal glucose toward the reducing end. LC/MS analysis of the residual product obtained by digesting the mGLP with pancreatic α-amylase revealed that the product is an oligosaccharide terminated by α-(1→4)–linked 6-O-methyl-d-glucosyl residues. This oligosaccharide retained none of the acyl groups, except for the octanoyl group, and was unable to induce protective γ9δ2 T cells. This observation confirmed that mGLP induces γ9δ2 T cells and indicated that the acylated glucosyl residues at the nonreducing terminus of mGLP are required for this activity.
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Affiliation(s)
- Prithwiraj De
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology and
| | - Michael McNeil
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology and
| | - Mei Xia
- Department of Internal Medicine, Saint Louis University, St. Louis, Missouri 63104
| | - Claudia M Boot
- Central Instrument Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 and
| | - Danny C Hesser
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology and
| | - Karolien Denef
- Central Instrument Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 and
| | - Christopher Rithner
- Central Instrument Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 and
| | - Tyler Sours
- Central Instrument Facility, Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523 and
| | - Karen M Dobos
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology and
| | - Daniel Hoft
- Department of Internal Medicine, Saint Louis University, St. Louis, Missouri 63104
| | - Delphi Chatterjee
- From the Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology and
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27
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Chen LC, Tsutsui S, Naito T, Ninomiya S, Hiraoka K. Electrospray ionization source with a rear extractor. JOURNAL OF MASS SPECTROMETRY : JMS 2018; 53:400-407. [PMID: 29453773 DOI: 10.1002/jms.4072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 06/08/2023]
Abstract
A new electrospray source design is introduced by having an extractor electrode placed at 1 to 2 mm behind the emitter tip. The extractor was integrated into the sprayer body as a single device. An insulating tube was used to isolate the emitter from the extractor and to deliver the sheath gas for the electrospray. The electric field strength at the emitter was primarily determined by the relative position and the potential between the needle and the extractor; therefore, the spraying condition was insusceptible to the change of sprayer position or orientation with respect to the ion sampling inlet. Such design allowed the use of much lower operating voltage and facilitated the optimization of sprayer position by keeping the electric field parameter constant. Using an emitter capillary of 150 and 310 μm in inner and outer diameters, strong ion signal could still be acquired with 2-kV emitter potential even if the distance between the emitter and ion inlet was extended to >70 mm. Charge reduction of protein ions using 2 extractor-based electrosprays of opposite emitter polarities was also demonstrated.
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Affiliation(s)
- Lee Chuin Chen
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11, Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Satoru Tsutsui
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11, Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Tsubasa Naito
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11, Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Satoshi Ninomiya
- Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 4-3-11, Takeda, Kofu, Yamanashi, 400-8511, Japan
| | - Kenzo Hiraoka
- Clean Energy Research Center, University of Yamanashi, 4-3-11, Takeda, Kofu, Yamanashi, 400-8511, Japan
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28
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Hochberg GKA, Shepherd DA, Marklund EG, Santhanagoplan I, Degiacomi MT, Laganowsky A, Allison TM, Basha E, Marty MT, Galpin MR, Struwe WB, Baldwin AJ, Vierling E, Benesch JLP. Structural principles that enable oligomeric small heat-shock protein paralogs to evolve distinct functions. Science 2018; 359:930-935. [PMID: 29472485 PMCID: PMC6587588 DOI: 10.1126/science.aam7229] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 09/25/2017] [Accepted: 01/08/2018] [Indexed: 12/26/2022]
Abstract
Oligomeric proteins assemble with exceptional selectivity, even in the presence of closely related proteins, to perform their cellular roles. We show that most proteins related by gene duplication of an oligomeric ancestor have evolved to avoid hetero-oligomerization and that this correlates with their acquisition of distinct functions. We report how coassembly is avoided by two oligomeric small heat-shock protein paralogs. A hierarchy of assembly, involving intermediates that are populated only fleetingly at equilibrium, ensures selective oligomerization. Conformational flexibility at noninterfacial regions in the monomers prevents coassembly, allowing interfaces to remain largely conserved. Homomeric oligomers must overcome the entropic benefit of coassembly and, accordingly, homomeric paralogs comprise fewer subunits than homomers that have no paralogs.
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Affiliation(s)
- Georg K A Hochberg
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Dale A Shepherd
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Erik G Marklund
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Indu Santhanagoplan
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Matteo T Degiacomi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Arthur Laganowsky
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Timothy M Allison
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Eman Basha
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Michael T Marty
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Martin R Galpin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Weston B Struwe
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Andrew J Baldwin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Elizabeth Vierling
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Justin L P Benesch
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK.
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29
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Oh MI, Consta S. What factors determine the stability of a weak protein-protein interaction in a charged aqueous droplet? Phys Chem Chem Phys 2018; 19:31965-31981. [PMID: 29177351 DOI: 10.1039/c7cp05043g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Maintaining the interface of a weak transient protein complex transferred from bulk solution to the gaseous state via evaporating droplets is a critical question in the detection of the complex association (dissociation) constant by using electrospray ionization mass spectrometry (ESI-MS). Here we explore the factors that may affect the stability of a protein-protein interaction (PPI) using atomistic molecular dynamics (MD) modelling of a complex of ubiquitin (Ub) and the ubiquitin-associated domain (UbA) (RCSB PDB code ) and a non-covalent complex of diubiquitin (RCSB PDB code ) in aqueous droplets. A general method is presented to determine the protonation states of the complexes we investigate in particular, and that of a protein in general, under various pH conditions that an evaporating droplet acquires due to its change in size. We find that the combination of high temperature and high charge states of the protein complexes may destabilize the interface by creating new interfaces instead of a direct rupture of the initial stable interface. We provide evidence that highly charged protein complexes are found in droplets that form conical extrusions of the solvent on the surface due to charge-induced instability. This distinct droplet morphology leads to a higher solvent evaporation rate that assists in transferring the complex in the gaseous state without dissociation. The conical solvent protrusions expose on the droplet surface certain amino acids that otherwise would be solvated in a droplet with the protein complex of low charge states. The new vapor-protein interface does not have a direct effect on the stability of the PPI. A common way in experiments to stabilize the protein complexes in droplets is to reduce the protonation state of the proteins. Here we find that weakly bound protein complexes even at high protonation states can be stabilized by the presence of a small number of counterions, without affecting the protonation state of the protein. Our findings may provide guiding principles in ESI-MS experiments to stabilize weak transient PPIs.
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Affiliation(s)
- Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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30
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Oh MI, Consta S. Charging and Release Mechanisms of Flexible Macromolecules in Droplets. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2262-2279. [PMID: 28801879 DOI: 10.1007/s13361-017-1754-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 05/28/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
We study systematically the charging and release mechanisms of a flexible macromolecule, modeled by poly(ethylene glycol) (PEG), in a droplet by using molecular dynamics simulations. We compare how PEG is solvated and charged by sodium Na+ ions in a droplet of water (H2O), acetonitrile (MeCN), and their mixtures. Initially, we examine the location and the conformation of the macromolecule in a droplet bearing no net charge. It is revealed that the presence of charge carriers do not affect the location of PEG in aqueous and MeCN droplets compared with that in the neutral droplets, but the location of the macromolecule and the droplet size do affect the PEG conformation. PEG is charged on the surface of a sodiated aqueous droplet that is found close to the Rayleigh limit. Its charging is coupled to the extrusion mechanism, where PEG segments leave the droplet once they coordinate a Na+ ion or in a correlated motion with Na+ ions. In contrast, as PEG resides in the interior of a MeCN droplet, it is sodiated inside the droplet. The compact macro-ion transitions through partially unwound states to an extended conformation, a process occurring during the final stage of desolvation and in the presence of only a handful of MeCN molecules. For charged H2O/MeCN droplets, the sodiation of PEG is determined by the H2O component, reflecting its slower evaporation and preference over MeCN for solvating Na+ ions. We use the simulation data to construct an analytical model that suggests that the droplet surface electric field may play a role in the macro-ion-droplet interactions that lead to the extrusion of the macro-ion. This study provides the first evidence of the effect of the surface electric field by using atomistic simulations. Graphical Abstract ᅟ.
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Affiliation(s)
- Myong In Oh
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada.
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31
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Zhuang X, Gavriilidou AFM, Zenobi R. Influence of Alkylammonium Acetate Buffers on Protein-Ligand Noncovalent Interactions Using Native Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:341-346. [PMID: 27830529 DOI: 10.1007/s13361-016-1526-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 06/06/2023]
Abstract
We investigate the influence of three volatile alkylammonium acetate buffers on binding affinities for protein-ligand interactions determined by native electrospray ionization-mass spectrometry (ESI-MS). Four different types of proteins were chosen for this study. A charge-reduction effect was observed for all the cases studied, in comparison to the ions formed in ammonium acetate solution. When increasing the collision energy, the complexes of trypsin and the ligand were found to be more stable when sprayed from alkylammonium acetate buffers than from ammonium acetate. The determined dissociation constant (Kd) also exhibited a drop (up to 40%) when ammonium acetate was replaced by alkylammonium acetate buffers for the case of lysozyme and the ligand. The prospective uses of these ammonium acetate analogs in native ESI-MS are discussed in this paper as well. Graphical Abstract ᅟ.
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Affiliation(s)
- Xiaoyu Zhuang
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
- National Center of Mass Spectrometry in Changchun, Jilin Province Key Laboratory of Chinese Medicine Chemistry and Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Agni F M Gavriilidou
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, CH-8093, Zurich, Switzerland.
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32
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Miller CF, Kulyk DS, Kim JW, Badu-Tawiah AK. Re-configurable, multi-mode contained-electrospray ionization for protein folding and unfolding on the millisecond time scale. Analyst 2017; 142:2152-2160. [DOI: 10.1039/c7an00362e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Contained-electrospray ionization enables online selection of protein charge states by a direct infusion of reactive vapors and liquids into charged micro-droplets.
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Affiliation(s)
- Colbert F. Miller
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Dmytro S. Kulyk
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Jongin W. Kim
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
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33
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Chan DSH, Matak-Vinković D, Coyne AG, Abell C. Insight into Protein Conformation and Subcharging by DMSO from Native Ion Mobility Mass Spectrometry. ChemistrySelect 2016. [DOI: 10.1002/slct.201601402] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Daniel Shiu-Hin Chan
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW United Kingdom
| | - Dijana Matak-Vinković
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW United Kingdom
| | - Anthony G. Coyne
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW United Kingdom
| | - Chris Abell
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW United Kingdom
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34
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Liko I, Hopper JTS, Allison TM, Benesch JLP, Robinson CV. Negative Ions Enhance Survival of Membrane Protein Complexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1099-104. [PMID: 27106602 PMCID: PMC4869745 DOI: 10.1007/s13361-016-1381-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/07/2016] [Accepted: 03/08/2016] [Indexed: 05/08/2023]
Abstract
Membrane protein complexes are commonly introduced to the mass spectrometer solubilized in detergent micelles. The collisional activation used to remove the detergent, however, often causes protein unfolding and dissociation. As in the case for soluble proteins, electrospray in the positive ion mode is most commonly used for the study of membrane proteins. Here we show several distinct advantages of employing the negative ion mode. Negative polarity can yield lower average charge states for membrane proteins solubilized in saccharide detergents, with enhanced peak resolution and reduced adduct formation. Most importantly, we demonstrate that negative ion mode electrospray ionization (ESI) minimizes subunit dissociation in the gas phase, allowing access to biologically relevant oligomeric states. Together, these properties mean that intact membrane protein ions can be generated in a greater range of solubilizing detergents. The formation of negative ions, therefore, greatly expands the possibilities of using mass spectrometry on this intractable class of protein. Graphical Abstract ᅟ.
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Affiliation(s)
- Idlir Liko
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Jonathan T S Hopper
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Timothy M Allison
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 5QY, UK.
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35
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Allison TM, Landreh M, Benesch JLP, Robinson CV. Low Charge and Reduced Mobility of Membrane Protein Complexes Has Implications for Calibration of Collision Cross Section Measurements. Anal Chem 2016; 88:5879-5884. [PMID: 27153188 DOI: 10.1021/acs.analchem.6b00691] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ion mobility mass spectrometry of integral membrane proteins provides valuable insights into their architecture and stability. Here we show that, due to their lower charge, the average mobility of native-like membrane protein ions is approximately 30% lower than that of soluble proteins of similar mass. This has implications for drift time measurements, made on traveling wave ion mobility mass spectrometers, which have to be calibrated to extract collision cross sections (Ω). Common calibration strategies employ unfolded or native-like soluble protein standards with masses and mobilities comparable to the protein of interest. We compare Ω values for membrane proteins, derived from standard calibration protocols using soluble proteins, to values measured using an RF-confined drift tube. Our results demonstrate that, while common calibration methods underestimate Ω for native-like or unfolded membrane protein complexes, higher mass soluble calibration standards consistently yield more accurate Ω values. These findings enable us to obtain directly structural information for highly charge-reduced complexes by traveling wave ion mobility mass spectrometry.
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Affiliation(s)
- Timothy M Allison
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Michael Landreh
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Carol V Robinson
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, United Kingdom
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36
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Stutzman JR, Crowe MC, Alexander JN, Bell BM, Dunkle MN. Coupling Charge Reduction Mass Spectrometry to Liquid Chromatography for Complex Mixture Analysis. Anal Chem 2016; 88:4130-9. [DOI: 10.1021/acs.analchem.6b00485] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John R. Stutzman
- Analytical
Sciences, The Dow Chemical Company, 1897 Building, Midland, Michigan 48667, United States
| | - Matthew C. Crowe
- Analytical
Sciences, The Dow Chemical Company, Collegeville, Pennsylvania 19426, United States
| | - James N. Alexander
- Analytical
Sciences, The Dow Chemical Company, Collegeville, Pennsylvania 19426, United States
| | - Bruce M. Bell
- Analytical
Sciences, The Dow Chemical Company, 1897 Building, Midland, Michigan 48667, United States
| | - Melissa N. Dunkle
- Analytical
Sciences, The Dow Chemical Company, Herbert H. Dowweg 5, ADD2/8, 4542 NM Hoek, Netherlands
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37
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Yao Y, Richards MR, Kitova EN, Klassen JS. Influence of Sulfolane on ESI-MS Measurements of Protein-Ligand Affinities. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:498-506. [PMID: 26667179 DOI: 10.1007/s13361-015-1312-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 11/22/2015] [Accepted: 11/24/2015] [Indexed: 06/05/2023]
Abstract
The results of an investigation into the influence of sulfolane, a commonly used supercharging agent, on electrospray ionization mass spectrometry (ESI-MS) measurements of protein-ligand affinities are described. Binding measurements carried out on four protein-carbohydrate complexes, lysozyme with β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-β-D-GlcNAc-(1→4)-D-GlcNAc, a single chain variable fragment and α-D-Gal-(1→2)-[α-D-Abe-(1→3)]-α-D-Man-OCH3, cholera toxin B subunit homopentamer with β-D-Gal-(1→3)-β-D-GalNAc-(1→4)[α-D-Neu5Ac-(2→3)]-β-D-Gal-(1→4)-β-D-Glc, and a fragment of galectin 3 and α-L-Fuc-(1→2)-β-D-Gal-(1→3)-β-D-GlcNAc-(1→3)-β-D-Gal-(1→4)-β-D-Glc, revealed that sulfolane generally reduces the apparent (as measured by ESI-MS) protein-ligand affinities. To establish the origin of this effect, a detailed study was undertaken using the lysozyme-tetrasaccharide interaction as a model system. Measurements carried out using isothermal titration calorimetry (ITC), circular dichroism, and nuclear magnetic resonance spectroscopies reveal that sulfolane reduces the binding affinity in solution but does not cause any significant change in the higher order structure of lysozyme or to the intermolecular interactions. These observations confirm that changes to the structure of lysozyme in bulk solution are not responsible for the supercharging effect induced by sulfolane. Moreover, the agreement between the ESI-MS and ITC-derived affinities indicates that there is no dissociation of the complex during ESI or in the gas phase (i.e., in-source dissociation). This finding suggests that supercharging of lysozyme by sulfolane is not related to protein unfolding during the ESI process. Binding measurements performed using liquid sample desorption ESI-MS revealed that protein supercharging with sulfolane can be achieved without a reduction in affinity.
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Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Michele R Richards
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Elena N Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - John S Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada.
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38
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Fukuda T, Hike H, Usui F, Bando Y, Nishimura T, Kodama T, Kawamura T. An improvement on mass spectrometry-based epigenetic analysis of large histone-derived peptides by using the Ionization Variable Unit interface. Anal Biochem 2015; 486:14-6. [DOI: 10.1016/j.ab.2015.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 05/31/2015] [Accepted: 06/01/2015] [Indexed: 11/28/2022]
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39
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DeMuth JC, Bu J, McLuckey SA. Electrospray droplet exposure to polar vapors: delayed desolvation of protein complexes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:973-981. [PMID: 26407312 DOI: 10.1002/rcm.7188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/08/2015] [Accepted: 03/05/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Fragile non-covalent complexes are susceptible to dissociation upon introduction into and transmission through the mass spectrometer. The exposure of nanoelectrospray droplets to various polar vapors, which are introduced into the curtain gas, is shown to stabilize non-covalent protein complexes even under relatively energetic ion transfer conditions. This study probes the mechanism by which polar vapor exposure appears to stabilize non-covalent protein complex ions in the gas phase. METHODS Holomyoglobin and hemoglobin were dissolved in either aqueous 1 mM ammonium acetate or ammonium bicarbonate solutions and ionized via nanoelectrospray ionization in the positive polarity. Polar vapors were entrained within the counter-current drying gas and exposed to nanoelectrospray droplets for circa 1 ms within the interface of a quadrupole/time-of-flight mass spectrometer. Mass spectra were acquired using various voltage gradients within the mass spectrometer. RESULTS In the absence of added reagent vapors, significant fragmentation of holomyoglobin ions is noted with high voltage gradients for ions either entering or departing q0, a transmission quadrupole closely coupled to the skimmer exit. However, upon the introduction of reagent vapors, essentially 100% of the holomyoglobin complex can be preserved. Significant stabilization is noted at both relatively high q0 entrance and exit gradients when ions are transmitted through q0. These results indicate that upon vapor exposure the holomyoglobin ions are not completely desolvated as they enter or exit q0 under normal ion transmission conditions. CONCLUSIONS The apparent stabilization of protein complexes and other non-covalent complexes noted here and elsewhere is attributed to the delayed desolvation of the ions. This allows the solvated ions to be transmitted through relatively high voltage gradients without disrupting the non-covalent interactions holding the complexes together.
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Affiliation(s)
- J Corinne DeMuth
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
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40
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Kondrat FDL, Struwe WB, Benesch JLP. Native mass spectrometry: towards high-throughput structural proteomics. Methods Mol Biol 2015; 1261:349-371. [PMID: 25502208 DOI: 10.1007/978-1-4939-2230-7_18] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Native mass spectrometry (MS) has become a sensitive method for structural proteomics, allowing practitioners to gain insight into protein self-assembly, including stoichiometry and three-dimensional architecture, as well as complementary thermodynamic and kinetic aspects. Although MS is typically performed in vacuum, a body of literature has described how native solution-state structure is largely retained on the timescale of the experiment. Native MS offers the benefit that it requires substantially smaller quantities of a sample than traditional structural techniques such as NMR and X-ray crystallography, and is therefore well suited to high-throughput studies. Here we first describe the native MS approach and outline the structural proteomic data that it can deliver. We then provide practical details of experiments to examine the structural and dynamic properties of protein assemblies, highlighting potential pitfalls as well as principles of best practice.
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Affiliation(s)
- Frances D L Kondrat
- Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
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41
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Yao Y, Shams-Ud-Doha K, Daneshfar R, Kitova EN, Klassen JS. Quantifying protein-carbohydrate interactions using liquid sample desorption electrospray ionization mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:98-106. [PMID: 25315460 DOI: 10.1007/s13361-014-1008-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/03/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
The application of liquid sample desorption electrospray ionization mass spectrometry (liquid sample DESI-MS) for quantifying protein-carbohydrate interactions in vitro is described. Association constants for the interactions between lysozyme and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc, and between a single chain antibody and α-D-Galp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 and β-D-Glcp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 measured using liquid sample DESI-MS were found to be in good agreement with values measured by isothermal titration calorimetry and the direct ESI-MS assay. The reference protein method, which was originally developed to correct ESI mass spectra for the occurrence of nonspecific ligand-protein binding, was shown to reliably correct liquid sample DESI mass spectra for nonspecific binding. The suitability of liquid sample DESI-MS for quantitative binding measurements carried out using solutions containing high concentrations of the nonvolatile biological buffer phosphate buffered saline (PBS) was also explored. Binding of lysozyme to β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc in aqueous solutions containing up to 1× PBS was successfully monitored using liquid sample DESI-MS; with ESI-MS the binding measurements were limited to concentrations less than 0.02 X PBS.
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Affiliation(s)
- Yuyu Yao
- Alberta Glycomics Center and Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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42
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DeMuth JC, McLuckey SA. Electrospray Droplet Exposure to Organic Vapors: Metal Ion Removal from Proteins and Protein Complexes. Anal Chem 2014; 87:1210-8. [PMID: 25517019 DOI: 10.1021/ac503865v] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- J. Corinne DeMuth
- Department of Chemistry Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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43
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Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
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Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
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Mehmood S, Marcoux J, Hopper JTS, Allison TM, Liko I, Borysik AJ, Robinson CV. Charge reduction stabilizes intact membrane protein complexes for mass spectrometry. J Am Chem Soc 2014; 136:17010-2. [PMID: 25402655 DOI: 10.1021/ja510283g] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The study of intact soluble protein assemblies by means of mass spectrometry is providing invaluable contributions to structural biology and biochemistry. A recent breakthrough has enabled similar study of membrane protein complexes, following their release from detergent micelles in the gas phase. Careful optimization of mass spectrometry conditions, particularly with respect to energy regimes, is essential for maintaining compact folded states as detergent is removed. However, many of the saccharide detergents widely employed in structural biology can cause unfolding of membrane proteins in the gas phase. Here, we investigate the potential of charge reduction by introducing three membrane protein complexes from saccharide detergents and show how reducing their overall charge enables generation of compact states, as evidenced by ion mobility mass spectrometry. We find that charge reduction stabilizes the oligomeric state and enhances the stability of lipid-bound complexes. This finding is significant since maintaining native-like membrane proteins enables ligand binding to be assessed from a range of detergents that retain solubility while protecting the overall fold.
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Affiliation(s)
- Shahid Mehmood
- Department of Chemistry, University of Oxford , Oxford, U.K
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Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Li Z, Li L. Chemical-Vapor-Assisted Electrospray Ionization for Increasing Analyte Signals in Electrospray Ionization Mass Spectrometry. Anal Chem 2013; 86:331-5. [DOI: 10.1021/ac4036263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Zhendong Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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Hilton GR, Hochberg GKA, Laganowsky A, McGinnigle SI, Baldwin AJ, Benesch JLP. C-terminal interactions mediate the quaternary dynamics of αB-crystallin. Philos Trans R Soc Lond B Biol Sci 2013; 368:20110405. [PMID: 23530258 PMCID: PMC3638394 DOI: 10.1098/rstb.2011.0405] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
αB-crystallin is a highly dynamic, polydisperse small heat-shock protein that can form oligomers ranging in mass from 200 to 800 kDa. Here we use a multifaceted mass spectrometry approach to assess the role of the C-terminal tail in the self-assembly of αB-crystallin. Titration experiments allow us to monitor the binding of peptides representing the C-terminus to the αB-crystallin core domain, and observe individual affinities to both monomeric and dimeric forms. Notably, we find that binding the second peptide equivalent to the core domain dimer is considerably more difficult than the first, suggesting a role of the C-terminus in regulating assembly. This finding motivates us to examine the effect of point mutations in the C-terminus in the full-length protein, by quantifying the changes in oligomeric distribution and corresponding subunit exchange rates. Our results combine to demonstrate that alterations in the C-terminal tail have a significant impact on the thermodynamics and kinetics of αB-crystallin. Remarkably, we find that there is energy compensation between the inter- and intra-dimer interfaces: when one interaction is weakened, the other is strengthened. This allosteric communication between binding sites on αB-crystallin is likely important for its role in binding target proteins.
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Affiliation(s)
- Gillian R Hilton
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK
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Sokratous K, Layfield R, Oldham NJ. The effects of cation adduction upon the conformation of three-helix bundle protein domains. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s12127-012-0114-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Harvey SR, Porrini M, Stachl C, MacMillan D, Zinzalla G, Barran PE. Small-molecule inhibition of c-MYC:MAX leucine zipper formation is revealed by ion mobility mass spectrometry. J Am Chem Soc 2012; 134:19384-92. [PMID: 23106332 DOI: 10.1021/ja306519h] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The leucine zipper interaction between MAX and c-MYC has been studied using mass spectrometry and drift time ion mobility mass spectrometry (DT IM-MS) in addition to circular dichroism spectroscopy. Peptides comprising the leucine zipper sequence with (c-MYC-Zip residues 402-434) and without a postulated small-molecule binding region (c-MYC-ZipΔDT residues 406-434) have been synthesized, along with the corresponding MAX leucine zipper (MAX-Zip residues 74-102). c-MYC-Zip:MAX-Zip complexes are observed both in the absence and in the presence of the reported small-molecule inhibitor 10058-F4 for both forms of c-MYC-Zip. DT IM-MS, in combination with molecular dynamics (MD), shows that the c-MYC-Zip:MAX-Zip complex [M+5H](5+) exists in two conformations, one extended with a collision cross section (CCS) of 1164 ± 9.3 Å(2) and one compact with a CCS of 982 ± 6.6 Å(2); similar values are observed for the two forms of c-MYC-ZipΔDT:MAX-Zip. Candidate geometries for the complexes have been evaluated with MD simulations. The helical leucine zipper structure previously determined from NMR measurements (Lavigne, P.; et al. J. Mol. Biol. 1998, 281, 165), altered to include the DT region and subjected to a gas-phase minimization, yields a CCS of 1247 Å(2), which agrees with the extended conformation we observe experimentally. More extensive MD simulations provide compact complexes which are found to be highly disordered, with CCSs that correspond to the compact form from experiment. In the presence of the ligand, the leucine zipper conformation is completely inhibited and only the more disordered species is observed, providing a novel method to study the effect of interactions of disordered systems and subsequent inhibition of the formation of an ordered helical complex.
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Affiliation(s)
- Sophie R Harvey
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
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Hopper JTS, Rawlings A, Afonso JP, Channing D, Layfield R, Oldham NJ. Evidence for the preservation of native inter- and intra-molecular hydrogen bonds in the desolvated FK-binding protein·FK506 complex produced by electrospray ionization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1757-1767. [PMID: 22797884 DOI: 10.1007/s13361-012-0430-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 06/06/2012] [Accepted: 06/06/2012] [Indexed: 06/01/2023]
Abstract
It is now well established that electrospray ionization (ESI) is capable of introducing noncovalent protein assemblies into a desolvated environment, thereby allowing their analysis by mass spectrometry. The degree to which native interactions from the solution phase are preserved in this environment is less clear. Site-directed mutagenesis of FK506-binding protein (FKBP) has been employed to probe specific intra- and inter-molecular interactions within the complex between FKBP and its ligand FK506. Collisional activation of wild-type and mutant-FKBP•FK506 ions, generated by ESI, demonstrated that removal of native protein-ligand interactions formed between residues Asp37, Tyr82, and FK506 significantly destabilized the complex. Mutation of Arg42 to Ala42, or Tyr26 to Phe26 also resulted in lower energy dissociation of the FKBP·FK506 complex. Although these residues do not form direct H-bonds to FK506, they interact with Asp37, ensuring its correct orientation to associate with the ligand. Comparison with solution-based affinity measurements of these mutants has been discussed, including the stabilization afforded by ordered water molecules. Ion mobility spectrometry (IMS) has been employed to provide gas-phase structural information on the unfolding of the complexes. The [M + 6H](6+) complexes of the wild-type and mutants have been shown to resist unfolding and retain compact conformations. However, removal of the basic Arg42 residue was found to induce significant structural weakening of the [M + 7H](7+) complex when raised to dissociation-level energies. Overall, destabilization of the FKBP·FK506 complex, resulting from targeted removal of specific H-bonds, provides evidence for the preservation of these interactions in the desolvated wild-type complex.
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