201
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Pyle E, Guo C, Hofmann T, Schmidt C, Ribiero O, Politis A, Byrne B. Protein–Lipid Interactions Stabilize the Oligomeric State of BOR1p from Saccharomyces cerevisiae. Anal Chem 2019; 91:13071-13079. [DOI: 10.1021/acs.analchem.9b03271] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Euan Pyle
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
- Department of Chemistry, Kings College London, 7 Trinity Street, London SE1 1DB, U.K
| | - Chengzhi Guo
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Tommy Hofmann
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str 3a, D-06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str 3a, D-06120 Halle, Germany
| | - Orquidea Ribiero
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
| | - Argyris Politis
- Department of Chemistry, Kings College London, 7 Trinity Street, London SE1 1DB, U.K
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, Exhibition Road, London SW7 2AZ, U.K
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202
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Sengupta A, Wu J, Seffernick JT, Sabag-Daigle A, Thomsen N, Chen TH, Capua AD, Bell CE, Ahmer BMM, Lindert S, Wysocki VH, Gopalan V. Integrated Use of Biochemical, Native Mass Spectrometry, Computational, and Genome-Editing Methods to Elucidate the Mechanism of a Salmonella deglycase. J Mol Biol 2019; 431:4497-4513. [PMID: 31493410 DOI: 10.1016/j.jmb.2019.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 01/18/2023]
Abstract
Salmonellais a foodborne pathogen that causes annually millions of cases of salmonellosis globally, yet Salmonella-specific antibacterials are not available. During inflammation, Salmonella utilizes the Amadori compound fructose-asparagine (F-Asn) as a nutrient through the successive action of three enzymes, including the terminal FraB deglycase. Salmonella mutants lacking FraB are highly attenuated in mouse models of inflammation due to the toxic build-up of the substrate 6-phosphofructose-aspartate (6-P-F-Asp). This toxicity makes Salmonella FraB an appealing drug target, but there is currently little experimental information about its catalytic mechanism. Therefore, we sought to test our postulated mechanism for the FraB-catalyzed deglycation of 6-P-F-Asp (via an enaminol intermediate) to glucose-6-phosphate and aspartate. A FraB homodimer model generated by RosettaCM was used to build substrate-docked structures that, coupled with sequence alignment of FraB homologs, helped map a putative active site. Five candidate active-site residues-including three expected to participate in substrate binding-were mutated individually and characterized. Native mass spectrometry and ion mobility were used to assess collision cross sections and confirm that the quaternary structure of the mutants mirrored the wild type, and that there are two active sites/homodimer. Our biochemical studies revealed that FraB Glu214Ala, Glu214Asp, and His230Ala were inactive in vitro, consistent with deprotonated-Glu214 and protonated-His230 serving as a general base and a general acid, respectively. Glu214Ala or His230Ala introduced into the Salmonella chromosome by CRISPR/Cas9-mediated genome editing abolished growth on F-Asn. Results from our computational and experimental approaches shed light on the catalytic mechanism of Salmonella FraB and of phosphosugar deglycases in general.
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Affiliation(s)
- Anindita Sengupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Jikang Wu
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Justin T Seffernick
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Anice Sabag-Daigle
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Nicholas Thomsen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Tien-Hao Chen
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Angela Di Capua
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Charles E Bell
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Brian M M Ahmer
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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203
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El-Baba TJ, Clemmer DE. Solution thermochemistry of concanavalin A tetramer conformers measured by variable-temperature ESI-IMS-MS. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 443:93-100. [PMID: 32226278 PMCID: PMC7100878 DOI: 10.1016/j.ijms.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Variable-temperature nano-electrospray ionization coupled with ion mobility spectrometry-mass spectrometry is used to investigate the thermal denaturation of the tetrameric protein concanavalin A. As the solution temperature is increased, changes in mass spectra and collision cross section distributions provide evidence for discrete structural changes that occur at temperatures that are ~40 to 50 degrees below the temperature required for tetramer dissociation. The subtle structural changes are associated with four distinct tetramer conformations with unique melting temperatures. Gibbs-Helmholtz analysis of the free energies determined with respect to the most abundant "native" state yields heat capacities of ΔCp = 1.6 ± 0.3, -2.2 ± 0.4, and -2.9 ± 1.6 kJ·K-1·mol-1, and temperature dependent enthalpies and entropies for the three non-native conformations. Analysis of the thermochemistry indicates that the high-temperature products are entropically stable until the threshold for tetramer dissociation, and changes in heat capacity are consistent with increases in solvation of polar residues. Our findings suggest these high-temperature non-native states result from an increase in disorder at surface exposed regions. Such studies provide valuable insight towards the structural details of non-native states.
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Affiliation(s)
- Tarick J El-Baba
- Department of Chemistry, Indiana University, Bloomington IN, 47401 USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, Bloomington IN, 47401 USA
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204
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Talbert LE, Julian RR. Methionine and Selenomethionine as Energy Transfer Acceptors for Biomolecular Structure Elucidation in the Gas Phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1601-1608. [PMID: 31222676 PMCID: PMC6697561 DOI: 10.1007/s13361-019-02262-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/31/2019] [Accepted: 06/01/2019] [Indexed: 06/09/2023]
Abstract
Mass spectrometry affords rapid and sensitive analysis of peptides and proteins. Coupling spectroscopy with mass spectrometry allows for the development of new methods to enhance biomolecular structure determination. Herein, we demonstrate two new energy acceptors that can be utilized for action-excitation energy transfer experiments. In the first system, C-S bonds in methionine act as energy acceptors from native chromophores, including tyrosine, tryptophan, and phenylalanine. Comparison among chromophores reveals that tyrosine transfers energy most efficiently at 266 nm, but phenylalanine and tryptophan also transfer energy with comparable efficiencies. Overall, the C-S bond dissociation yields following energy transfer are low for methionine, which led to an investigation of selenomethionine, a common analog that is found in many naturally occurring proteins. Sulfur and selenium are chemically similar, but C-Se bonds are weaker than C-S bonds and have lower lying σ* anti-bonding orbitals. Excitation of peptides containing tyrosine and tryptophan results in efficient energy transfer to selenomethionine and abundant C-Se bond dissociation. A series of helical peptides were examined where the positions of the donor or acceptor were systematically scanned to explore the influence of distance and helix orientation on energy transfer. The distance was found to be the primary factor affecting energy transfer efficiency, suggesting that selenomethionine may be a useful acceptor for probing protein structure in the gas phase.
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Affiliation(s)
- Lance E Talbert
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA
| | - Ryan R Julian
- Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA, 92521, USA.
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205
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Hartmann L, Botzanowski T, Galibert M, Jullian M, Chabrol E, Zeder-Lutz G, Kugler V, Stojko J, Strub JM, Ferry G, Frankiewicz L, Puget K, Wagner R, Cianférani S, Boutin JA. VHH characterization. Comparison of recombinant with chemically synthesized anti-HER2 VHH. Protein Sci 2019; 28:1865-1879. [PMID: 31423659 DOI: 10.1002/pro.3712] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/14/2019] [Accepted: 08/14/2019] [Indexed: 12/12/2022]
Abstract
In the continuous exploration of the VHH chemistry, biochemistry and therapeutic future use, we investigated two different production strategies of this small antibody-like protein, using an anti-HER2 VHH as a model. The total chemical synthesis of the 125 amino-acid peptide was performed with reasonable yield, even if optimization will be necessary to upgrade this kind of production. In parallel, we expressed the same sequence in two different hosts: Escherichia coli and Pichia pastoris. Both productions were successful and led to a fair amount of VHHs. The integrity and conformation of the VHH were characterized by complementary mass spectrometry approaches, while surface plasmon resonance experiments were used to assess the VHH recognition capacity and affinity toward its "antigen." Using this combination of orthogonal techniques, it was possible to show that the three VHHs-whether synthetic or recombinant ones-were properly and similarly folded and recognized the "antigen" HER2 with similar affinities, in the nanomolar range. This opens a route toward further exploration of modified VHH with unnatural amino acids and subsequently, VHH-drug conjugates.
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Affiliation(s)
- Lucie Hartmann
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Thomas Botzanowski
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
| | | | | | - Eric Chabrol
- PEX de Biotechnologie, Chimie et Biologie, Institut de REchercehs Servier, Croissy-sur-Seine, France
| | - Gabrielle Zeder-Lutz
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Valérie Kugler
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Johann Stojko
- PEX de Biotechnologie, Chimie et Biologie, Institut de REchercehs Servier, Croissy-sur-Seine, France
| | - Jean-Marc Strub
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
| | - Gilles Ferry
- PEX de Biotechnologie, Chimie et Biologie, Institut de REchercehs Servier, Croissy-sur-Seine, France
| | | | | | - Renaud Wagner
- Plateforme IMPReSs, Laboratoire de Biotechnologie et Signalisation Cellulaire, CNRS, Université de Strasbourg, Illkirch, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, Strasbourg, France
| | - Jean A Boutin
- Institut de Recherches Internationales Servier, Suresnes, France
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206
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Szymkowicz L, Lento C, Wilson DJ. Impact of Cardiolipin and Phosphatidylcholine Interactions on the Conformational Ensemble of Cytochrome c. Biochemistry 2019; 58:3617-3626. [DOI: 10.1021/acs.biochem.9b00495] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Lisa Szymkowicz
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Cristina Lento
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
| | - Derek J. Wilson
- Department of Chemistry, York University, Toronto, Ontario, Canada M3J 1P3
- Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada M3J 1P3
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207
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Ezpeleta J, Baudouin V, Arellano-Anaya ZE, Boudet-Devaud F, Pietri M, Baudry A, Haeberlé AM, Bailly Y, Kellermann O, Launay JM, Schneider B. Production of seedable Amyloid-β peptides in model of prion diseases upon PrP Sc-induced PDK1 overactivation. Nat Commun 2019; 10:3442. [PMID: 31371707 PMCID: PMC6672003 DOI: 10.1038/s41467-019-11333-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 07/09/2019] [Indexed: 02/07/2023] Open
Abstract
The presence of amyloid beta (Aβ) plaques in the brain of some individuals with Creutzfeldt-Jakob or Gertsmann-Straussler-Scheinker diseases suggests that pathogenic prions (PrPSc) would have stimulated the production and deposition of Aβ peptides. We here show in prion-infected neurons and mice that deregulation of the PDK1-TACE α-secretase pathway reduces the Amyloid Precursor Protein (APP) α-cleavage in favor of APP β-processing, leading to Aβ40/42 accumulation. Aβ predominates as monomers, but is also found as trimers and tetramers. Prion-induced Aβ peptides do not affect prion replication and infectivity, but display seedable properties as they can deposit in the mouse brain only when seeds of Aβ trimers are co-transmitted with PrPSc. Importantly, brain Aβ deposition accelerates death of prion-infected mice. Our data stress that PrPSc, through deregulation of the PDK1-TACE-APP pathway, provokes the accumulation of Aβ, a prerequisite for the onset of an Aβ seeds-induced Aβ pathology within a prion-infectious context. Aβ plaques have been detected in brains of patients with prion diseases. Here, using mice, the authors show that prion infection enhances Aβ production via a PDK1-TACE mechanism and that brain deposition of Aβ induced by Aβ seeds co-transmitted with PrPSc contributes to mortality in prion disease.
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Affiliation(s)
- Juliette Ezpeleta
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - Vincent Baudouin
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - Zaira E Arellano-Anaya
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - François Boudet-Devaud
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - Mathéa Pietri
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - Anne Baudry
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - Anne-Marie Haeberlé
- Trafic Membranaire dans les Cellules du Système Nerveux, Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 67000, Strasbourg, France
| | - Yannick Bailly
- Trafic Membranaire dans les Cellules du Système Nerveux, Institut des Neurosciences Cellulaires et Intégratives, CNRS UPR 3212, 67000, Strasbourg, France
| | - Odile Kellermann
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France.,INSERM, UMR 1124, 75006, Paris, France
| | - Jean-Marie Launay
- Assistance Publique des Hôpitaux de Paris, INSERM UMR 942, Hôpital Lariboisière, 75010, Paris, France. .,Pharma Research Department, Hoffmann La Roche Ltd, 4070, Basel, Switzerland.
| | - Benoit Schneider
- Université Paris Descartes, Sorbonne Paris Cité, UFR des Sciences Fondamentales et Biomédicales, UMR 1124, 75006, Paris, France. .,INSERM, UMR 1124, 75006, Paris, France.
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208
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Structural mechanism of synergistic activation of Aurora kinase B/C by phosphorylated INCENP. Nat Commun 2019; 10:3166. [PMID: 31320618 PMCID: PMC6639382 DOI: 10.1038/s41467-019-11085-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/19/2019] [Indexed: 12/27/2022] Open
Abstract
Aurora kinases B and C (AURKB/AURKC) are activated by binding to the C-terminal domain of INCENP. Full activation requires phosphorylation of two serine residues of INCENP that are conserved through evolution, although the mechanism of this activation has not been explained. Here we present crystal structures of the fully active complex of AURKC bound to INCENP, consisting of phosphorylated, activated, AURKC and INCENP phosphorylated on its TSS motif, revealing the structural and biochemical mechanism of synergistic activation of AURKC:INCENP. The structures show that TSS motif phosphorylation stabilises the kinase activation loop of AURKC. The TSS motif phosphorylations alter the substrate-binding surface consistent with a mechanism of altered kinase substrate selectivity and stabilisation of the protein complex against unfolding. We also analyse the binding of the most specific available AURKB inhibitor, BRD-7880, and demonstrate that the well-known Aurora kinase inhibitor VX-680 disrupts binding of the phosphorylated INCENP TSS motif.
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209
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Riboni N, Quaranta A, Motwani HV, Österlund N, Gräslund A, Bianchi F, Ilag LL. Solvent-Assisted Paper Spray Ionization Mass Spectrometry (SAPSI-MS) for the Analysis of Biomolecules and Biofluids. Sci Rep 2019; 9:10296. [PMID: 31311939 PMCID: PMC6635430 DOI: 10.1038/s41598-019-45358-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 05/24/2019] [Indexed: 12/23/2022] Open
Abstract
Paper Spray Ionization (PSI) is commonly applied for the analysis of small molecules, including drugs, metabolites, and pesticides in biological fluids, due to its high versatility, simplicity, and low costs. In this study, a new setup called Solvent Assisted Paper Spray Ionization (SAPSI), able to increase data acquisition time, signal stability, and repeatability, is proposed to overcome common PSI drawbacks. The setup relies on an integrated solution to provide ionization potential and constant solvent flow to the paper tip. Specifically, the ion source was connected to the instrument fluidics along with the voltage supply systems, ensuring a close control over the ionization conditions. SAPSI was successfully applied for the analysis of different classes of biomolecules: amyloidogenic peptides, proteins, and N-glycans. The prolonged analysis time allowed real-time monitoring of processes taking places on the paper tip, such as amyloid peptides aggregation and disaggregation phenomena. The enhanced signal stability allowed to discriminate protein species characterized by different post translational modifications and adducts with electrophilic compounds, both in aqueous solutions and in biofluids, such as serum and cerebrospinal fluid, without any sample pretreatment. In the next future, application to clinical relevant modifications, could lead to the development of quick and cost-effective diagnostic tools.
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Affiliation(s)
- Nicoló Riboni
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, Sweden.,Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, IT, Italy
| | - Alessandro Quaranta
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, Sweden
| | - Hitesh V Motwani
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, Sweden
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, SE, Sweden
| | - Federica Bianchi
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, IT, Italy
| | - Leopold L Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, SE, Sweden.
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210
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Lee JH, Pollert K, Konermann L. Testing the Robustness of Solution Force Fields for MD Simulations on Gaseous Protein Ions. J Phys Chem B 2019; 123:6705-6715. [DOI: 10.1021/acs.jpcb.9b04014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Justin H. Lee
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Katja Pollert
- 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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211
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Jin C, Harvey DJ, Struwe WB, Karlsson NG. Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography–Mass Spectrometry. Anal Chem 2019; 91:10604-10613. [DOI: 10.1021/acs.analchem.9b01772] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - David J. Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Weston B. Struwe
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
- Chemistry Research laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Niclas G. Karlsson
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
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212
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Kirk SR, Liu FC, Cropley TC, Carlock HR, Bleiholder C. On the Preservation of Non-covalent Peptide Assemblies in a Tandem-Trapped Ion Mobility Spectrometer-Mass Spectrometer (TIMS-TIMS-MS). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1204-1212. [PMID: 31025294 DOI: 10.1007/s13361-019-02200-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 03/05/2019] [Accepted: 03/14/2019] [Indexed: 05/21/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) has demonstrated the ability to characterize structures of weakly-bound peptide assemblies. However, these assemblies can potentially dissociate during the IMS-MS measurement if they undergo energetic ion-neutral collisions. Here, we investigate the ability of tandem-trapped ion mobility spectrometry-mass spectrometry (TIMS-TIMS-MS) to retain weakly-bound peptide assemblies. We assess ion heating and dissociaton in the tandem-TIMS instrument using bradykinin and its assemblies as reference systems. Our data indicate that non-covalent bradykinin assemblies are largely preserved in TIMS-TIMS under carefully selected operating conditions. Importantly, we observe quadruply-charged bradykinin tetramers, which attests to the "softness" of our instrument. Graphical Abstract.
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Affiliation(s)
- Samuel R Kirk
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Fanny C Liu
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Tyler C Cropley
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Hunter R Carlock
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA
| | - Christian Bleiholder
- Department of Chemistry & Biochemistry, Florida State University, 95 Chieftan Way, Tallahassee, FL, 32306-4390, USA.
- Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32306-4390, USA.
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213
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Rolland AD, Prell JS. Computational Insights into Compaction of Gas-Phase Protein and Protein Complex Ions in Native Ion Mobility-Mass Spectrometry. Trends Analyt Chem 2019; 116:282-291. [PMID: 31983791 PMCID: PMC6979403 DOI: 10.1016/j.trac.2019.04.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Native ion mobility-mass spectrometry (IM-MS) is a rapidly growing field for studying the composition and structure of biomolecules and biomolecular complexes using gas-phase methods. Typically, ions are formed in native IM-MS using gentle nanoelectrospray ionization conditions, which in many cases can preserve condensed-phase stoichiometry. Although much evidence shows that large-scale condensed-phase structure, such as quaternary structure and topology, can also be preserved, it is less clear to what extent smaller-scale structure is preserved in native IM-MS. This review surveys computational and experimental efforts aimed at characterizing compaction and structural rearrangements of protein and protein complex ions upon transfer to the gas phase. A brief summary of gas-phase compaction results from molecular dynamics simulations using multiple common force fields and a wide variety of protein ions is presented and compared to literature IM-MS data.
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Affiliation(s)
- Amber D. Rolland
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
| | - James S. Prell
- Department of Chemistry and Biochemistry, 1253 University
of Oregon, Eugene, OR, USA, 97403-1253
- Materials Science Institute, 1252 University of Oregon,
Eugene, OR, USA 97403-1252
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214
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Pukala T. Importance of collision cross section measurements by ion mobility mass spectrometry in structural biology. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 3:72-82. [PMID: 30265417 DOI: 10.1002/rcm.8294] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/17/2018] [Accepted: 09/19/2018] [Indexed: 06/08/2023]
Abstract
The field of ion mobility mass spectrometry (IM-MS) has developed rapidly in recent decades, with new fundamental advances underpinning innovative applications. This has been particularly noticeable in the field of biomacromolecular structure determination and structural biology, with pioneering studies revealing new structural insight for complex protein assemblies which control biological function. This perspective offers a review of recent developments in IM-MS which have enabled expanding applications in protein structural biology, principally focusing on the quantitative measurement of collision cross sections and their interpretation to describe higher order protein structures.
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Affiliation(s)
- Tara Pukala
- Discipline of Chemistry, University of Adelaide, North Terrace, Adelaide, South Australia, 5005
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215
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Kerr RA, Keire DA, Ye H. The impact of standard accelerated stability conditions on antibody higher order structure as assessed by mass spectrometry. MAbs 2019; 11:930-941. [PMID: 30913973 PMCID: PMC6601562 DOI: 10.1080/19420862.2019.1599632] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/23/2019] [Accepted: 03/21/2019] [Indexed: 01/12/2023] Open
Abstract
Protein therapeutic higher order structure (HOS) is a quality attribute that can be assessed to help predict shelf life. To model product shelf-life values, possible sample-dependent pathways of degradation that may affect drug efficacy or safety need to be evaluated. As changes in drug thermal stability over time can be correlated with an increased risk of HOS perturbations, the effect of long-term storage on the product should be measured as a function of temperature. Here, complementary high-resolution mass spectrometry methods for HOS analysis were used to identify storage-dependent changes of biotherapeutics (bevacizumab (Avastin), trastuzumab (Herceptin), rituximab (Rituxan), and the NIST reference material 8671 (NISTmAb)) under accelerated or manufacturer-recommended storage conditions. Collision-induced unfolding ion mobility-mass spectrometry data showed changes in monoclonal antibody folded stability profiles that were consistent with the appearance of a characteristic unfolded population. Orthogonal hydrogen-deuterium exchange-mass spectrometry data revealed that the observed changes in unfolding occurred in parallel to changes in HOS localized to the periphery of the hinge region. Using intact reverse-phase liquid chromatography-mass spectrometry, we identified several mass species indicative of peptide backbone hydrolysis, located between the variable and constant domains of the heavy chain of bevacizumab. Taken together, our data highlighted the capability of these approaches to identify age- or temperature-dependent changes in biotherapeutic HOS.
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Affiliation(s)
- Richard A. Kerr
- Division of Pharmaceutical Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, USA
| | - David A. Keire
- Division of Pharmaceutical Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, USA
| | - Hongping Ye
- Division of Pharmaceutical Analysis, Office of Testing and Research, Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, St. Louis, USA
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216
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Chang CM, Prabhu GRD, Tseng CM, Urban PL. Temporal Analysis of Conformers in the Course of pH Scan Directed by Urea–Urease Reaction—A “Protein Clock”. Anal Chem 2019; 91:8814-8819. [DOI: 10.1021/acs.analchem.9b02199] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Chun-Ming Chang
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Gurpur Rakesh D. Prabhu
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Chien-Ming Tseng
- Department of Applied Chemistry, National Chiao Tung University, 1001 University Road, Hsinchu 300, Taiwan
| | - Pawel L. Urban
- Department of Chemistry, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
- Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, 101, Section 2, Kuang-Fu Road, Hsinchu 30013, Taiwan
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217
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Monge ME, Dodds JN, Baker ES, Edison AS, Fernández FM. Challenges in Identifying the Dark Molecules of Life. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:177-199. [PMID: 30883183 PMCID: PMC6716371 DOI: 10.1146/annurev-anchem-061318-114959] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Metabolomics is the study of the metabolome, the collection of small molecules in living organisms, cells, tissues, and biofluids. Technological advances in mass spectrometry, liquid- and gas-phase separations, nuclear magnetic resonance spectroscopy, and big data analytics have now made it possible to study metabolism at an omics or systems level. The significance of this burgeoning scientific field cannot be overstated: It impacts disciplines ranging from biomedicine to plant science. Despite these advances, the central bottleneck in metabolomics remains the identification of key metabolites that play a class-discriminant role. Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate. In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task.
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Affiliation(s)
- María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQD, Ciudad de Buenos Aires, Argentina
| | - James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Arthur S Edison
- Department of Genetics, Department of Biochemistry and Molecular Biology, and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology and Petit Institute for Biochemistry and Bioscience, Atlanta, Georgia 30332, USA;
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218
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Giles K, Ujma J, Wildgoose J, Pringle S, Richardson K, Langridge D, Green M. A Cyclic Ion Mobility-Mass Spectrometry System. Anal Chem 2019; 91:8564-8573. [PMID: 31141659 DOI: 10.1021/acs.analchem.9b01838] [Citation(s) in RCA: 290] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Improvements in the performance and availability of commercial instrumentation have made ion mobility-mass spectrometry (IM-MS) an increasingly popular approach for the structural analysis of ionic species as well as for separation of complex mixtures. Here, a new research instrument is presented which enables complex experiments, extending the current scope of IM technology. The instrument is based on a Waters SYNAPT G2-S i IM-MS platform, with the IM separation region modified to accept a cyclic ion mobility (cIM) device. The cIM region consists of a 98 cm path length, closed-loop traveling wave (TW)-enabled IM separator positioned orthogonally to the main ion optical axis. A key part of this geometry and its flexibility is the interface between the ion optical axis and the cIM, where a planar array of electrodes provides control over the TW direction and subsequent ion motion. On either side of the array, there are ion guides used for injection, ejection, storage, and activation of ions. In addition to single and multipass separations around the cIM, providing selectable mobility resolution, the instrument design and control software enable a range of "multifunction" experiments such as mobility selection, activation, storage, IMS n, and importantly custom combinations of these functions. Here, the design and performance of the cIM-MS instrument is highlighted, with a mobility resolving power of approximately 750 demonstrated for 100 passes around the cIM device using a reverse sequence peptide pair. The multifunction capabilities are demonstrated through analysis of three isomeric pentasaccharide species and the small protein ubiquitin.
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Affiliation(s)
- Kevin Giles
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jakub Ujma
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Jason Wildgoose
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Steven Pringle
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Keith Richardson
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - David Langridge
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
| | - Martin Green
- Waters Corporation , Stamford Avenue, Altrincham Road , Wilmslow SK9 4AX , U.K
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219
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Chen X, Raab SA, Poe T, Clemmer DE, Larriba-Andaluz C. Determination of Gas-Phase Ion Structures of Locally Polar Homopolymers Through High-Resolution Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:905-918. [PMID: 30993642 DOI: 10.1007/s13361-019-02184-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 03/05/2019] [Indexed: 06/09/2023]
Abstract
The strong synergy arising from coupling two orthogonal analytical techniques such as ion mobility and mass spectrometry can be used to separate complex mixtures and determine structural information of analytes in the gas phase. A tandem study is performed using two systems with different gases and pressures to ascertain gas-phase conformations of homopolymer ions. Aside from spherical and stretched configurations, intermediate configurations formed by a multiply charged globule and a "bead-on-a-string" appendix are confirmed for polyethylene-glycol (PEG), polycaprolactone (PCL), and polydimethylsiloxane (PDMS). These intermediate configurations are shown to be ubiquitous for all charge states and masses present. For each charge state, configurations evolve in two distinctive patterns: an inverse evolution which occurs as an elementary charge attached to the polymer leaves the larger globule and incorporates itself into the appendage, and a forward evolution which reduces the globule without relinquishing a charge while leaving the appendix relatively constant. Forward evolutions are confirmed to form self-similar family shapes that transcend charge states for all polymers. Identical structural changes occur at the same mass over charge regardless of the system, gas or pressure strongly suggesting that conformations are only contingent on number of charges and chain length, and start arranging once the ion is at least partially ejected from the droplet, supporting a charge extrusion mechanism. Configurational changes are smoother for PDMS which is attributed to the larger steric hindrance caused by protruding pendant groups. This study has implications in the study of the configurational space of more complex homopolymers and heteropolymers. Graphical Abstract.
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Affiliation(s)
- Xi Chen
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA
- Department of Mechanical Engineering, Purdue Universiy, West Lafayette, IN, 47907, USA
| | - Shannon A Raab
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Timothy Poe
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA
| | - David E Clemmer
- Department of Chemistry, Indiana University, 800 E Kirkwood Ave, Bloomington, IN, 47405, USA
| | - Carlos Larriba-Andaluz
- Department of Mechanical Engineering, IUPUI, 723 W Michigan st, Indianapolis, IN, 46202, USA.
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220
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Eaton RM, Allen SJ, Bush MF. Principles of Ion Selection, Alignment, and Focusing in Tandem Ion Mobility Implemented Using Structures for Lossless Ion Manipulations (SLIM). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1115-1125. [PMID: 30963456 DOI: 10.1007/s13361-019-02170-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 06/09/2023]
Abstract
Tandem ion mobility (IM) enables the characterization of subpopulations of ions from larger ensembles, including differences that cannot be resolved in a single dimension of IM. Tandem IM consists of at least two IM regions that are each separated by an ion selection region. In many implementations of tandem IM, ions eluting from a dimension of separation are filtered and immediately transferred to the subsequent dimension of separation (selection-only experiments). We recently reported a mode of operation in which ions eluting from a dimension are trapped prior to the subsequent dimension (selection-trapping experiments), which was implemented on an instrument constructed using the structures for lossless ion manipulations (SLIM) architecture. Here, we use a combination of experiments and trajectory simulations to characterize aspects of the selection, trapping, and separation processes underlying these modes of operation. For example, the actual temporal profile of filtered ions can be very similar to the width of the waveforms used for selection, but depending on experimental parameters, can differ by up to ± 500 μs. Experiments and simulations indicate that ions in selection-trapping experiments can be spatially focused between dimensions, which removes the broadening that occurred during the preceding dimension. During focusing, individual ions are thermalized, which aligns and establishes common initial conditions for the subsequent dimension. Therefore, selection-trapping experiments appear to offer significant advantages relative to selection-only experiments, which we anticipate will become more pronounced in future experiments that make use of longer IM separations, additional dimensions of analysis, and the outcomes of this study. Graphical Abstract.
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Affiliation(s)
- Rachel M Eaton
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Samuel J Allen
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA
| | - Matthew F Bush
- Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195-1700, USA.
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221
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Jeanne Dit Fouque K, Hegemann JD, Zirah S, Rebuffat S, Lescop E, Fernandez-Lima F. Evidence of Cis/Trans-Isomerization at Pro7/Pro16 in the Lasso Peptide Microcin J25. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1038-1045. [PMID: 30834511 DOI: 10.1007/s13361-019-02134-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/08/2019] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Microcin J25 is a ribosomal synthesized and post-translationally modified peptide (RiPP) characterized by a mechanically interlocked topology called the lasso fold. This structure provides microcin J25 a potent antimicrobial activity resulting from internalization via the siderophore receptor FhuA and further inhibition of the RNA polymerase. In the present work, nuclear magnetic resonance (NMR) and trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) were used to investigate the lasso structure of microcin J25. NMR experiments showed that the lasso peptide microcin J25 can adopt conformational states where Pro16 can be found in the cis- and trans-orientations. The high-resolution mobility analysis, aided by site-directed mutagenesis ([P7A], [P16A], and [P7A/P16A] variants), demonstrated that microcin J25 can adopt cis/cis-, cis/trans-, trans/cis-, and trans/trans-conformations at the Pro7 and Pro16 peptide bonds. It was also shown that interconversion between the conformers can occur as a function of the starting solvent conditions and ion heating (collision-induced activation, CIA) despite the lasso topology. Complementary to NMR findings, the cis-conformations at Pro7 were assigned using TIMS-MS. This study highlights the analytical power of TIMS-MS and site-directed mutagenesis for the study of biological systems with large micro-heterogeneity as a way to further increase our understanding of the receptor-binding dynamics and biological activity.
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Affiliation(s)
- Kevin Jeanne Dit Fouque
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, FL, 33199, USA
| | - Julian D Hegemann
- M Department of Chemistry, University of Illinois, Urbana-Champaign, IL, 61801, USA
| | - Séverine Zirah
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS UMR 7245, 75005, Paris, France
| | - Sylvie Rebuffat
- Laboratory Molecules of Communication and Adaptation of Microorganisms, National Museum of Natural History, CNRS UMR 7245, 75005, Paris, France
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Saclay, 91198, Gif sur Yvette Cedex, France
| | - Francisco Fernandez-Lima
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., AHC4-233, Miami, FL, 33199, USA.
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222
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Österlund N, Moons R, Ilag LL, Sobott F, Gräslund A. Native Ion Mobility-Mass Spectrometry Reveals the Formation of β-Barrel Shaped Amyloid-β Hexamers in a Membrane-Mimicking Environment. J Am Chem Soc 2019; 141:10440-10450. [DOI: 10.1021/jacs.9b04596] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Nicklas Österlund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rani Moons
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
| | - Leopold L. Ilag
- Department of Environmental Science and Analytical Chemistry, Stockholm University, Stockholm, Sweden
| | - Frank Sobott
- Department of Chemistry, University of Antwerp, Antwerp, Belgium
- The Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, The United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, The United Kingdom
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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223
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Woodall DW, El-Baba TJ, Fuller DR, Liu W, Brown CJ, Laganowsky A, Russell DH, Clemmer DE. Variable-Temperature ESI-IMS-MS Analysis of Myohemerythrin Reveals Ligand Losses, Unfolding, and a Non-Native Disulfide Bond. Anal Chem 2019; 91:6808-6814. [PMID: 31038926 DOI: 10.1021/acs.analchem.9b00981] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Variable-temperature electrospray ionization combined with ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques are used to monitor structural transitions of the protein myohemerythrin from peanut worm in aqueous ammonium acetate solutions from ∼15 to 92 °C. At physiological temperatures, myohemerythrin favors a four-helix bundle motif and has a diiron oxo cofactor that binds oxygen. As the solution temperature is increased from ∼15 to 35 °C, some bound oxygen dissociates; at ∼66 °C, the cofactor dissociates to produce populations of both folded and unfolded apoprotein. At higher temperatures (∼85 °C and above), the IMS-MS spectrum indicates that the folded apoprotein dominates, and provides evidence for stabilization of the structure by formation of a non-native disulfide bond. In total, we find evidence for 18 unique forms of myohemerythrin as well as information about the structures and stabilities of these states. The high-fidelity of IMS-MS techniques provides a means of examining the stabilities of individual components of complex mixtures that are inaccessible by traditional calorimetric and spectroscopic methods.
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Affiliation(s)
- Daniel W Woodall
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Tarick J El-Baba
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Daniel R Fuller
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Wen Liu
- Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
| | - Christopher J Brown
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Arthur Laganowsky
- 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
| | - David E Clemmer
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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224
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Peters I, Metwally H, Konermann L. Mechanism of Electrospray Supercharging for Unfolded Proteins: Solvent-Mediated Stabilization of Protonated Sites During Chain Ejection. Anal Chem 2019; 91:6943-6952. [DOI: 10.1021/acs.analchem.9b01470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Insa Peters
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Haidy Metwally
- 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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225
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Gabelica V, Shvartsburg AA, Afonso C, Barran P, Benesch JL, Bleiholder C, Bowers MT, Bilbao A, Bush MF, Campbell JL, Campuzano ID, Causon T, Clowers BH, Creaser CS, De Pauw E, Far J, Fernandez‐Lima F, Fjeldsted JC, Giles K, Groessl M, Hogan CJ, Hann S, Kim HI, Kurulugama RT, May JC, McLean JA, Pagel K, Richardson K, Ridgeway ME, Rosu F, Sobott F, Thalassinos K, Valentine SJ, Wyttenbach T. Recommendations for reporting ion mobility Mass Spectrometry measurements. MASS SPECTROMETRY REVIEWS 2019; 38:291-320. [PMID: 30707468 PMCID: PMC6618043 DOI: 10.1002/mas.21585] [Citation(s) in RCA: 304] [Impact Index Per Article: 60.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 05/02/2023]
Abstract
Here we present a guide to ion mobility mass spectrometry experiments, which covers both linear and nonlinear methods: what is measured, how the measurements are done, and how to report the results, including the uncertainties of mobility and collision cross section values. The guide aims to clarify some possibly confusing concepts, and the reporting recommendations should help researchers, authors and reviewers to contribute comprehensive reports, so that the ion mobility data can be reused more confidently. Starting from the concept of the definition of the measurand, we emphasize that (i) mobility values (K0 ) depend intrinsically on ion structure, the nature of the bath gas, temperature, and E/N; (ii) ion mobility does not measure molecular surfaces directly, but collision cross section (CCS) values are derived from mobility values using a physical model; (iii) methods relying on calibration are empirical (and thus may provide method-dependent results) only if the gas nature, temperature or E/N cannot match those of the primary method. Our analysis highlights the urgency of a community effort toward establishing primary standards and reference materials for ion mobility, and provides recommendations to do so. © 2019 The Authors. Mass Spectrometry Reviews Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Valérie Gabelica
- University of Bordeaux, INSERM and CNRS, ARNA Laboratory, IECB site2 rue Robert Escarpit, 33600PessacFrance
| | | | | | - Perdita Barran
- Michael Barber Centre for Collaborative Mass SpectrometryManchester Institute for Biotechnology, University of ManchesterManchesterUK
| | - Justin L.P. Benesch
- Department of Chemistry, Chemistry Research LaboratoryUniversity of Oxford, Mansfield Road, OX1 3TAOxfordUK
| | - Christian Bleiholder
- Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeFlorida32311
| | | | - Aivett Bilbao
- Biological Sciences DivisionPacific Northwest National LaboratoryRichlandWashington
| | - Matthew F. Bush
- Department of ChemistryUniversity of WashingtonSeattleWashington
| | | | | | - Tim Causon
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Brian H. Clowers
- Department of ChemistryWashington State UniversityPullmanWashington
| | - Colin S. Creaser
- Centre for Analytical ScienceDepartment of Chemistry, Loughborough UniversityLoughboroughUK
| | - Edwin De Pauw
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | - Johann Far
- Laboratoire de spectrométrie de masse (L.S.M.) − Molecular SystemsUniversité de LiègeLiègeBelgium
| | | | | | | | - Michael Groessl
- Department of Nephrology and Hypertension and Department of BioMedical ResearchInselspital, Bern University Hospital, University of Bern, Switzerland and TofwerkThunSwitzerland
| | | | - Stephan Hann
- University of Natural Resources and Life Sciences (BOKU)Department of Chemistry, Division of Analytical ChemistryViennaAustria
| | - Hugh I. Kim
- Department of ChemistryKorea UniversitySeoulKorea
| | | | - Jody C. May
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - John A. McLean
- Department of ChemistryCenter for Innovative Technology, Vanderbilt UniversityNashvilleTennessee
| | - Kevin Pagel
- Freie Universitaet BerlinInstitute for Chemistry and BiochemistryBerlinGermany
| | | | | | - Frédéric Rosu
- CNRS, INSERM and University of BordeauxInstitut Européen de Chimie et BiologiePessacFrance
| | - Frank Sobott
- Antwerp UniversityBiomolecular & Analytical Mass SpectrometryAntwerpBelgium
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsUK
- School of Molecular and Cellular BiologyUniversity of LeedsLeedsUK
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of BiosciencesUniversity College LondonLondonWC1E 6BTUK
- United Kingdom and Institute of Structural and Molecular BiologyDepartment of Biological Sciences, Birkbeck College, University of LondonLondonWC1E 7HXUK
| | - Stephen J. Valentine
- C. Eugene Bennett Department of ChemistryWest Virginia UniversityMorgantownWest Virginia
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226
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Burnum-Johnson KE, Zheng X, Dodds JN, Ash J, Fourches D, Nicora CD, Wendler JP, Metz TO, Waters KM, Jansson JK, Smith RD, Baker ES. Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples. Trends Analyt Chem 2019; 116:292-299. [PMID: 31798197 DOI: 10.1016/j.trac.2019.04.022] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.
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Affiliation(s)
| | - Xueyun Zheng
- Department of Chemistry, Texas A &M University, College Station, TX
| | - James N Dodds
- Department of Chemistry, NC State University, Raleigh, NC
| | - Jeremy Ash
- Department of Chemistry, NC State University, Raleigh, NC
| | - Denis Fourches
- Department of Chemistry, NC State University, Raleigh, NC
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Jason P Wendler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Katrina M Waters
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Janet K Jansson
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Erin S Baker
- Department of Chemistry, NC State University, Raleigh, NC
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227
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Kaldmäe M, Sahin C, Saluri M, Marklund EG, Landreh M. A strategy for the identification of protein architectures directly from ion mobility mass spectrometry data reveals stabilizing subunit interactions in light harvesting complexes. Protein Sci 2019; 28:1024-1030. [PMID: 30927297 PMCID: PMC6511732 DOI: 10.1002/pro.3609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/04/2019] [Accepted: 03/28/2019] [Indexed: 12/18/2022]
Abstract
Biotechnological applications of protein complexes require detailed information about their structure and composition, which can be challenging to obtain for proteins from natural sources. Prominent examples are the ring-shaped phycoerythrin (PE) and phycocyanin (PC) complexes isolated from the light-harvesting antennae of red algae and cyanobacteria. Despite their widespread use as fluorescent probes in biotechnology and medicine, the structures and interactions of their noncrystallizable central subunits are largely unknown. Here, we employ ion mobility mass spectrometry to reveal varying stabilities of the PC and PE complexes and identify their closest architectural homologues among all protein assemblies in the Protein Data Bank (PDB). Our results suggest that the central subunits of PC and PE complexes, although absent from the crystal structures, may be crucial for their stability, and thus of unexpected importance for their biotechnological applications.
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Affiliation(s)
- Margit Kaldmäe
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, SE-171 65, Stockholm, Sweden
| | - Cagla Sahin
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, SE-171 65, Stockholm, Sweden
| | - Mihkel Saluri
- School of Natural Sciences and Health, Tallinn University, Narva mnt 25, 10120, Tallinn, Estonia
| | - Erik G Marklund
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Michael Landreh
- Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Tomtebodavägen 23A, SE-171 65, Stockholm, Sweden
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228
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Donor MT, Mroz AM, Prell JS. Experimental and theoretical investigation of overall energy deposition in surface-induced unfolding of protein ions. Chem Sci 2019; 10:4097-4106. [PMID: 31049192 PMCID: PMC6471915 DOI: 10.1039/c9sc00644c] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/06/2019] [Indexed: 12/15/2022] Open
Abstract
Recent advances in native mass spectrometry have enabled its use to probe the structure of and interactions within biomolecular complexes. Surface-induced dissociation, in which inter- and intramolecular interactions are disrupted following an energetic ion-surface collision, is a method that can directly interrogate the topology of protein complexes. However, a quantitative relationship between the ion kinetic energy at the moment of surface collision and the internal energy deposited into the ion has not yet been established for proteins. The factors affecting energy deposition in surface-induced unfolding (SIU) of protein monomers were investigated and a calibration relating laboratory-frame kinetic energy to internal energy developed. Protein monomers were unfolded by SIU and by collision-induced unfolding (CIU). CIU and SIU cause proteins to undergo the same unfolding transitions at different values of laboratory-frame kinetic energy. There is a strong correlation between the SIU and CIU energies, demonstrating that SIU, like CIU, can largely be understood as a thermal process. The change in internal energy in CIU was modeled using a Monte Carlo approach and theory. Computed values of the overall efficiency were found to be approximately 25% and used to rescale the CIU energy axis and relate nominal SIU energies to internal energy. The energy deposition efficiency in SIU increases with mass and kinetic energy from a low of ∼20% to a high of ∼68%, indicating that the effective mass of the surface increases along with the mass of the ion. The effect of ion structure on energy deposition was probed using multiple stages of ion activation. Energy deposition in SIU strongly depends on structure, decreasing as the protein is elongated, due to decreased effective protein-surface collisional cross section and increased transfer to rotational modes.
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Affiliation(s)
- Micah T Donor
- Department of Chemistry and Biochemistry , 1253 University of Oregon , Eugene , OR 97403-1253 , USA
| | - Austin M Mroz
- Department of Chemistry and Biochemistry , 1253 University of Oregon , Eugene , OR 97403-1253 , USA
| | - James S Prell
- Department of Chemistry and Biochemistry , 1253 University of Oregon , Eugene , OR 97403-1253 , USA
- Materials Science Institute , University of Oregon , 1252 University of Oregon , Eugene , OR 97403-1252 , USA . ; ; Tel: +1 541 346 2597
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229
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Kirk AT, Bohnhorst A, Raddatz CR, Allers M, Zimmermann S. Ultra-high-resolution ion mobility spectrometry-current instrumentation, limitations, and future developments. Anal Bioanal Chem 2019; 411:6229-6246. [PMID: 30957205 DOI: 10.1007/s00216-019-01807-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 12/29/2022]
Abstract
With recent advances in ionization sources and instrumentation, ion mobility spectrometers (IMS) have transformed from a detector for chemical warfare agents and explosives to a widely used tool in analytical and bioanalytical applications. This increasing measurement task complexity requires higher and higher analytical performance and especially ultra-high resolution. In this review, we will discuss the currently used ion mobility spectrometers able to reach such ultra-high resolution, defined here as a resolving power greater than 200. These instruments are drift tube IMS, traveling wave IMS, trapped IMS, and field asymmetric or differential IMS. The basic operating principles and the resulting effects of experimental parameters on resolving power are explained and compared between the different instruments. This allows understanding the current limitations of resolving power and how ion mobility spectrometers may progress in the future. Graphical abstract.
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Affiliation(s)
- Ansgar T Kirk
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany.
| | - Alexander Bohnhorst
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Christian-Robert Raddatz
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Maria Allers
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
| | - Stefan Zimmermann
- Institute of Electrical Engineering and Measurement Technology, Department of Sensors and Measurement Technology, Leibniz Universität Hannover, Appelstr. 9A, 30167, Hannover, Germany
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230
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Bashyal A, Sanders JD, Holden DD, Brodbelt JS. Top-Down Analysis of Proteins in Low Charge States. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:704-717. [PMID: 30796622 PMCID: PMC6447437 DOI: 10.1007/s13361-019-02146-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 05/08/2023]
Abstract
The impact of charging methods on the dissociation behavior of intact proteins in low charge states is investigated using HCD and 193 nm UVPD. Low charge states are produced for seven different proteins using the following four different methods: (1) proton transfer reactions of ions in high charge states generated from conventional denaturing solutions; (2) ESI of proteins in solutions of high ionic strength to enhance retention of folded native-like conformations; (3) ESI of proteins in high pH solutions to limit protonation; and (4) ESI of carbamylated proteins. Comparison of sequence coverages, degree of preferential cleavages, and types and distribution of fragment ions reveals a number of differences in the fragmentation patterns depending on the method used to generate the ions. More notable differences in these metrics are observed upon HCD than upon UVPD. The fragmentation caused by HCD is influenced more significantly by the presence/absence of mobile protons, a factor that modulates the degree of preferential cleavages and net sequence coverages. Carbamylation of the lysines and the N-terminus of the proteins alters the proton mobility by reducing the number of proton-sequestering, highly basic sites as evidenced by decreased preferential fragmentation C-terminal to Asp or N-terminal to Pro upon HCD. UVPD is less dependent on the method used to generate the low charge states and favors non-specific fragmentation, an outcome which is important for obtaining high sequence coverage of intact proteins.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - James D Sanders
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Dustin D Holden
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX, 78712, USA.
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231
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Zhao B, Zhuang X, Bian X, Pi Z, Liu S, Liu Z, Song F. Effects of aprotic solvents on the stability of metal-free superoxide dismutase probed by native electrospray ionization-ion mobility-mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2019; 54:351-358. [PMID: 30734979 DOI: 10.1002/jms.4341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Considering that aprotic solvents are often used as cosolvents in investigating the interactions between small molecules and proteins, we assessed the effects of five aprotic solvents represented by dimethylformamide (DMF) on the structure stabilities of metal-free SOD1 (apo-SOD1) by native electrospray ionization-ion mobility-mass spectrometry (ESI-IM-MS). These aprotic solvents include DMF, 1,3-dimethyl-2-imidazolidinone (DMI), dimethyl sulfoxide (DMSO), acetonitrile (ACN), and tetrahydrofuran (THF). Results indicated that DMI, DMSO, and DMF at low percentage concentration could reduce the average charge and the dimer dissociation of apo-SOD1. By contrast, ACN and THF at low concentration have no similar effect. DMF was selected as a representative solvent to further investigate the detailed effects on the structure stability of apo-SOD1 by using collision-induced dissociation and unfolding. The results reveal that the addition of minimal DMF to an aqueous protein solution can protect against the unfolding and dissociation of dimer, even under destabilizing conditions (such as low pH or high cone voltage). When the different percentage concentrations of DMF were added, the average collision cross section of apo-SOD1 showed that apo-SOD1 became compacted when the DMF concentration increased from 0% to 1% and eventually started extending when increased from 1% to 20%. The results indicated that DMF has similar effects to DMSO in native mass spectrometry (MS) and it can also be used as a cosolvent besides DMSO in investigating the stabilities of proteins and the interactions between small molecules and proteins.
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Affiliation(s)
- Bing Zhao
- 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, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
| | - Xiaoyu Zhuang
- School of Pharmacy, Fudan University, Shanghai, China
| | - Xinyu Bian
- 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, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
| | - Zifeng Pi
- 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, China
| | - Shu Liu
- 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, China
| | - Zhiqiang Liu
- 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, China
| | - Fengrui Song
- 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, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
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232
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Humphreys SC, Thayer MB, Campuzano IDG, Netirojjanakul C, Rock BM. Quantification of siRNA-Antibody Conjugates in Biological Matrices by Triplex-Forming Oligonucleotide ELISA. Nucleic Acid Ther 2019; 29:161-166. [PMID: 30801231 DOI: 10.1089/nat.2018.0770] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The potential repertoire of short interfering RNA (siRNA) therapeutics is expanding as targeting strategies evolve. One approach to enable organ-specific delivery has been to directly conjugate siRNA to a monoclonal antibody (siRNA-mAb), analogous to antibody-drug conjugates. Detection of intact siRNA-mAb conjugates presents a bioanalytical challenge given that certain synthetic nucleotide chemical modifications and low-temperature requirements render common oligonucleotide detection assays, such as reverse transcription-polymerase chain reaction, incompatible with the immunoassay component. To circumvent these issues, we developed a triplex-forming oligonucleotide ELISA using locked nucleic acid (LNA) containing oligonucleotide probes. We demonstrate that the incorporation of these LNAs allow for an enrichment and immobilization of siRNA directly conjugated to an antibody at nondenaturing temperatures. Without further requirement for extraction or amplification, we can sensitively and specifically detect intact siRNA-mAb conjugates in complex matrices such as serum and tissue homogenate.
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Affiliation(s)
- Sara C Humphreys
- 1 Amgen, Inc., Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California
| | - Mai B Thayer
- 1 Amgen, Inc., Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California
| | - Iain D G Campuzano
- 2 Amgen, Inc., Discovery Attribute Sciences, Amgen Research, Thousand Oaks, California
| | | | - Brooke M Rock
- 1 Amgen, Inc., Pharmacokinetics and Drug Metabolism, Amgen Research, South San Francisco, California
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233
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Hernychová L, Rosůlek M, Kádek A, Mareška V, Chmelík J, Adámková L, Grobárová V, Šebesta O, Kukačka Z, Skála K, Spiwok V, Černý J, Novák P. The C-type lectin-like receptor Nkrp1b: Structural proteomics reveals features affecting protein conformation and interactions. J Proteomics 2019; 196:162-172. [DOI: 10.1016/j.jprot.2018.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/31/2018] [Accepted: 11/05/2018] [Indexed: 11/24/2022]
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234
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Paul M, Detmar E, Schlangen M, Breugst M, Neudörfl JM, Schwarz H, Berkessel A, Schäfer M. Intermediates of N-Heterocyclic Carbene (NHC) Dimerization Probed in the Gas Phase by Ion Mobility Mass Spectrometry: C-H⋅⋅⋅:C Hydrogen Bonding Versus Covalent Dimer Formation. Chemistry 2019; 25:2511-2518. [PMID: 30488654 DOI: 10.1002/chem.201803641] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/27/2018] [Indexed: 11/06/2022]
Abstract
N-Heterocyclic carbenes (NHCs, :C) can interact with azolium salts (C-H+ ) by either forming a hydrogen-bonded aggregate (CHC+ ) or a covalent C-C bond (CCH+ ). In this study, the intramolecular NHC-azolium salt interactions of aromatic imidazolin-2-ylidenes and saturated imidazolidin-2-ylidenes have been investigated in the gas phase by traveling wave ion mobility mass spectrometry (TW IMS) and DFT calculations. The TW IMS experiments provided evidence for the formation of these important intermediates in the gas phase, and they identified the predominant aggregation mode (hydrogen bond vs. covalent C-C) as a function of the nature of the interacting carbene-azolium pairs.
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Affiliation(s)
- Mathias Paul
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Eric Detmar
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Maria Schlangen
- Institute of Chemistry, Technical University Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Martin Breugst
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Jörg-Martin Neudörfl
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Helmut Schwarz
- Institute of Chemistry, Technical University Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Albrecht Berkessel
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
| | - Mathias Schäfer
- Department of Chemistry, Organic Chemistry, University of Cologne, Greinstrasse 4, 50939, Cologne, Germany
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235
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Pitts-McCoy AM, Harrilal CP, McLuckey SA. Gas-Phase Ion/Ion Chemistry as a Probe for the Presence of Carboxylate Groups in Polypeptide Cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:329-338. [PMID: 30341581 PMCID: PMC6347497 DOI: 10.1007/s13361-018-2079-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/04/2018] [Indexed: 05/31/2023]
Abstract
The reactivity of 1-hydroxybenzoyl triazole (HOBt) esters with the carboxylate functionality present in peptides is demonstrated in the gas phase with a doubly deprotonated dianion. The reaction forms an anhydride linkage at the carboxylate site. Upon ion trap collisional-induced dissociation (CID) of the modified peptide, the resulting spectrum shows a nominal loss of the mass of the reagent and a water molecule. Analogous phenomenology was also noted for model peptide cations that likely contain zwitterionic/salt-bridged motifs in reactions with a negatively charged HOBt ester. Control experiments indicate that a carboxylate group is the likely reactive site, rather than other possible nucleophilic sites present in the peptide. These observations suggest that HOBt ester chemistry may be used as a chemical probe for the presence and location of carboxylate groups in net positively charged polypeptide ions. As an illustration, deprotonated sulfobenzoyl HOBt was reacted with the [M+7H]7+ ion of ubiquitin. The ion was shown to react with the reagent and CID of the covalent reaction product yielded an abundant [M+6H-H2O]6+ ion. Comparison of the CID product ion spectrum of this ion with that of the water loss product generated from CID of the unmodified [M+6H]6+ ion revealed the glutamic acid at residue 64 as a reactive site, suggesting that it is present in the deprotonated form. Graphical Abstract ᅟ.
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Affiliation(s)
- Anthony M Pitts-McCoy
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Christopher P Harrilal
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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236
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Harrison JA, Kelso C, Pukala TL, Beck JL. Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:256-267. [PMID: 30324262 DOI: 10.1007/s13361-018-2074-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/14/2018] [Accepted: 09/20/2018] [Indexed: 06/08/2023]
Abstract
Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes. Stable hetero-oligomeric phospholipase A2 (PDx) and its subunits were characterized as calibrants for TWIM-MS. Conditions for acquisition of native-like TWIM (Synapt G1 HDMS) and DTIM (Agilent 6560 IM-Q-TOF) mass spectra were optimized to ensure the spectra exhibited similar charge state distributions. CCS measurements (DTIM-MS) for ubiquitin, cytochrome c, holo-myoglobin, serum albumin and glutamate dehydrogenase were in good agreement with other recent results determined using this and other DTIM-MS instruments. PDx and its β and γ subunits were stable across a wide range of cone and trap voltages in TWIM-MS and were stable in the presence of organic solvents. The CCS of PDx and its subunits were determined by DTIM-MS and were used as calibrants in determination of CCS of native-like cytochrome c, holo-myoglobin, carbonic anhydrase, serum albumin and haemoglobin in TWIM-MS. The CCS values were in good agreement with those measured by DTIM-MS where available. These experiments demonstrate conditions for analysis of native-like proteins using a commercially available DTIM-MS instrument, characterize robust calibrants for TWIM-MS, and present CCS values determined by DTIM-MS and TWIM-MS for native proteins to add to the current literature database. Graphical Abstract ᅟ.
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Affiliation(s)
- Julian A Harrison
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Celine Kelso
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - Tara L Pukala
- Discipline of Chemistry, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jennifer L Beck
- School of Chemistry, University of Wollongong, Wollongong, NSW, 2522, Australia.
- Molecular Horizons, University of Wollongong, Wollongong, NSW, 2522, Australia.
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237
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He M, Luo P, Hong J, Wang X, Wu H, Zhang R, Qu F, Xiang Y, Xu W. Structural Analysis of Biomolecules through a Combination of Mobility Capillary Electrophoresis and Mass Spectrometry. ACS OMEGA 2019; 4:2377-2386. [PMID: 31459477 PMCID: PMC6648644 DOI: 10.1021/acsomega.8b03224] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/24/2019] [Indexed: 05/08/2023]
Abstract
The 3D structures of biomolecules determine their biological function. Established methods in biomolecule structure determination typically require purification, crystallization, or modification of target molecules, which limits their applications for analyzing trace amounts of biomolecules in complex matrices. Here, we developed instruments and methods of mobility capillary electrophoresis (MCE) and its coupling with MS for the 3D structural analysis of biomolecules in the liquid phase. Biomolecules in complex matrices could be separated by MCE and sequentially detected by MS. The effective radius and the aspect ratio of each separated biomolecule were simultaneously determined through the separation by MCE, which were then used as restraints in determining biomolecule conformations through modeling. Feasibility of this method was verified by analyzing a mixture of somatostatin and bradykinin, two peptides with known liquid-phase structures. Proteins could also be structurally analyzed using this method, which was demonstrated for lysozyme. The combination of MCE and MS for complex sample analysis was also demonstrated. MCE and MCE-MS would allow us to analyze trace amounts of biomolecules in complex matrices, which has the potential to be an alternative and powerful biomolecule structure analysis technique.
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Affiliation(s)
- Muyi He
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Pan Luo
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jie Hong
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaofeng Wang
- Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Haimei Wu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ye Xiang
- Beijing
Advanced Innovation Center for Structural Biology, Department of Basic
Medical Sciences, School of Medicine, Tsinghua
University, Beijing 100084, China
- E-mail: (Y.X.)
| | - Wei Xu
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
- E-mail: (W.X.)
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238
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Ion Mobility in Structural Biology. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.10.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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239
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Konermann L, Metwally H, Duez Q, Peters I. Charging and supercharging of proteins for mass spectrometry: recent insights into the mechanisms of electrospray ionization. Analyst 2019; 144:6157-6171. [DOI: 10.1039/c9an01201j] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Molecular dynamics simulations have uncovered mechanistic details of the protein ESI process under various experimental conditions.
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Affiliation(s)
- Lars Konermann
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Haidy Metwally
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Quentin Duez
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
| | - Insa Peters
- Department of Chemistry
- The University of Western Ontario
- London
- Canada
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240
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Li C, Hogan Jr CJ. Direct observation of C60− nano-ion gas phase ozonation via ion mobility-mass spectrometry. Phys Chem Chem Phys 2019; 21:10470-10476. [DOI: 10.1039/c9cp01394f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Atmospheric pressure differential mobility analysis-mass spectrometry facilitates determination of nano-ion-neutral reaction rates approaching the collision controlled limit.
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Affiliation(s)
- Chenxi Li
- Department of Mechanical Engineering
- University of Minnesota
- Minneapolis
- USA
- Laboratory for Physical Chemistry
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241
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Prell JS. Modelling Collisional Cross Sections. ADVANCES IN ION MOBILITY-MASS SPECTROMETRY: FUNDAMENTALS, INSTRUMENTATION AND APPLICATIONS 2019. [DOI: 10.1016/bs.coac.2018.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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242
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Ben-Nissan G, Vimer S, Tarnavsky M, Sharon M. Structural mass spectrometry approaches to study the 20S proteasome. Methods Enzymol 2019; 619:179-223. [DOI: 10.1016/bs.mie.2018.12.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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243
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McKenna KR, Li L, Baker AG, Ujma J, Krishnamurthy R, Liotta CL, Fernández FM. Carbohydrate isomer resolutionviamulti-site derivatization cyclic ion mobility-mass spectrometry. Analyst 2019; 144:7220-7226. [DOI: 10.1039/c9an01584a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Cyclic ion mobility-tandem mass spectrometry enhances the separation and identification of small carbohydrate isomers.
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Affiliation(s)
- Kristin R. McKenna
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | - Li Li
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | | | | | | | - Charles L. Liotta
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
| | - Facundo M. Fernández
- NSF/NASA Center for Chemical Evolution
- Georgia Institute of Technology
- Atlanta
- USA
- School of Chemistry and Biochemistry
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244
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Rabuck-Gibbons JN, Lodge JM, Mapp AK, Ruotolo BT. Collision-Induced Unfolding Reveals Unique Fingerprints for Remote Protein Interaction Sites in the KIX Regulation Domain. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:94-102. [PMID: 30136215 PMCID: PMC6320266 DOI: 10.1007/s13361-018-2043-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 07/24/2018] [Accepted: 07/28/2018] [Indexed: 06/08/2023]
Abstract
The kinase-inducible domain (KIX) of the transcriptional coactivator CBP binds multiple transcriptional regulators through two allosterically connected sites. Establishing a method for observing activator-specific KIX conformations would facilitate the discovery of drug-like molecules that capture specific conformations and further elucidate how distinct activator-KIX complexes produce differential transcriptional effects. However, the transient and low to moderate affinity interactions between activators and KIX are difficult to capture using traditional biophysical assays. Here, we describe a collision-induced unfolding-based approach that produces unique fingerprints for peptides bound to each of the two available sites within KIX, as well as a third fingerprint for ternary KIX complexes. Furthermore, we evaluate the analytical utility of unfolding fingerprints for KIX complexes using CIUSuite, and conclude by speculating as to the structural origins of the conformational families created from KIX:peptide complexes following collisional activation. Graphical Abstract ᅟ.
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Affiliation(s)
- Jessica N Rabuck-Gibbons
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N Torrey Pines Rd., La Jolla, CA, 92037, USA
| | - Jean M Lodge
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA
- Life Science Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
- University of Wisconsin, Genome Center, 425 Henry Mall, Madison, WI, 53706, USA
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA
- Life Science Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI, 48109, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, 930 N University, Ann Arbor, MI, 48109, USA.
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245
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Dyachenko A, Tamara S, Heck AJR. Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:7-15. [PMID: 29736602 PMCID: PMC6318259 DOI: 10.1007/s13361-018-1910-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 02/01/2018] [Accepted: 02/01/2018] [Indexed: 05/06/2023]
Abstract
The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. Graphical Abstract.
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Affiliation(s)
- Andrey Dyachenko
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Sem Tamara
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
- Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
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246
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Li J, Begbie A, Boehm BJ, Button A, Whidborne C, Pouferis Y, Huang DM, Pukala TL. Ion Mobility-Mass Spectrometry Reveals Details of Formation and Structure for GAA·TCC DNA and RNA Triplexes. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:103-112. [PMID: 30341580 DOI: 10.1007/s13361-018-2077-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
DNA and RNA triplexes are thought to play key roles in a range of cellular processes such as gene regulation and epigenetic remodeling and have been implicated in human disease such as Friedreich's ataxia. In this work, ion mobility-mass spectrometry (IM-MS) is used with supporting UV-visible spectroscopy to investigate DNA triplex assembly, considering stability and specificity, for GAA·TTC oligonucleotide sequences of relevance to Friedreich's ataxia. We demonstrate that, contrary to other examples, parallel triplex structures are favored for these sequences and that stability is enhanced by increasing oligonucleotide length and decreasing pH. We also provide evidence for the self-association of these triplexes, consistent with a proposed model of higher order DNA structures formed in Friedreich's ataxia. By comparing triplex assembly using DNA- and RNA-based triplex-forming oligonucleotides, we demonstrate more favorable formation of RNA triplexes, suggesting a role for their formation in vivo. Finally, we interrogate the binding properties of netropsin, a known polyamide triplex destabilizer, with RNA-DNA hybrid triplexes, where preference for duplex binding is evident. We show that IM-MS is able to report on relevant solution-phase populations of triplex DNA structures, thereby further highlighting the utility of this technology in structural biology. Our data therefore provides new insights into the possible DNA and RNA assemblies that may form as a result of GAA triplet repeats. Graphical Abstract ᅟ.
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Affiliation(s)
- Jiawei Li
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Alexander Begbie
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Belinda J Boehm
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Alexander Button
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Charles Whidborne
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Yannii Pouferis
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - David M Huang
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia
| | - Tara L Pukala
- School of Physical Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.
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247
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Tian Y, Lippens JL, Netirojjanakul C, Campuzano IDG, Ruotolo BT. Quantitative collision-induced unfolding differentiates model antibody-drug conjugates. Protein Sci 2018; 28:598-608. [PMID: 30499138 DOI: 10.1002/pro.3560] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/15/2022]
Abstract
Antibody-drug conjugates (ADCs) are antibody-based therapeutics that have proven to be highly effective cancer treatment platforms. They are composed of monoclonal antibodies conjugated with highly potent drugs via chemical linkers. Compared to cysteine-targeted chemistries, conjugation at native lysine residues can lead to a higher degree of structural heterogeneity, and thus it is important to evaluate the impact of conjugation on antibody conformation. Here, we present a workflow involving native ion mobility (IM)-MS and gas-phase unfolding for the structural characterization of lysine-linked monoclonal antibody (mAb)-biotin conjugates. Following the determination of conjugation states via denaturing Liquid Chromatography-Mass Spectrometry (LC-MS) measurements, we performed both size exclusion chromatography (SEC) and native IM-MS measurements in order to compare the structures of biotinylated and unmodified IgG1 molecules. Hydrodynamic radii (Rh) and collision cross-sectional (CCS) values were insufficient to distinguish the conformational changes in these antibody-biotin conjugates owing to their flexible structures and limited instrument resolution. In contrast, collision induced unfolding (CIU) analyses were able to detect subtle structural and stability differences in the mAb upon biotin conjugation, exhibiting a sensitivity to mAb conjugation that exceeds native MS analysis alone. Destabilization of mAb-biotin conjugates was detected by both CIU and differential scanning calorimetry (DSC) data, suggesting a previously unknown correlation between the two measurement tools. We conclude by discussing the impact of IM-MS and CIU technologies on the future of ADC development pipelines.
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Affiliation(s)
- Yuwei Tian
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Jennifer L Lippens
- Amgen Discovery Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, California, 91320
| | - Chawita Netirojjanakul
- Amgen Discovery Research, Hybrid Modality Engineering, Amgen, Thousand Oaks, California, 91320
| | - Iain D G Campuzano
- Amgen Discovery Research, Discovery Attribute Sciences, Amgen, Thousand Oaks, California, 91320
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
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248
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Ben-Nissan G, Vimer S, Warszawski S, Katz A, Yona M, Unger T, Peleg Y, Morgenstern D, Cohen-Dvashi H, Diskin R, Fleishman SJ, Sharon M. Rapid characterization of secreted recombinant proteins by native mass spectrometry. Commun Biol 2018; 1:213. [PMID: 30534605 PMCID: PMC6277423 DOI: 10.1038/s42003-018-0231-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/12/2018] [Indexed: 12/22/2022] Open
Abstract
Characterization of overexpressed proteins is essential for assessing their quality, and providing input for iterative redesign and optimization. This process is typically carried out following purification procedures that require pronounced cost of time and labor. Therefore, quality assessment of recombinant proteins with no prior purification offers a major advantage. Here, we report a native mass spectrometry method that enables characterization of overproduced proteins directly from culture media. Properties such as solubility, molecular weight, folding, assembly state, overall structure, post-translational modifications and binding to relevant biomolecules are immediately revealed. We show the applicability of the method for in-depth characterization of secreted recombinant proteins from eukaryotic systems such as yeast, insect, and human cells. This method, which can be readily extended to high-throughput analysis, considerably shortens the time gap between protein production and characterization, and is particularly suitable for characterizing engineered and mutated proteins, and optimizing yield and quality of overexpressed proteins.
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Affiliation(s)
- Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shay Vimer
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Shira Warszawski
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Aliza Katz
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Meital Yona
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Yoav Peleg
- Israel Structural Proteomics Center, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - David Morgenstern
- The De Botton protein Profiling Institute of the Nancy and Stephen Grand Israel national Center for Personalized Medicine, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Hadas Cohen-Dvashi
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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249
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Ouyang H, Bo T, Zhang Z, Guo X, He M, Li J, Yang S, Ma X, Feng Y. Ion mobility mass spectrometry with molecular modelling to reveal bioactive isomer conformations and underlying relationship with isomerization. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:1931-1940. [PMID: 30151930 DOI: 10.1002/rcm.8271] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/21/2018] [Accepted: 08/20/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE In medicine and drug development, molecular modelling is an important tool. It is attractive to develop a platform connecting the theoretical structural modelling and the results from experimental measurement. In addition, the separation and structural analysis of bioactive constituent isomers are still challenging tasks. METHODS Drift tube ion mobility (IM) mass spectrometry (MS) provides the experimental collision cross section (CCS) which contains the structural information. The experimental CCS can be compared with the calculated CCS of the molecular modelling structures. This technique is especially useful for bioactive constituents in herbal medicine because active isomers with the same chemical formula are common in these samples. IM helps separate and identify these isomers and reveals details about their structures and conformations. RESULTS Two model bioactive constituents, caffeoylquinic acids (CQAs) and dicaffeoylquinic acids (di-CQAs), were selected to systematically investigate the influence of solution, ion source conditions and ion heating on the isomer CCS distributions. By comparing the calculated CCS with the experimental value, we identified the favorable conformations of CQAs. The most compact conformation of a CQA was less likely to isomerize than the more extended conformation. It was found that the isomerization tendency was in accord with the conformation favorability. CONCLUSIONS This study offers an effective approach to predict and demystify the conformation and isomerization of the active constituents in herbal medicines.
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Affiliation(s)
- Hui Ouyang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Tao Bo
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Zhengxiang Zhang
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Xinqiu Guo
- Ming De Tian Sheng Biotech Inc., Changping Campus of Peking University, Beijing, 102200, China
| | - Mingzhen He
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Junmao Li
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
| | - Shilin Yang
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, No. 56 Yangming Road, Nanchang, 330006, China
| | - Xin Ma
- Agilent Technologies, No. 3, Wang Jing Bei Lu, Beijing, 100102, China
| | - Yulin Feng
- Jiangxi University of Traditional Chinese Medicine, No. 818 Yunwan Road, Nanchang, 330002, China
- State Key Laboratory of Innovative Drug and Efficient Energy-Saving Pharmaceutical Equipment, No. 56 Yangming Road, Nanchang, 330006, China
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250
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Nam E, Derrick JS, Lee S, Kang J, Han J, Lee SJC, Chung SW, Lim MH. Regulatory Activities of Dopamine and Its Derivatives toward Metal-Free and Metal-Induced Amyloid-β Aggregation, Oxidative Stress, and Inflammation in Alzheimer's Disease. ACS Chem Neurosci 2018; 9:2655-2666. [PMID: 29782798 DOI: 10.1021/acschemneuro.8b00122] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A catecholamine neurotransmitter, dopamine (DA), is suggested to be linked to the pathology of dementia; however, the involvement of DA and its structural analogues in the pathogenesis of Alzheimer's disease (AD), the most common form of dementia, composed of multiple pathogenic factors has not been clear. Herein, we report that DA and its rationally designed structural derivatives (1-6) based on DA's oxidative transformation are able to modulate multiple pathological elements found in AD [i.e., metal ions, metal-free amyloid-β (Aβ), metal-bound Aβ (metal-Aβ), and reactive oxygen species (ROS)], with demonstration of detailed molecular-level mechanisms. Our multidisciplinary studies validate that the protective effects of DA and its derivatives on Aβ aggregation and Aβ-mediated toxicity are induced by their oxidative transformation with concomitant ROS generation under aerobic conditions. In particular, DA and the derivatives (i.e., 3 and 4) show their noticeable anti-amyloidogenic ability toward metal-free Aβ and/or metal-Aβ, verified to occur via their oxidative transformation that facilitates Aβ oxidation. Moreover, in primary pan-microglial marker (CD11b)-positive cells, the major producers of inflammatory mediators in the brain, DA and its derivatives significantly diminish inflammation and oxidative stress triggered by lipopolysaccharides and Aβ through the reduced induction of inflammatory mediators as well as upregulated expression of heme oxygenase-1, the enzyme responsible for production of antioxidants. Collectively, we illuminate how DA and its derivatives could prevent multiple pathological features found in AD. The overall studies could advance our understanding regarding distinct roles of neurotransmitters in AD and identify key interactions for alleviation of AD pathology.
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Affiliation(s)
- Eunju Nam
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jeffrey S. Derrick
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Seunghee Lee
- School of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Juhye Kang
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jiyeon Han
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Shin Jung C. Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Su Wol Chung
- School of Biological Sciences, College of Natural Sciences, University of Ulsan, Ulsan 44610, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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