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Ivanov DG, Cheung K, Kaltashov IA. Probing the Architecture of Multisubunit Protein Complexes with In-line Disulfide Reduction and Native MS Analysis. Anal Chem 2024. [PMID: 38733603 DOI: 10.1021/acs.analchem.4c00879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024]
Abstract
Native mass spectrometry (MS) continues to enjoy growing popularity as a means of providing a wealth of information on noncovalent biopolymer assemblies ranging from composition and binding stoichiometry to characterization of the topology of these assemblies. The latter frequently relies on supplementing MS measurements with limited fragmentation of the noncovalent complexes in the gas phase to identify the pairs of neighboring subunits. While this approach has met with much success in the past two decades, its implementation remains difficult (and the success record relatively modest) within one class of noncovalent assemblies: protein complexes in which at least one binding partner has multiple subunits cross-linked by disulfide bonds. We approach this problem by inducing chemical reduction of disulfide bonds under nondenaturing conditions in solution followed by native MS analysis with online buffer exchange to remove unconsumed reagents that are incompatible with the electrospray ionization process. While this approach works well with systems comprised of thiol-linked subunits that remain stable upon reduction of the disulfide bridges (such as immunoglobulins), chemical reduction frequently gives rise to species that are unstable (prone to aggregation). This problem is circumvented by taking advantage of the recently introduced cross-path reactive chromatography platform (XPRC), which allows the disulfide reduction to be carried out in-line, thereby minimizing the loss of metastable protein subunits and their noncovalent complexes with the binding partners prior to MS analysis. The feasibility of this approach is demonstrated using hemoglobin complexes with haptoglobin 1-1, a glycoprotein consisting of four polypeptide chains cross-linked by disulfide bonds.
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Affiliation(s)
- Daniil G Ivanov
- Department of Chemistry, University of Massachusetts─Amherst, Amherst, Massachusetts 01002, United States
| | - Kevin Cheung
- Department of Chemistry, University of Massachusetts─Amherst, Amherst, Massachusetts 01002, United States
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts─Amherst, Amherst, Massachusetts 01002, United States
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2
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Nguyen SN, Le SH, Ivanov DG, Ivetic N, Nazy I, Kaltashov IA. Structural Characterization of a Pathogenic Antibody Underlying Vaccine-Induced Immune Thrombotic Thrombocytopenia (VITT). Anal Chem 2024; 96:6209-6217. [PMID: 38607319 DOI: 10.1021/acs.analchem.3c05253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare but dangerous side effect of adenoviral-vectored COVID-19 vaccines. VITT had been linked to production of autoantibodies recognizing platelet factor 4 (PF4). Here, we characterize anti-PF4 antibodies obtained from a VITT patient's blood. Intact mass measurements indicate that a significant fraction of these antibodies represent a limited number of clones. MS analysis of large antibody fragments (the light chain and the Fc/2 and Fd fragments of the heavy chain) confirms the monoclonal nature of this component of the anti-PF4 antibodies repertoire and reveals the presence of a mature complex biantennary N-glycan within the Fd segment. Peptide mapping using two complementary proteases and LC-MS/MS was used to determine the amino acid sequence of the entire light chain and over 98% of the heavy chain (excluding a short N-terminal segment). The sequence analysis allows the monoclonal antibody to be assigned to the IgG2 subclass and verifies that the light chain belongs to the λ-type. Incorporation of enzymatic de-N-glycosylation into the peptide mapping routine allows the N-glycan in the Fab region of the antibody to be localized to the framework 3 region of the VH domain. This novel N-glycosylation site is the result of a single mutation within the germline sequence. Peptide mapping also provides information on lower-abundance (polyclonal) components of the anti-PF4 antibody ensemble, revealing the presence of all four subclasses (IgG1-IgG4) and both types of the light chain (λ and κ). This case study demonstrates the power of combining the intact, middle-down, and bottom-up MS approaches for meaningful characterization of ultralow quantities of pathogenic antibodies extracted directly from patients' blood.
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Affiliation(s)
- Son N Nguyen
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Si-Hung Le
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Nikola Ivetic
- Department of Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Ishac Nazy
- Department of Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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3
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Yang Y, Du Y, Ivanov D, Niu C, Clare R, Smith JW, Nazy I, Kaltashov IA. Molecular architecture and platelet-activating properties of small immune complexes assembled on heparin and platelet factor 4. Commun Biol 2024; 7:308. [PMID: 38467823 PMCID: PMC10928113 DOI: 10.1038/s42003-024-05982-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Heparin-induced thrombocytopenia (HIT) is an adverse reaction to heparin leading to a reduction in circulating platelets with an increased risk of thrombosis. It is precipitated by polymerized immune complexes consisting of pathogenic antibodies that recognize a small chemokine platelet factor 4 (PF4) bound to heparin. Characterization of these immune complexes is extremely challenging due to the enormous structural heterogeneity of such macromolecular assemblies and their constituents. Native mass spectrometry demonstrates that up to three PF4 tetramers can be assembled on a heparin chain, consistent with the molecular modeling studies showing facile polyanion wrapping along the polycationic belt on the PF4 surface. Although these assemblies can accommodate a maximum of only two antibodies, the resulting immune complexes are capable of platelet activation despite their modest size. Taken together, these studies provide further insight into molecular mechanisms of HIT and other immune disorders where anti-PF4 antibodies play a central role.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Yi Du
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Daniil Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Chendi Niu
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Rumi Clare
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - James W Smith
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Ishac Nazy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
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4
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Yang Y, Ivanov DG, Levin MD, Olenyuk B, Cordova-Robles O, Cederstrom B, Schnitzer JE, Kaltashov IA. Characterization of Large Immune Complexes with Size Exclusion Chromatography and Native Mass Spectrometry Supplemented with Gas Phase Ion Chemistry. Anal Chem 2024. [PMID: 38319243 DOI: 10.1021/acs.analchem.3c03278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Large immune complexes formed by the cross-linking of antibodies with polyvalent antigens play critical roles in modulating cell-mediated immunity. While both the size and the shape of immune complexes are important determinants in Fc receptor-mediated signaling responsible for phagocytosis, degranulation, and, in some instances, autoimmune pathologies, their characterization remains extremely challenging due to their large size and structural heterogeneity. We use native mass spectrometry (MS) supplemented with limited charge reduction in the gas phase to determine the stoichiometry of immune complexes formed by a bivalent (homodimeric) antigen, a 163 kDa aminopeptidase P2 (APP2), and a monoclonal antibody (mAb) to APP2. The observed (APP2·mAb)n complexes populate a wide range of stoichiometries (n = 1-4) with the largest detected species exceeding 1 MDa, although the gas-phase dissociation products are also evident in the mass spectra. While frequently considering a nuisance that complicates interpretation of native MS data, limited dissociation provides an additional dimension for characterization of the immune complex quaternary structure. APP2/mAb associations with identical composition but slightly different elution times in size exclusion chromatography exhibit notable differences in their spontaneous fragmentation profiles. The latter indicates the presence of both extended linear and cyclized (APP2·mAb)n configurations. The unique ability of MS to distinguish between such isomeric structures will be invaluable for a variety of applications where the biological effects of immune complexes are determined by their ability to assemble Fc receptor clusters of certain density on cell surfaces, such as platelet activation by clustering the low-affinity receptors FcγRIIa on their surface.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
| | - Michael D Levin
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Bogdan Olenyuk
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Oscar Cordova-Robles
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Brittany Cederstrom
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Jan E Schnitzer
- Proteogenomics Research Institute for Systems Medicine, La Jolla, California 92037, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, USA
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Kaltashov IA, Ivanov DG, Yang Y. Mass spectrometry-based methods to characterize highly heterogeneous biopharmaceuticals, vaccines, and nonbiological complex drugs at the intact-mass level. Mass Spectrom Rev 2024; 43:139-165. [PMID: 36582075 PMCID: PMC10307928 DOI: 10.1002/mas.21829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
The intact-mass MS measurements are becoming increasingly popular in characterization of a range of biopolymers, especially those of interest to biopharmaceutical industry. However, as the complexity of protein therapeutics and other macromolecular medicines increases, the new challenges arise, one of which is the high levels of structural heterogeneity that are frequently exhibited by such products. The very notion of the molecular mass measurement loses its clear and intuitive meaning when applied to an extremely heterogenous system that cannot be characterized by a unique mass, but instead requires that a mass distribution be considered. Furthermore, convoluted mass distributions frequently give rise to unresolved ionic signal in mass spectra, from which little-to-none meaningful information can be extracted using standard approaches that work well for homogeneous systems. However, a range of technological advances made in the last decade, such as the hyphenation of intact-mass MS measurements with front-end separations, better integration of ion mobility in MS workflows, development of an impressive arsenal of gas-phase ion chemistry tools to supplement MS methods, as well as the revival of the charge detection MS and its triumphant entry into the field of bioanalysis already made impressive contributions towards addressing the structural heterogeneity challenge. An overview of these techniques is accompanied by critical analysis of the strengths and weaknesses of different approaches, and a brief overview of their applications to specific classes of biopharmaceutical products, vaccines, and nonbiological complex drugs.
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Affiliation(s)
- Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst MA 01003
| | - Daniil G. Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst MA 01003
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Ivanov DG, Ivetic N, Du Y, Nguyen SN, Le SH, Favre D, Nazy I, Kaltashov IA. Reverse Engineering of a Pathogenic Antibody Reveals the Molecular Mechanism of Vaccine-Induced Immune Thrombotic Thrombocytopenia. J Am Chem Soc 2023; 145:25203-25213. [PMID: 37949820 DOI: 10.1021/jacs.3c07846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The massive COVID-19 vaccine roll-out campaign illuminated a range of rare side effects, the most dangerous of which─vaccine-induced immune thrombotic thrombocytopenia (VITT)─is caused by adenoviral (Ad)-vectored vaccines. VITT occurrence had been linked to the production of pathogenic antibodies that recognize an endogenous chemokine, platelet factor 4 (PF4). Mass spectrometry (MS)-based evaluation of the ensemble of anti-PF4 antibodies obtained from a VITT patient's blood indicates that the major component is a monoclonal antibody. Structural characterization of this antibody reveals several unusual characteristics, such as the presence of an N-glycan in the Fab segment and high density of acidic amino acid residues in the complementarity-determining regions. A recombinant version of this antibody (RVT1) was generated by transient expression in mammalian cells based on the newly determined sequence. It captures the key properties of VITT antibodies such as their ability to activate platelets in a PF4 concentration-dependent fashion. Homology modeling of the Fab segment reveals a well-defined polyanionic paratope, and the docking studies indicate that the polycationic segment of PF4 readily accommodates two Fab segments, cross-linking the antibodies to yield polymerized immune complexes. Their existence was verified with native MS by detecting assemblies as large as (RVT1)3(PF4)2, pointing out at FcγRIIa-mediated platelet activation as the molecular mechanism underlying VITT clinical manifestations. In addition to the high PF4 affinity, RVT1 readily binds other polycationic targets, indicating a polyreactive nature of this antibody. This surprising promiscuity not only sheds light on VITT etiology but also opens up a range of opportunities to manage this pathology.
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Affiliation(s)
- Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Nikola Ivetic
- Department of Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Yi Du
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Son N Nguyen
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - S Hung Le
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Daniel Favre
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Ishac Nazy
- Department of Medicine, Michael G. DeGroote School of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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7
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Nguyen SN, Le SH, Ivanov DG, Ivetic N, Nazy I, Kaltashov IA. Structural characterization of a pathogenic antibody underlying vaccine-induced immune thrombotic thrombocytopenia (VITT). bioRxiv 2023:2023.05.28.542636. [PMID: 37398203 PMCID: PMC10312456 DOI: 10.1101/2023.05.28.542636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Vaccine-induced immune thrombotic thrombocytopenia (VITT) is a rare but extremely dangerous side effect that has been reported for several adenoviral (Ad)-vectored COVID-19 vaccines. VITT pathology had been linked to production of antibodies that recognize platelet factor 4 (PF4), an endogenous chemokine. In this work we characterize anti-PF4 antibodies obtained from a VITT patient's blood. Intact-mass MS measurements indicate that a significant fraction of this ensemble is comprised of antibodies representing a limited number of clones. MS analysis of large antibody fragments (the light chain, as well as the Fc/2 and Fd fragments of the heavy chain) confirms the monoclonal nature of this component of the anti-PF4 antibodies repertoire, and reveals the presence of a fully mature complex biantennary N-glycan within its Fd segment. Peptide mapping using two complementary proteases and LC-MS/MS analysis were used to determine the amino acid sequence of the entire light chain and over 98% of the heavy chain (excluding a short N-terminal segment). The sequence analysis allows the monoclonal antibody to be assigned to IgG2 subclass and verify that the light chain belongs to the λ-type. Incorporation of enzymatic de- N -glycosylation into the peptide mapping routine allows the N -glycan in the Fab region of the antibody to be localized to the framework 3 region of the V H domain. This novel N -glycosylation site (absent in the germline sequence) is a result of a single mutation giving rise to an NDT motif in the antibody sequence. Peptide mapping also provides a wealth of information on lower-abundance proteolytic fragments derived from the polyclonal component of the anti-PF4 antibody ensemble, revealing the presence of all four subclasses (IgG1 through IgG4) and both types of the light chain (λ and κ). The structural information reported in this work will be indispensable for understanding the molecular mechanism of VITT pathogenesis.
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8
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Yang Y, Du Y, Ivanov D, Niu C, Clare R, Smith JW, Nazy I, Kaltashov IA. Molecular architecture and platelet-activating properties of small immune complexes assembled on intact heparin and their possible involvement in heparin-induced thrombocytopenia. bioRxiv 2023:2023.02.11.528150. [PMID: 36798284 PMCID: PMC9934687 DOI: 10.1101/2023.02.11.528150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Heparin-induced thrombocytopenia (HIT) is an adverse reaction to heparin leading to a reduction in circulating platelets with an increased risk of thrombosis. It is precipitated by polymerized immune complexes consisting of pathogenic antibodies that recognize a small chemokine platelet factor 4 (PF4) bound to heparin, which trigger platelet activation and a hypercoagulable state. Characterization of these immune complexes is extremely challenging due to the enormous structural heterogeneity of such macromolecular assemblies and their constituents (especially heparin). We use native mass spectrometry to characterize small immune complexes formed by PF4, heparin and monoclonal HIT-specific antibodies. Up to three PF4 tetramers can be assembled on a heparin chain, consistent with the results of molecular modeling studies showing facile polyanion wrapping along the polycationic belt on the PF4 surface. Although these assemblies can accommodate a maximum of only two antibodies, the resulting immune complexes are capable of platelet activation despite their modest size. Taken together, these studies provide further insight into molecular mechanisms of HIT and other immune disorders where anti-PF4 antibodies play a central role.
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Chang MJ, Ollivault-Shiflett M, Schuman R, Ngoc Nguyen S, Kaltashov IA, Bobst C, Rajagopal SP, Przedpelski A, Barbieri JT, Lees A. Genetically detoxified tetanus toxin as a vaccine and conjugate carrier protein. Vaccine 2022; 40:5103-5113. [PMID: 35871872 DOI: 10.1016/j.vaccine.2022.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022]
Abstract
Tetanus toxoid (TTxd), developed over 100 years ago, is a clinically effective, legacy vaccine against tetanus. Due to the extreme potency of native tetanus toxin, manufacturing and regulatory efforts often focus on TTxd production, standardization, and safety, rather than product modernization. Recently, a genetically detoxified, full-length tetanus toxin protein (8MTT) was reported as a tetanus vaccine alternative to TTxd (Przedpelski et al. mBio, 2020). Here we describe the production of 8MTT in Gor/MetTM E. coli, a strain engineered to have an oxidative cytoplasm, allowing for the expression of soluble, disulfide-bonded proteins. The strain was also designed to efficiently cleave N-terminal methionine, the obligatory start amino acid for E. coli expressed proteins. 8MTT was purified as a soluble protein from the cytoplasm in a two-column protocol to > 99 % purity, yielding 0.5 g of purified 8MTT/liter of fermentation broth with low endotoxin contamination, and antigenic purity of 3500 Lf/mg protein nitrogen. Mouse immunizations showed 8MTT to be an immunogenic vaccine and effective as a carrier protein for peptide and polysaccharide conjugates. These studies validate 8MTT as commercially viable and, unlike the heterogenous tetanus toxoid, a uniform carrier protein for conjugate vaccines. The development of a recombinant, genetically detoxified toxin produced in E. coli aligns the tetanus vaccine with modern manufacturing, regulatory, standardization, and safety requirements.
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Affiliation(s)
- Min-Ju Chang
- Fina Biosolutions LLC, 9430 Key West Ave, Suite 200, Rockville, MD 20850, United States
| | | | - Richard Schuman
- Antibody and Immunoassay Consultants, 9430 Key West Ave, Suite 201, Rockville, MD 20850, United States
| | - Son Ngoc Nguyen
- University of Massachusetts, 240 Thatcher Way, Life Science Laboratories N369, Amherst, MA 01003, United States
| | - Igor A Kaltashov
- University of Massachusetts, 240 Thatcher Way, Life Science Laboratories N369, Amherst, MA 01003, United States
| | - Cedric Bobst
- University of Massachusetts, 240 Thatcher Way, Life Science Laboratories N369, Amherst, MA 01003, United States
| | - Shalini P Rajagopal
- National Institute for Biological Standards and Control, Medicines and Healthcare products Regulatory Agency, Blanche Lane, South Mimms, Potters Bar EN6 3QG, UK
| | - Amanda Przedpelski
- Medical College of Wisconsin, 8701 Watertown Plank Rd., Microbiology and Immunology BSB-2830, Milwaukee, WI 53226, United States
| | - Joseph T Barbieri
- Medical College of Wisconsin, 8701 Watertown Plank Rd., Microbiology and Immunology BSB-2830, Milwaukee, WI 53226, United States
| | - Andrew Lees
- Fina Biosolutions LLC, 9430 Key West Ave, Suite 200, Rockville, MD 20850, United States
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Cheng LL, Zhong AB, Muti IH, Eyles SJ, Vachet RW, Stopka SA, Sikora KN, Bobst CE, Agar JN, Mino-Kenudson MA, Wu CL, Christiani DC, Kaltashov IA, Agar NY. Abstract 2322: Multiplatform metabolomics studies of human cancers with NMR and mass spectrometry imaging. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Unfortunately, at present, there is no single technique that possesses all the characteristics needed to be considered an ideal global metabolite profiling tool. Thus, the use of multiple analytical platforms, such as combining the strengths of Mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), for metabolic profiling can maximize coverage and generate more global metabolomic profiles. In this study, we demonstrate the utilities of the combined NMR and MSI multiplatform in our metabolomics results on human prostate and lung cancers.
Statistical data on the natural history of prostate cancer (PCa) show that >70% of patients diagnosed by PSA screening will likely experience indolent disease with little impact on well-being. For about 17% of newly PSA-diagnosed patients, however, aggressive PCa proliferation ensues, truncating life expectancy. At present, no reliable clinical test can differentiate between these two groups. Using HRMAS 1HNMR followed by quantitative histology, we showed statistically significant correlations between concentrations of Spm and the amount of histologically-benign epithelial (Hb Epi) prostatic cells and glands in human cancerous prostates. However, as above discussed that using HRMAS NMR alone we cannot prove that Spm was indeed generated or resided in the Hb Epi cells. Nevertheless, using MALDI MSI, we were able to locate Spm (m/z: 203.223 ± 0.001Da) onto Hb Epi, where spermine on the PCa lesions appeared below detection limits. From these maps, for the first time, we could visualize and confirm the differential localizations of Spm in prostates. This proof of Sym relationship to prostate pathologies and its proposed PCa inhibitory effects may support further studies that are critical in differentiating aggressive from indolent PCa for disease evaluations and patient personalized treatment strategies.
To search for such screening metabolomics biomarkers in lung cancer, we used HRMAS NMR to analyze 93 pairs of human LuCa tissue and serum samples, and 29 healthy human sera. A number of potential metabolite candidates capable to differentiate LuCa characteristics were identified, including glutamate, lipids, alanine, glycerylphosphorylcholine, glutamine, phosphorylcholine, etc. This list can be further expanded by analyzing metabolite composition in the serum of cancer patients and control healthy subjects using LC-MS, which offers a dramatic increase in sensitivity compared to HRMAS NMR and, therefore, is better suited for the biomarker discovery. In addition to acquiring high-resolution mass data, the high data acquisition rate allows the fragment ion mass spectra (MS/MS) to be generated for the most abundant ionic species in each chromatographic peak. This feature allows specific classes of tumor-attenuated metabolites to be identified based on the presence of unique structurally diagnostic fragment ions in MS/MS spectra.
Citation Format: Leo L. Cheng, Anya B. Zhong, Isabella H. Muti, Stephen J. Eyles, Richard W. Vachet, Sylwia A. Stopka, Kristen N. Sikora, Cedric E. Bobst, Jeffrey N. Agar, Mari A. Mino-Kenudson, Chin-Lee Wu, David C. Christiani, Igor A. Kaltashov, Nathalie Y. Agar. Multiplatform metabolomics studies of human cancers with NMR and mass spectrometry imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2322.
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Affiliation(s)
- Leo L. Cheng
- 1Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Anya B. Zhong
- 1Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | - Isabella H. Muti
- 1Massachusetts General Hospital, Harvard Medical School, Charlestown, MA
| | | | | | - Sylwia A. Stopka
- 3Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | | | | | | | | | - Chin-Lee Wu
- 5Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | | | | | - Nathalie Y. Agar
- 3Brigham and Women's Hospital, Harvard Medical School, Boston, MA
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Favre D, Harmon JF, Zhang A, Miller MS, Kaltashov IA. Decavanadate interactions with the elements of the SARS-CoV-2 spike protein highlight the potential role of electrostatics in disrupting the infectivity cycle. J Inorg Biochem 2022; 234:111899. [PMID: 35716549 PMCID: PMC9183239 DOI: 10.1016/j.jinorgbio.2022.111899] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/02/2022] [Accepted: 06/05/2022] [Indexed: 12/15/2022]
Abstract
Polyoxidometalates (POMs) exhibit a range of biological properties that can be exploited for a variety of therapeutic applications. However, their potential utility as antivirals has been largely overlooked in the ongoing efforts to identify safe, effective and robust therapeutic agents to combat COVID-19. We focus on decavanadate (V10), a paradigmatic member of the POM family, to highlight the utility of electrostatic forces as a means of disrupting molecular processes underlying the SARS-CoV-2 entry into the host cell. While the departure from the traditional lock-and-key approach to the rational drug design relies on less-specific and longer-range interactions, it may enhance the robustness of therapeutic agents by making them less sensitive to the viral mutations. Native mass spectrometry (MS) not only demonstrates the ability of V10 to associate with the receptor-binding domain of the SARS-CoV-2 spike protein, but also provides evidence that this association disrupts the protein binding to its host cell-surface receptor. Furthermore, V10 is also shown to be capable of binding to the polybasic furin cleavage site within the spike protein, which is likely to decrease the effectiveness of the proteolytic processing of the latter (a pre-requisite for the viral fusion with the host cell membrane). Although in vitro studies carried out with SARS-CoV-2 infected cells identify V10 cytotoxicity as a major factor limiting its utility as an antiviral agent, the collected data provide a compelling stimulus for continuing the search for effective, robust and safe therapeutics targeting the novel coronavirus among members of the POM family.
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Affiliation(s)
- Daniel Favre
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, United States of America
| | - Jackson F Harmon
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, MA 01003, United States of America
| | - Ali Zhang
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Matthew S Miller
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster Immunology Research Centre, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003, United States of America; Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, MA 01003, United States of America.
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12
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Zhong AB, Muti IH, Eyles SJ, Vachet RW, Sikora KN, Bobst CE, Calligaris D, Stopka SA, Agar JN, Wu CL, Mino-Kenudson MA, Agar NYR, Christiani DC, Kaltashov IA, Cheng LL. Multiplatform Metabolomics Studies of Human Cancers With NMR and Mass Spectrometry Imaging. Front Mol Biosci 2022; 9:785232. [PMID: 35463966 PMCID: PMC9024335 DOI: 10.3389/fmolb.2022.785232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/02/2022] [Indexed: 11/22/2022] Open
Abstract
The status of metabolomics as a scientific branch has evolved from proof-of-concept to applications in science, particularly in medical research. To comprehensively evaluate disease metabolomics, multiplatform approaches of NMR combining with mass spectrometry (MS) have been investigated and reported. This mixed-methods approach allows for the exploitation of each individual technique's unique advantages to maximize results. In this article, we present our findings from combined NMR and MS imaging (MSI) analysis of human lung and prostate cancers. We further provide critical discussions of the current status of NMR and MS combined human prostate and lung cancer metabolomics studies to emphasize the enhanced metabolomics ability of the multiplatform approach.
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Affiliation(s)
- Anya B. Zhong
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Isabella H. Muti
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Richard W. Vachet
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Kristen N. Sikora
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Cedric E. Bobst
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA, United States
| | - David Calligaris
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Sylwia A. Stopka
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Jeffery N. Agar
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, United States
| | - Chin-Lee Wu
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
| | | | - Nathalie Y. R. Agar
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, MA, United States
| | - David C. Christiani
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
- Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Igor A. Kaltashov
- Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Leo L. Cheng
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, United States
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13
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Ivanov DG, Yang Y, Pawlowski JW, Carrick IJ, Kaltashov IA. Rapid Evaluation of the Extent of Haptoglobin Glycosylation Using Orthogonal Intact-Mass MS Approaches and Multivariate Analysis. Anal Chem 2022; 94:5140-5148. [PMID: 35285615 DOI: 10.1021/acs.analchem.1c05585] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intact-mass measurements are becoming increasingly popular in mass spectrometry (MS) based protein characterization, as they allow the entire complement of proteoforms to be evaluated within a relatively short time. However, applications of this approach are currently limited to systems exhibiting relatively modest degrees of structural diversity, as the high extent of heterogeneity frequently prevents straightforward MS measurements. Incorporation of limited charge reduction into electrospray ionization (ESI) MS is an elegant way to obtain meaningful information on most heterogeneous systems, yielding not only the average mass of the protein but also the mass range populated by the entire complement of proteoforms. Application of this approach to characterization of two different phenotypes of haptoglobin (1-1 and 2-1) provides evidence of a significant difference in their extent of glycosylation (with the glycan load of phenotype 2-1 being notably lighter) despite a significant overlap of their ionic signals. More detailed characterization of their glycosylation patterns is enabled by the recently introduced technique of cross-path reactive chromatography (XP-RC) with online MS detection, which combines chromatographic separation with in-line reduction of disulfide bonds to generate metastable haptoglobin subunits. Application of XP-RC to both haptoglobin phenotypes confirms that no modifications are present within their light chains and provides a wealth of information on glycosylation patterns of the heavy chains. N-Glycosylation patterns of both haptoglobin phenotypes were found to be consistent with bi- and triantennary structures of complex type that exhibit significant level of fucosylation and sialylation. However, multivariate analysis of haptoglobin 1-1 reveals higher number of the triantennary structures, in comparison to haptoglobin 2-1, as well as a higher extent of fucosylation. The glycosylation patterns deduced from the XP-RC/MS measurements are in agreement with the conclusions of the intact-mass analysis supplemented by limited charge reduction, suggesting that the latter technique can be employed in situations when fast assessment of protein heterogeneity is needed (e.g., process analytical technology applications).
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Affiliation(s)
- Daniil G Ivanov
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Yang Yang
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Jake W Pawlowski
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Ian J Carrick
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts─Amherst, 240 Thatcher Road, Amherst, Massachusetts 01003, United States
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14
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Muneeruddin K, Kaltashov IA, Wang G. Characterizing Soluble Protein Aggregates Using Native Mass Spectrometry Coupled with Temperature-Controlled Electrospray Ionization and Size-Excl usion Chromatography. Methods Mol Biol 2022; 2406:455-468. [PMID: 35089574 DOI: 10.1007/978-1-0716-1859-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Characterization of soluble protein aggregates provides valuable information for revealing mechanisms of protein aggregation process and assessing the activity and safety of protein therapeutics. However, the noncovalent interaction, the transient nature and higher degree of structural heterogeneity of the soluble aggregation system hinders precise characterization at the molecular level. Here, we describe methods using native mass spectrometry coupled with temperature-control electrospray ionization and size-exclusion chromatography to monitor the aggregation process and profile the aggregates in detail.
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Affiliation(s)
- Khaja Muneeruddin
- The Mass Spectrometry Facility, University of Massachusetts Medical School, Shrewsbury, MA, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Guanbo Wang
- Biomedical Pioneering Innovation Center, Peking University, Beijing, China.
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, China.
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15
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Yang W, Ivanov DG, Kaltashov IA. Extending the capabilities of intact-mass analyses to monoclonal immunoglobulins of the E-isotype (IgE). MAbs 2022; 14:2103906. [PMID: 35895856 PMCID: PMC9336480 DOI: 10.1080/19420862.2022.2103906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Mass spectrometry (MS) has become an indispensable tool in structural characterization and quality control of monoclonal antibodies (mAbs). Intact-mass analysis is a particularly attractive option that provides a powerful and cost-effective means to not only confirm the structural integrity of the protein, but also probe its interactions with therapeutic targets. To a certain extent, this success can be attributed to relatively modest glycosylation levels exhibited by IgG molecules, which limits their structural heterogeneity and enables straightforward mass measurements at the intact molecule level. The recent surge of interest in expanding the repertoire of mAbs to include other classes of immunoglobulins places a premium on efforts to adapt the IgG-tailored experimental strategies to other classes of antibodies, but their dramatically higher levels of glycosylation may create insurmountable obstacles. The monoclonal murine IgE antibody explored in this work provides a challenging model system, as its glycosylation level exceeds that of conventional IgG mAbs by a factor of nine. The commercial sample, which included various IgE fragments, yields a poorly resolved ionic signal in intact-mass measurements, from which little useful information can be extracted. However, coupling MS measurements with the limited charge reduction of select polycationic species in the gas phase gives rise to well-defined charge ladders, from which both ionic masses and charges can be readily determined. The measurements reveal significant variation of the extent of glycosylation within intact IgE molecules, as well as the presence of low-molecular weight impurities in the commercial IgE sample. Furthermore, incubation of the monoclonal IgE with its antigen (ovalbumin) gives rise to the formation of complexes with varying stoichiometries, which can also be uniquely identified using a combination of native MS, limited charge reduction in the gas phase and data fitting procedures. This work demonstrates that following appropriate modifications, intact-mass analysis measurements can be successfully applied to mAbs beyond the IgG isotype, providing a wealth of information not only on the mass distribution of the intact IgE molecules, but also their large-scale conformational integrity, the integrity of their covalent structure, and their interactions with antigens.
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Affiliation(s)
- Wenhua Yang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA.,College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Daniil G Ivanov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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16
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Favre D, Bobst CE, Eyles SJ, Murakami H, Crans DC, Kaltashov IA. Solution- and gas-phase behavior of decavanadate: implications for mass spectrometric analysis of redox-active polyoxidometalates. Inorg Chem Front 2022; 9:1556-1564. [PMID: 35756945 PMCID: PMC9216222 DOI: 10.1039/d1qi01618k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work explores the utility of high-resolution electrospray ionization (ESI) mass spectrometry (MS) and ion exclusion chromatography LC/MS for structural analysis of decavanadate (V10O286 ̄ or V10), a paradigmatic member...
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Affiliation(s)
- Daniel Favre
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA
| | - Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA
| | - Stephen J. Eyles
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, MA
| | - Heide Murakami
- Department of Chemistry, Colorado State University, Ft. Collins, CO
| | - Debbie C. Crans
- Department of Chemistry, Colorado State University, Ft. Collins, CO
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA
- Corresponding Author: All correspondence should be addressed to Igor A. Kaltashov at
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17
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Yang W, Tu Z, Li Q, Kaltashov IA, McClements DJ. Utilization of sonication-glycation to improve the functional properties of ovalbumin: A high-resolution mass spectrometry study. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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18
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Abstract
Ovalbumin (OVA), one of the major allergens in hen egg, exhibits extensive structural heterogeneity due to a range of post-translational modifications (PTMs). However, analyzing the structural heterogeneity of native OVA is challenging, and the relationship between heterogeneity and IgG/IgE-binding of OVA remains unclear. In this work, ion exchange chromatography (IXC) with salt gradient elution and on-line detection by native electrospray ionization mass spectrometry (ESI MS) was used to assess the structural heterogeneity of OVA, while inhibition-ELISA was used to assess the IgG/IgE binding characteristics of OVA. Over 130 different OVA proteoforms (including glycan-free species and 32 pairs of isobaric species) were identified. Proteoforms with acetylation, phosphorylation, oxidation and succinimide modifications had reduced IgG/IgE binding capacities, whereas those with few structural modifications had higher IgG/IgE binding capacities. OVA isoforms with a sialic acid-containing glycan modification had the highest IgG/IgE binding capacity. Our results demonstrate that on-line native IXC/MS with salt gradient elution can be used for rapid assessment of the structural heterogeneity of proteins. An improved understanding of the relationship between IgG/IgE binding capacity and OVA structure provides a basis for developing biotechnology or food processing methods for reducing protein allergenicity reduction.
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Affiliation(s)
- Wenhua Yang
- College of Chemistry and Bioengineering, Yichun University, Yichun, Jiangxi 336000, People's Republic of China.
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19
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Bobst CE, Sperry J, Friese OV, Kaltashov IA. Simultaneous Evaluation of a Vaccine Component Microheterogeneity and Conformational Integrity Using Native Mass Spectrometry and Limited Charge Reduction. J Am Soc Mass Spectrom 2021; 32:1631-1637. [PMID: 34006091 PMCID: PMC8514165 DOI: 10.1021/jasms.1c00091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Analytical characterization of extensively modified proteins (such as haptenated carrier proteins in synthetic vaccines) remains a challenging task due to the high degree of structural heterogeneity. Native mass spectrometry (MS) combined with limited charge reduction allows these obstacles to be overcome and enables meaningful characterization of a heavily haptenated carrier protein CRM197 (inactivated diphtheria toxin conjugated with nicotine), a major component of a smoking cessation vaccine. The extensive conjugation results in a near-continuum distribution of ionic signal in electrospray ionization (ESI) mass spectra of haptenated CRM197 even after size-exclusion chromatographic fractionation. However, supplementing the ESI MS measurements with limited charge reduction of ionic populations selected within narrow m/z windows gives rise to well-resolved charge ladders, from which both masses and charge states of the ionic species can be readily deduced. Application of this technique to a research-grade material of CRM197/H7 conjugate not only reveals its marginal conformational stability (manifested by the appearance of high charge-density ions in ESI MS) but also establishes a role of the extent of haptenation as a major factor driving the loss of the higher order structure integrity. The unique information provided by native MS used in combination with limited charge reduction provides a strong argument for this technique to become a standard/required tool in the analytical arsenal in the field of biotechnology and biopharmaceutical analysis, where protein conjugates are becoming increasingly common.
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Affiliation(s)
- Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003
| | - Justin Sperry
- BioTherapeutics Pharmaceutical Sciences, Pfizer, St. Louis, MO 63017
| | - Olga V. Friese
- BioTherapeutics Pharmaceutical Sciences, Pfizer, St. Louis, MO 63017
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA 01003
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20
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Yang Y, Ivanov DG, Kaltashov IA. The challenge of structural heterogeneity in the native mass spectrometry studies of the SARS-CoV-2 spike protein interactions with its host cell-surface receptor. bioRxiv 2021. [PMID: 34189525 DOI: 10.1101/2021.06.20.449191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Native mass spectrometry (MS) enjoyed tremendous success in the past two decades in a wide range of studies aiming at understanding the molecular mechanisms of physiological processes underlying a variety of pathologies and accelerating the drug discovery process. However, the success record of native MS has been surprisingly modest with respect to the most recent challenge facing the biomedical community â€" the novel coronavirus infection (COVID-19). The major reason for the paucity of successful studies that use native MS to target various aspects of SARS-CoV-2 interaction with its host is the extreme degree of structural heterogeneity of the viral protein playing a key role in the host cell invasion. Indeed, the SARS-CoV-2 spike protein (S-protein) is extensively glycosylated, presenting a formidable challenge for native mass spectrometry (MS) as a means of characterizing its interactions with both the host cell-surface receptor ACE2 and the drug candidates capable of disrupting this interaction. In this work we evaluate the utility of native MS complemented with the experimental methods using gas-phase chemistry (limited charge reduction) to obtain meaningful information on the association of the S1 domain of the S-protein with the ACE2 ectodomain, and the influence of a small synthetic heparinoid on this interaction. Native MS reveals the presence of several different S1 oligomers in solution and allows the stoichiometry of the most prominent S1/ACE2 complexes to be determined. This enables meaningful interpretation of the changes in native MS that are observed upon addition of a small synthetic heparinoid (the pentasaccharide fondaparinux) to the S1/ACE2 solution, confirming that the small polyanion destabilizes the protein/receptor binding.
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21
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Niu C, Du Y, Kaltashov IA. Towards better understanding of the heparin role in NETosis: feasibility of using native mass spectrometry to monitor interactions of neutrophil elastase with heparin oligomers. Int J Mass Spectrom 2021; 463:116550. [PMID: 33692650 PMCID: PMC7939139 DOI: 10.1016/j.ijms.2021.116550] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Neutrophil elastase is a serine protease released by neutrophils, and its dysregulation has been associated with a variety of debilitating pathologies, most notably cystic fibrosis. This protein is also a prominent component of the so-called neutrophil extracellular traps (NETs), whose formation is a part of the innate immunity response to invading pathogens, but also contributes to a variety of pathologies ranging from autoimmune disorders and inflammation to cancer to thrombotic complications in COVID-19. Retention of neutrophil elastase within NETs is provided by ejected DNA chains, although this protein is also capable of interacting with a range of other endogenous polyanions, such as heparin and heparan sulfate. In this work, we evaluate the feasibility of using native mass spectrometry (MS) as a means of studying interactions of neutrophil elastase with heparin oligomers ranging from structurally homogeneous synthetic pentasaccharide fondaparinux to relatively long (up to twenty saccharide units) and structurally heterogeneous chains produced by partial depolymerization of heparin. The presence of heterogeneous glycan chains on neutrophil elastase and the structural heterogeneity of heparin oligomers render the use of standard MS to study their complexes impractical. However, supplementing MS with limited charge reduction in the gas phase allows meaningful data to be extracted from MS measurements. In contrast to earlier molecular modeling studies where a single heparin-binding site was identified, our work reveals the existence of multiple binding sites, with a single protein molecule being able to accommodate up to three decasaccharides. The measurements also reveal the ability of even relatively short heparin oligomers to bridge two protein molecules, suggesting that characterization of these complexes using native MS can shed light on the structural properties of NETs. Lastly, the use of MS allows the binding preferences of heparin oligomers to neutrophil elastase to be studied with respect to specific structural properties of heparin, such as the level of sulfation (i.e., charge density). All experimental measurements are carried out in parallel with molecular dynamics simulations of the protein/heparin oligomer systems, which are in remarkable agreement with the experimental data and highlight the role of electrostatic interactions as dominant forces governing the formation of these complexes.
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Affiliation(s)
| | | | - Igor A. Kaltashov
- Corresponding author: Igor A. Kaltashov; address: 240 Thatcher Way, Life Sciences Laboratories N369, Amherst, MA 01003; ; phone: 413-545-1460; fax: 413-545-4490
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22
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Yang Y, Niu C, Bobst CE, Kaltashov IA. Charge Manipulation Using Solution and Gas-Phase Chemistry to Facilitate Analysis of Highly Heterogeneous Protein Complexes in Native Mass Spectrometry. Anal Chem 2021; 93:3337-3342. [PMID: 33566581 PMCID: PMC8514162 DOI: 10.1021/acs.analchem.0c05249] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structural heterogeneity is a significant challenge complicating (and in some cases making impossible) electrospray ionization mass spectrometry (ESI MS) analysis of noncovalent complexes comprising structurally heterogeneous biopolymers. The broad mass distribution exhibited by such species inevitably gives rise to overlapping ionic signals representing different charge states, resulting in a continuum spectrum with no discernible features that can be used to assign ionic charges and calculate their masses. This problem can be circumvented by using limited charge reduction, which utilizes gas-phase chemistry to induce charge-transfer reactions within ionic populations selected within narrow m/z windows, thereby producing well-defined and readily interpretable charge ladders. However, the ionic signal in native MS typically populates high m/z regions of mass spectra, which frequently extend beyond the precursor ion isolation limits of most commercial mass spectrometers. While the ionic signal of single-chain proteins can be shifted to lower m/z regions simply by switching to a denaturing solvent, this approach cannot be applied to noncovalent assemblies due to their inherent instability under denaturing conditions. An alternative approach explored in this work relies on adding supercharging reagents to protein solutions as a means of increasing the extent of multiple charging of noncovalent complexes in ESI MS without compromising their integrity. This shifts the ionic signal down the m/z scale to the region where ion selection and isolation can be readily accomplished with a front-end quadrupole, followed by limited charge reduction of the isolated ionic population. The feasibility of the new approach is demonstrated using noncovalent complexes formed by hemoglobin with structurally heterogeneous haptoglobin.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003
| | | | - Cedric E. Bobst
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Road, Amherst, MA 01003
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23
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Zhao Y, Kaltashov IA. Evaluation of top-down mass spectrometry and ion-mobility spectroscopy as a means of mapping protein-binding motifs within heparin chains. Analyst 2021; 145:3090-3099. [PMID: 32150181 DOI: 10.1039/d0an00097c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Identifying structural elements within heparin (as well as other glycosaminoglycan) chains that enable their interaction with a specific client protein remains a challenging task due to the high degree of both intra- and inter-chain heterogeneity exhibited by this polysaccharide. The new experimental approach explored in this work is based on the assumption that the heparin chain segments bound to the protein surface will be less prone to collision-induced dissociation (CID) in the gas phase compared to the chain regions that are not involved in binding. Facile removal of the unbound chain segments from the protein/heparin complex should allow the length and the number of sulfate groups within the protein-binding segment of the heparin chain to be determined by measuring the mass of the truncated heparin chain that remains bound to the protein. Conformational integrity of the heparin-binding interface on the protein surface in the course of CID is ensured by monitoring the evolution of collisional cross-section (CCS) of the protein/heparin complexes as a function of collisional energy. A dramatic increase in CCS signals the occurrence of large-scale conformational changes within the protein and identifies the energy threshold, beyond which relevant information on the protein-binding segments of heparin chains is unlikely to be obtained. Testing this approach using a 1 : 1 complex formed by a recombinant form of an acidic fibroblast growth factor (FGF-1) and a synthetic pentasaccharide GlcNS,6S-GlcA-GlcNS,3S,6S-IdoA2S-GlcNS,6S-Me as a model system indicated that a tri-saccharide fragment is the minimal-length FGF-binding segment. Extension of this approach to a decameric heparin chain (dp10) allowed meaningful binding data to be obtained for a 1 : 1 protein/dp10 complex, while the ions representing the higher stoichiometry complex (2 : 1) underwent dissociation via asymmetric charge partitioning without generating truncated heparin chains that remain bound to the protein.
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Affiliation(s)
- Yunlong Zhao
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003, USA.
| | - Igor A Kaltashov
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003, USA.
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24
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Yang Y, Du Y, Kaltashov IA. The Utility of Native MS for Understanding the Mechanism of Action of Repurposed Therapeutics in COVID-19: Heparin as a Disruptor of the SARS-CoV-2 Interaction with Its Host Cell Receptor. Anal Chem 2020; 92:10930-10934. [PMID: 32678978 PMCID: PMC7384394 DOI: 10.1021/acs.analchem.0c02449] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 07/17/2020] [Indexed: 02/06/2023]
Abstract
The emergence and rapid proliferation of the novel coronavirus (SARS-CoV-2) resulted in a global pandemic, with over 6,000,000 cases and nearly 400,000 deaths reported worldwide by the end of May 2020. A rush to find a cure prompted re-evaluation of a range of existing therapeutics vis-à-vis their potential role in treating COVID-19, placing a premium on analytical tools capable of supporting such efforts. Native mass spectrometry (MS) has long been a tool of choice in supporting the mechanistic studies of drug/therapeutic target interactions, but its applications remain limited in the cases that involve systems with a high level of structural heterogeneity. Both SARS-CoV-2 spike protein (S-protein), a critical element of the viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively glycosylated, making them challenging targets for native MS. However, supplementing native MS with a gas-phase ion manipulation technique (limited charge reduction) allows meaningful information to be obtained on the noncovalent complexes formed by ACE2 and the receptor-binding domain (RBD) of the S-protein. Using this technique in combination with molecular modeling also allows the role of heparin in destabilizing the ACE2/RBD association to be studied, providing critical information for understanding the molecular mechanism of its interference with the virus docking to the host cell receptor. Both short (pentasaccharide) and relatively long (eicosasaccharide) heparin oligomers form 1:1 complexes with RBD, indicating the presence of a single binding site. This association alters the protein conformation (to maximize the contiguous patch of the positive charge on the RBD surface), resulting in a notable decrease in its ability to associate with ACE2. The destabilizing effect of heparin is more pronounced in the case of the longer chains due to the electrostatic repulsion between the low-pI ACE2 and the heparin segments not accommodated on the RBD surface. In addition to providing important mechanistic information on attenuation of the ACE2/RBD association by heparin, the study demonstrates the yet untapped potential of native MS coupled to gas-phase ion chemistry as a means of facilitating rational repurposing of the existing medicines for treating COVID-19.
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Affiliation(s)
- Yang Yang
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003
| | - Yi Du
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, MA 01003
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25
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Yang Y, Du Y, Kaltashov IA. The utility of native MS for understanding the mechanism of action of repurposed therapeutics in COVID-19: heparin as a disruptor of the SARS-CoV-2 interaction with its host cell receptor. bioRxiv 2020. [PMID: 32577646 DOI: 10.1101/2020.06.09.142794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The emergence and rapid proliferation of the novel coronavirus (SARS-CoV-2) resulted in a global pandemic, with over six million cases and nearly four hundred thousand deaths reported world-wide by the end of May 2020. A rush to find the cures prompted re-evaluation of a range of existing therapeutics vis-à-vis their potential role in treating COVID-19, placing a premium on analytical tools capable of supporting such efforts. Native mass spectrometry (MS) has long been a tool of choice in supporting the mechanistic studies of drug/therapeutic target interactions, but its applications remain limited in the cases that involve systems with a high level of structural heterogeneity. Both SARS-CoV-2 spike protein (S-protein), a critical element of the viral entry to the host cell, and ACE2, its docking site on the host cell surface, are extensively glycosylated, making them challenging targets for native MS. However, supplementing native MS with a gas-phase ion manipulation technique (limited charge reduction) allows meaningful information to be obtained on the non-covalent complexes formed by ACE2 and the receptor-binding domain (RBD) of the S-protein. Using this technique in combination with molecular modeling also allows the role of heparin in destabilizing the ACE2/RBD association to be studied, providing critical information for understanding the molecular mechanism of its interference with the virus docking to the host cell receptor. Both short (pentasaccharide) and relatively long (eicosasaccharide) heparin oligomers form 1:1 complexes with RBD, indicating the presence of a single binding site. This association alters the protein conformation (to maximize the contiguous patch of the positive charge on the RBD surface), resulting in a notable decrease of its ability to associate with ACE2. The destabilizing effect of heparin is more pronounced in the case of the longer chains due to the electrostatic repulsion between the low-p I ACE2 and the heparin segments not accommodated on the RBD surface. In addition to providing important mechanistic information on attenuation of the ACE2/RBD association by heparin, the study demonstrates the yet untapped potential of native MS coupled to gas-phase ion chemistry as a means of facilitating rational repurposing of the existing medicines for treating COVID-19. Abstract Figure
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Niu C, Zhao Y, Bobst CE, Savinov SN, Kaltashov IA. Identification of Protein Recognition Elements within Heparin Chains Using Enzymatic Foot-Printing in Solution and Online SEC/MS. Anal Chem 2020; 92:7565-7573. [PMID: 32347711 DOI: 10.1021/acs.analchem.0c00115] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Understanding molecular mechanisms governing interactions of glycosaminoglycans (such as heparin) with proteins remains challenging due to their enormous structural heterogeneity. Commonly accepted approaches seek to reduce the structural complexity by searching for "binding epitopes" within the limited subsets of short heparin oligomers produced either enzymatically or synthetically. A top-down approach presented in this work seeks to preserve the chemical diversity displayed by heparin by allowing the longer and structurally diverse chains to interact with the client protein. Enzymatic lysis of the protein-bound heparin chains followed by the product analysis using size exclusion chromatography with online mass spectrometry detection (SEC/MS) reveals the oligomers that are protected from lysis due to their tight association with the protein, and enables their characterization (both the oligomer length, and the number of incorporated sulfate and acetyl groups). When applied to a paradigmatic heparin/antithrombin system, the new method generates a series of oligomers with surprisingly distinct sulfation levels. The extent of sulfation of the minimal-length binder (hexamer) is relatively modest yet persistent, consistent with the notion of six sulfate groups being both essential and sufficient for antithrombin binding. However, the masses of longer surviving chains indicate complete sulfation of disaccharides beyond the hexasaccharide core. Molecular dynamics simulations confirm the existence of favorable electrostatic interactions between the high charge-density saccharide residues flanking the "canonical" antithrombin-binding hexasaccharide and the positive patch on the surface of the overall negatively charged protein. Furthermore, electrostatics may rescue the heparin/protein interaction in the absence of the canonical binding element.
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Affiliation(s)
- Chendi Niu
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Yunlong Zhao
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Cedric E Bobst
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Sergey N Savinov
- Biochemistry and Molecular Biology Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
| | - Igor A Kaltashov
- Chemistry Department, University of Massachusetts-Amherst, 240 Thatcher Way, Amherst, Massachusetts 01003, United States
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Niu C, Yang Y, Huynh A, Nazy I, Kaltashov IA. Platelet Factor 4 Interactions with Short Heparin Oligomers: Implications for Folding and Assembly. Biophys J 2020; 119:1371-1379. [PMID: 32348723 DOI: 10.1016/j.bpj.2020.04.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/11/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022] Open
Abstract
Association of platelet factor 4 (PF4) with heparin is a first step in formation of aggregates implicated in the development of heparin-induced thrombocytopenia (HIT), a potentially fatal immune disorder affecting 1-5% of patients receiving heparin. Despite being a critically important element in HIT etiology, relatively little is known about the specific molecular mechanism of PF4-heparin interactions. This work uses native mass spectrometry to investigate PF4 interactions with relatively short heparin chains (up to decasaccharides). The protein is shown to be remarkably unstable at physiological ionic strength in the absence of polyanions; only monomeric species are observed, and the extent of multiple charging of corresponding ions indicates a partial loss of conformational integrity. The tetramer signal remains at or below the detection threshold in the mass spectra until the solution's ionic strength is elevated well above the physiological level, highlighting the destabilizing role played by electrostatic interactions vis-à-vis quaternary structure of this high-pI protein. The tetramer assembly is dramatically facilitated by relatively short polyanions (synthetic heparin-mimetic pentasaccharide), with the majority of the protein molecules existing in the tetrameric state even at physiological ionic strength. Each tetramer accommodates up to six pentasaccharides, with at least three such ligands required to guarantee the higher-order structure integrity. Similar results are obtained for PF4 association with longer and structurally heterogeneous heparin oligomers (decamers). These longer polyanions can also induce PF4 dimer assembly when bound to the protein in relatively low numbers, lending support to a model of PF4/heparin interaction in which the latter wraps around the protein, making contacts with multiple subunits. Taken together, these results provide a more nuanced picture of PF4-glycosaminoglycan interactions leading to complex formation. This work also advocates for a greater utilization of native mass spectrometry in elucidating molecular mechanisms underlying HIT, as well as other physiological processes driven by electrostatic interactions.
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Affiliation(s)
- Chendi Niu
- Chemistry Department, University of Massachusetts-Amherst, Amherst, Massachusetts
| | - Yang Yang
- Chemistry Department, University of Massachusetts-Amherst, Amherst, Massachusetts
| | - Angela Huynh
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Ishac Nazy
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Igor A Kaltashov
- Chemistry Department, University of Massachusetts-Amherst, Amherst, Massachusetts.
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Kaltashov IA, Bobst CE, Pawlowski J, Wang G. Mass spectrometry-based methods in characterization of the higher order structure of protein therapeutics. J Pharm Biomed Anal 2020; 184:113169. [PMID: 32092629 DOI: 10.1016/j.jpba.2020.113169] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
Higher order structure of protein therapeutics is an important quality attribute, which dictates both potency and safety. While modern experimental biophysics offers an impressive arsenal of state-of-the-art tools that can be used for the characterization of higher order structure, many of them are poorly suited for the characterization of biopharmaceutical products. As a result, these analyses were traditionally carried out using classical techniques that provide relatively low information content. Over the past decade, mass spectrometry made a dramatic debut in this field, enabling the characterization of higher order structure of biopharmaceuticals as complex as monoclonal antibodies at a level of detail that was previously unattainable. At present, mass spectrometry is an integral part of the analytical toolbox across the industry, which is critical not only for quality control efforts, but also for discovery and development.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
| | - Cedric E Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Jake Pawlowski
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province, PR China
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Kaltashov IA, El Khoury A, Ren C, Savinov SN. Ruthenium coordination preferences in imidazole-containing systems revealed by electrospray ionization mass spectrometry and molecular modeling: Possible cues for the surprising stability of the Ru (III)/tris (hydroxymethyl)-aminomethane/imidazole complexes. J Mass Spectrom 2020; 55:e4435. [PMID: 31508870 DOI: 10.1002/jms.4435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 07/19/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Ruthenium is a platinoid that exhibits a range of unique chemical properties in solution, which are exploited in a variety of applications, including luminescent probes, anticancer therapies, and artificial photosynthesis. This paper focuses on a recently demonstrated ability of this metal in its +3 oxidation state to form highly stable complexes with tris (hydroxymethyl)aminomethane (H2 NC(CH2 OH)3 , Tris-base or T) and imidazole (Im) ligands, where a single RuIII cation is coordinated by two molecules of each T and Im. High-resolution electrospray ionization mass spectrometry (ESI MS) is used to characterize RuIII complexes formed by placing a RuII complex [(NH3 )5 RuII Cl]Cl in a Tris buffer under aerobic conditions. The most abundant ionic species in ESI MS represent mononuclear complexes containing an oxidized form of the metal, ie, [Xn RuIII T2 - 2H]+ , where X could be an additional T (n = 1) or NH3 (n = 0-2). Di- and tri-metal complexes also give rise to a series of abundant ions, with the highest mass ion representing a metal complex with an empirical formula Ru3 C24 O21 N6 H66 (interpreted as cyclo(T2 RuO)3 , a cyclic oxo-bridged structure, where the coordination sphere of each metal is completed by two T ligands). The empirical formulae of the binuclear species are consistent with the structures representing acyclic fragments of cyclo(T2 RuO)3 with addition of various combinations of ammonia and dioxygen as ligands. Addition of histidine in large molar excess to this solution results in complete disassembly of poly-nuclear complexes and gives rise to a variety of ionic species in the ESI mass spectrum with a general formula [RuIII Hisk Tm (NH3 )n - 2H]+ , where k = 0 to 2, m = 0 to 3, and n = 0 to 4. Ammonia adducts are present for all observed combinations of k and m, except k = m = 2, suggesting that [His2 RuIII T2 - 2H]+ represents a complex with a fully completed coordination sphere. The observed cornucopia of RuIII complexes formed in the presence of histidine is in stark contrast to the previously reported selective reactivity of imidazole, which interacts with the metal by preserving the RuT2 core and giving rise to a single abundant ruthenium complex (represented by [Im2 RuIII T2 - 2H]+ in ESI mass spectra). Surprisingly, the behavior of a hexa-histidine peptide (HHHHHH) is similar to that of a single imidazole, rather than a single histidine amino acid: The RuT2 core is preserved, with the following ionic species observed in ESI mass spectra: [HHHHHH·(RuIII T2 )m - (3m-1)H]+ (m = 1-3). The remarkable selectivity of the imidazole interaction with the RuIII T2 core is rationalized using energetic considerations at the quantum mechanical level of theory.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Anton El Khoury
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Chengfeng Ren
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Sergey N Savinov
- Department of Biochemistry and Molecular Biology, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
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Dinges SS, Hohm A, Vandergrift LA, Nowak J, Habbel P, Kaltashov IA, Cheng LL. Cancer metabolomic markers in urine: evidence, techniques and recommendations. Nat Rev Urol 2020; 16:339-362. [PMID: 31092915 DOI: 10.1038/s41585-019-0185-3] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Urinary tests have been used as noninvasive, cost-effective tools for screening, diagnosis and monitoring of diseases since ancient times. As we progress through the 21st century, modern analytical platforms have enabled effective measurement of metabolites, with promising results for both a deeper understanding of cancer pathophysiology and, ultimately, clinical translation. The first study to measure metabolomic urinary cancer biomarkers using NMR and mass spectrometry (MS) was published in 2006 and, since then, these techniques have been used to detect cancers of the urological system (kidney, prostate and bladder) and nonurological tumours including those of the breast, ovary, lung, liver, gastrointestinal tract, pancreas, bone and blood. This growing field warrants an assessment of the current status of research developments and recommendations to help systematize future research.
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Affiliation(s)
- Sarah S Dinges
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Haematology and Oncology, CCM, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Hohm
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Diagnostic and Interventional Neuroradiology, University Hospital of Würzburg, Würzburg, Germany
| | - Lindsey A Vandergrift
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Johannes Nowak
- Department of Diagnostic and Interventional Radiology, University Hospital of Würzburg, Würzburg, Germany
| | - Piet Habbel
- Department of Haematology and Oncology, CCM, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
| | - Leo L Cheng
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 375] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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Ren C, Bobst CE, Kaltashov IA. Exploiting His-Tags for Absolute Quantitation of Exogenous Recombinant Proteins in Biological Matrices: Ruthenium as a Protein Tracer. Anal Chem 2019; 91:7189-7198. [PMID: 31083917 DOI: 10.1021/acs.analchem.9b00504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Metal labeling and ICP MS detection offer an alternative to commonly accepted techniques that are currently used to quantitate exogenous proteins in vivo, but modifying the protein surface with metal-containing groups inevitably changes its biophysical properties and is likely to affect trafficking and biodistribution. The approach explored in this work takes advantage of the presence of hexa-histidine tags in many recombinant proteins, which have high affinity toward a range of metals. While many divalent metals bind to poly histidine sequences reversibly, oxidation of imidazole-bound CoII or RuII is known to result in a dramatic increase of the binding strength. In order to evaluate the feasibility of using imidazole-bound metal oxidation as a means of attaching permanent tags to polyhistidine segments, a synthetic peptide YPDFEDYWMKHHHHHH was used as a model. RuII can be oxidized under ambient (aerobic) conditions, allowing any oxidation damage to the peptide beyond the metal-binding site to be avoided. The resulting peptide-RuIII complex is very stable, with the single hexa-histidine segment capable of accommodating up to three metal ions. Localization of RuIII within the hexa-histidine segment of the peptide was confirmed by tandem mass spectrometry. The RuIII/peptide binding appears to be irreversible, with both low- and high-molecular weight biologically relevant scavengers failing to strip the metal from the peptide. Application of this protocol to labeling a recombinant form of an 80 kDa protein transferrin allowed RuIII to be selectively placed within the His-tag segment. The metal label remained stable in the presence of ubiquitous scavengers and did not interfere with the receptor binding, while allowing the protein to be readily detected in serum at sub-nM concentrations. The results of this work suggest that ruthenium lends itself as an ideal metal tag for selective labeling of His-tag containing recombinant proteins to enable their sensitive detection and quantitation with ICP MS.
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Affiliation(s)
- Chengfeng Ren
- Department of Chemistry , University of Massachusetts-Amherst , Amherst , Massachusetts 01003 , United States
| | - Cedric E Bobst
- Department of Chemistry , University of Massachusetts-Amherst , Amherst , Massachusetts 01003 , United States
| | - Igor A Kaltashov
- Department of Chemistry , University of Massachusetts-Amherst , Amherst , Massachusetts 01003 , United States
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Minsky BB, Abzalimov RR, Niu C, Zhao Y, Kirsch Z, Dubin PL, Savinov SN, Kaltashov IA. Mass Spectrometry Reveals a Multifaceted Role of Glycosaminoglycan Chains in Factor Xa Inactivation by Antithrombin. Biochemistry 2018; 57:4880-4890. [PMID: 29999301 DOI: 10.1021/acs.biochem.8b00199] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Factor Xa (fXa) inhibition by antithrombin (AT) enabled by heparin or heparan sulfate is critical for controlling blood coagulation. AT activation by heparin has been investigated extensively, while interaction of heparin with trapped AT/fXa intermediates has received relatively little attention. We use native electrospray ionization mass spectrometry to study the role of heparin chains of varying length [hexa-, octa-, deca-, and eicosasaccharides (dp6, dp8, dp10, and dp20, respectively)] in AT/fXa complex assembly. Despite being critical promoters of AT/Xa binding, shorter heparin chains are excluded from the final products (trapped intermediates). However, replacement of short heparin segments with dp20 gives rise to a prominent ionic signal of ternary complexes. These species are also observed when the trapped intermediate is initially prepared in the presence of a short oligoheparin (dp6), followed by addition of a longer heparin chain (dp20), indicating that binding of heparin to AT/fXa complexes takes place after the inhibition event. The importance of the heparin chain length for its ability to associate with the trapped intermediate suggests that the binding likely occurs in a bidentate fashion (where two distinct segments of oligoheparin make contacts with the protein components, while the part of the chain separating these two segments is extended into solution to minimize electrostatic repulsion). This model is corroborated by both molecular dynamics simulations with an explicit solvent and ion mobility measurements in the gas phase. The observed post-inhibition binding of heparin to the trapped AT/fXa intermediates hints at the likely role played by heparan sulfate in their catabolism.
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Yang W, Tu Z, Wang H, Zhang L, Kaltashov IA, Zhao Y, Niu C, Yao H, Ye W. The mechanism of reduced IgG/IgE-binding of β-lactoglobulin by pulsed electric field pretreatment combined with glycation revealed by ECD/FTICR-MS. Food Funct 2018; 9:417-425. [PMID: 29220053 DOI: 10.1039/c7fo01082f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Bovine β-lactoglobulin (β-Lg) is a major allergen existing in milk and causes about 90% of IgE-mediated cow's milk allergies. Previous studies showed that pulsed electric field (PEF) treatment could partially unfold the protein, which may contribute to the improvement of protein glycation. In this study, the effect of PEF pretreatment combined with glycation on the IgG/IgE-binding ability and the structure of β-Lg was investigated. The result showed that PEF pretreatment combined with glycation significantly reduced the IgG and IgE binding abilities, which was attributed to the changes of secondary and tertiary structure and the increase in glycation sites and degree of substitution per peptide (DSP) value determined by electron capture dissociation Fourier transform ion cyclotron resonance mass spectrometry (ECD/FTICR-MS). Unexpectedly, glycation sites (K47, K91 and K135) added by two mannose molecules were identified in glycated β-Lg with PEF pretreatment. Moreover, the results indicated that PEF pretreatment at 25 kV cm-1 for 60 μs promoted the reduction of IgG/IgE-binding capacity by increasing the glycation degree of β-Lg, whereas single PEF treatment under the same conditions markedly enhanced the IgG/IgE-binding ability by partially unfolding the structure of β-Lg. The results suggested that ECD/FTICR-MS could help us to understand the mechanism of reduction in the IgG/IgE-binding of β-Lg by structural characterization at the molecular level. Therefore, PEF pretreatment combined with glycation may provide an alternative method for β-Lg desensitization.
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Affiliation(s)
- Wenhua Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi, 330047, P. R. China.
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Kaltashov IA. Mass spectrometry-based methods to study macromolecular higher order structure and interactions. Methods 2018; 144:1-2. [DOI: 10.1016/j.ymeth.2018.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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36
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Liu J, Tu ZC, Liu GX, Niu CD, Yao HL, Wang H, Sha XM, Shao YH, Kaltashov IA. Ultrasonic Pretreatment Combined with Dry-State Glycation Reduced the Immunoglobulin E/Immunoglobulin G-Binding Ability of α-Lactalbumin Revealed by High-Resolution Mass Spectrometry. J Agric Food Chem 2018; 66:5691-5698. [PMID: 29758985 DOI: 10.1021/acs.jafc.8b00489] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bovine α-lactalbumin (α-LA) is one of major food allergens in cow's milk. The present work sought to research the effects of ultrasonic pretreatment combined with dry heating-induced glycation between α-LA and galactose on the immunoglobulin E (IgE)/immunoglobulin G (IgG)-binding ability and glycation extent of α-LA, determined by inhibition enzyme-linked immunosorbent assay and high-resolution mass spectrometry, respectively. The IgE/IgG-binding ability of glycated α-LA was significantly decreased as a result of ultrasonic pretreatment, while the average molecular weight, incorporation ratio (IR) value, location and number of glycation sites, and degree of substitution per peptide (DSP) value were elevated. When the mixtures of α-LA and galactose were pretreated by ultrasonication at 150 W/cm2, glycated α-LA possesses seven glycation sites, the highest IR and DSP values, and the lowest IgE/IgG-binding ability. Therefore, the decrease in the IgE/IgG-binding ability of α-LA depends upon not only the shielding effect of the linear epitope found to be caused by the glycation of K13, K16, K58, K93, and K98 sites but also the intensified glycation extent, which reflected in the increase of the IR value, the number of glycation sites, and the DSP value. Moreover, allergenic proteins and monosaccharides pretreated by ultrasonication and then followed by dry-state glycation were revealed as a promising way of achieving lower allergenicity of proteins in food processing.
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Affiliation(s)
- Jun Liu
- College of Life Sciences , Jiangxi Normal University , Nanchang , Jiangxi 330022 , People's Republic of China
| | - Zong-Cai Tu
- College of Life Sciences , Jiangxi Normal University , Nanchang , Jiangxi 330022 , People's Republic of China
- State Key Laboratory of Food Science and Technology , Nanchang University , Nanchang , Jiangxi 330047 , People's Republic of China
| | - Guang-Xian Liu
- College of Life Sciences , Jiangxi Normal University , Nanchang , Jiangxi 330022 , People's Republic of China
| | - Chen-di Niu
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Hong-Lin Yao
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
| | - Hui Wang
- State Key Laboratory of Food Science and Technology , Nanchang University , Nanchang , Jiangxi 330047 , People's Republic of China
| | - Xiao-Mei Sha
- College of Life Sciences , Jiangxi Normal University , Nanchang , Jiangxi 330022 , People's Republic of China
| | - Yan-Hong Shao
- College of Life Sciences , Jiangxi Normal University , Nanchang , Jiangxi 330022 , People's Republic of China
| | - Igor A Kaltashov
- Department of Chemistry , University of Massachusetts Amherst , Amherst , Massachusetts 01003 , United States
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Kaltashov IA, Pawlowski JW, Yang W, Muneeruddin K, Yao H, Bobst CE, Lipatnikov AN. LC/MS at the whole protein level: Studies of biomolecular structure and interactions using native LC/MS and cross-path reactive chromatography (XP-RC) MS. Methods 2018; 144:14-26. [PMID: 29702225 DOI: 10.1016/j.ymeth.2018.04.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 04/18/2018] [Indexed: 11/25/2022] Open
Abstract
Interfacing liquid chromatography (LC) with electrospray ionization (ESI) to enable on-line MS detection had been initially implemented using reversed phase LC, which in the past three decades remained the default type of chromatography used for LC/MS and LC/MS/MS studies of protein structure. In contrast, the advantages of other types of LC as front-ends for ESI MS, particularly those that allow biopolymer higher order structure to be preserved throughout the separation process, enjoyed relatively little appreciation until recently. However, the past few years witnessed a dramatic surge of interest in the so-called "native" (with "non-denaturing" being perhaps a more appropriate adjective) LC/MS and LC/MS/MS analyses within the bioanalytical and biophysical communities. This review focuses on recent advances in this field, with an emphasis on size exclusion and ion exchange chromatography as front-end platforms for protein characterization by LC/MS. Also discussed are the benefits provided by the integration of chemical reactions in the native LC/MS analyses, including both ion chemistry in the gas phase (e.g., limited charge reduction for characterization of highly heterogeneous biopolymers) and solution-phase reactions (using the recently introduced technique cross-path reactive chromatography).
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Affiliation(s)
- Igor A Kaltashov
- Institute for Applied Life Sciences and Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, United States.
| | - Jake W Pawlowski
- Institute for Applied Life Sciences and Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Wenhua Yang
- Institute for Applied Life Sciences and Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Khaja Muneeruddin
- Institute for Applied Life Sciences and Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Honglin Yao
- Institute for Applied Life Sciences and Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Cedric E Bobst
- Institute for Applied Life Sciences and Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, United States
| | - Andrei N Lipatnikov
- Department of Mechanics and Maritime Sciences, Chalmers University of Technology, Göteborg, Sweden
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Pawlowski JW, Bajardi-Taccioli A, Houde D, Feschenko M, Carlage T, Kaltashov IA. Influence of glycan modification on IgG1 biochemical and biophysical properties. J Pharm Biomed Anal 2018; 151:133-144. [DOI: 10.1016/j.jpba.2017.12.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/29/2017] [Accepted: 12/31/2017] [Indexed: 02/04/2023]
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Wang G, Bondarenko PV, Kaltashov IA. Multi-step conformational transitions in heat-treated protein therapeutics can be monitored in real time with temperature-controlled electrospray ionization mass spectrometry. Analyst 2018; 143:670-677. [PMID: 29303166 DOI: 10.1039/c7an01655g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Heat-induced conformational transitions are frequently used to probe the free energy landscapes of proteins. However, the extraction of information from thermal denaturation profiles pertaining to non-native protein conformations remains challenging due to their transient nature and significant conformational heterogeneity. Previously we developed a temperature-controlled electrospray ionization (ESI) source that allowed unfolding and association of biopolymers to be monitored by mass spectrometry (MS) in real time as a function of temperature. The scope of this technique is now extended to systems that undergo multi-step denaturation upon heat stress, as well as relatively small-scale conformational changes that are precursors to protein aggregation. The behavior of two therapeutic proteins (human antithrombin and an IgG1 monoclonal antibody) under heat-stress conditions is monitored in real time, providing evidence that relatively small-scale conformational changes in each system lead to protein oligomerization, followed by aggregation. Temperature-controlled ESI MS is particularly useful for the studies of heat-stressed multi-domain proteins such as IgG, where it allows distinct transitions to be observed. The ability of native temperature-controlled ESI MS to monitor both the conformational changes and oligomerization/degradation with high selectivity complements the classic calorimetric methods, lending itself as a powerful experimental tool for the thermostability studies of protein therapeutics.
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Affiliation(s)
- Guanbo Wang
- Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, Jiangsu Key Laboratory of Biomedical Materials, and School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu, China.
| | - Pavel V Bondarenko
- Attribute Sciences, Process Development, Amgen, Inc., Thousand Oaks, CA, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
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Pawlowski JW, Carrick I, Kaltashov IA. Integration of On-Column Chemical Reactions in Protein Characterization by Liquid Chromatography/Mass Spectrometry: Cross-Path Reactive Chromatography. Anal Chem 2018; 90:1348-1355. [DOI: 10.1021/acs.analchem.7b04328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jake W. Pawlowski
- Department of Chemistry, University of Massachusetts—Amherst, Amherst, Massachusetts 01003, United States
| | - Ian Carrick
- Department of Chemistry, University of Massachusetts—Amherst, Amherst, Massachusetts 01003, United States
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts—Amherst, Amherst, Massachusetts 01003, United States
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Huang HT, Bobst CE, Iwig JS, Chivers PT, Kaltashov IA, Maroney MJ. Co(II) and Ni(II) binding of the Escherichia coli transcriptional repressor RcnR orders its N terminus, alters helix dynamics, and reduces DNA affinity. J Biol Chem 2017; 293:324-332. [PMID: 29150441 DOI: 10.1074/jbc.ra117.000398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/13/2017] [Indexed: 12/22/2022] Open
Abstract
RcnR, a transcriptional regulator in Escherichia coli, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered flexibility from the N terminus through helix 1 and modulated the RcnR-DNA interaction. Apo-RcnR and RcnR-DNA complexes and the Zn(II)-RcnR complex exhibited similar 2H uptake kinetics, with fast-exchanging segments located in the N terminus, in helix 1 (residues 14-24), and at the C terminus. The largest difference in 2H incorporation between apo- and Ni(II)- and Co(II)-bound RcnR was observed in helix 1, which contains the N terminus and His-3, and has been associated with cognate metal binding. 2H uptake in helix 1 was suppressed in the Ni(II)- and Co(II)-bound RcnR complexes, in particular in the peptide corresponding to residues 14-24, containing Arg-14 and Lys-17. Substitution of these two residues drastically affected DNA-binding affinity, resulting in rcnA expression in the absence of metal. Our results suggest that cognate metal binding to RcnR orders its N terminus, decreases helix 1 flexibility, and induces conformational changes that restrict DNA interactions with the positively charged residues Arg-14 and Lys-17. These metal-induced alterations decrease RcnR-DNA binding affinity, leading to rcnAB expression.
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Affiliation(s)
- Hsin-Ting Huang
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Cedric E Bobst
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Jeffrey S Iwig
- Carmot Therapeutics, Inc., San Francisco, California 94158
| | - Peter T Chivers
- Departments of Biosciences and Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Michael J Maroney
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003.
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Yang W, Tu Z, Wang H, Zhang L, Xu S, Niu C, Yao H, Kaltashov IA. Mechanism of Reduction in IgG and IgE Binding of β-Lactoglobulin Induced by Ultrasound Pretreatment Combined with Dry-State Glycation: A Study Using Conventional Spectrometry and High-Resolution Mass Spectrometry. J Agric Food Chem 2017; 65:8018-8027. [PMID: 28800703 DOI: 10.1021/acs.jafc.7b02842] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bovine β-lactoglobulin (β-Lg) is one of major allergens in cow's milk. Previous study showed that ultrasound treatment induced the conformational changes of β-Lg and promoted the glycation in aqueous solutions, which is, however, less efficient compared with dry-state. In this work, the effect of ultrasound pretreatment combined with dry-state glycation on the IgG and IgE binding of β-Lg was studied. Dry-state glycation with mannose after ultrasound pretreatment at 0-600 W significantly reduced the IgG and IgE binding of β-Lg, with the lowest values observed at 400 W. The decrease in the IgG and IgE binding of β-Lg was attributed to the increase in glycation extent and the changes of secondary and tertiary structure, which reflected in the increase of UV absorbance, α-helix and β-sheet contents, as well as the decrease of intrinsic fluorescence intensity, surface hydrophobicity, β-turn, and random coil contents. Moreover, ultrasound pretreatment promoted the reduction of IgG and IgE binding abilities by improving glycation, reflecting in the increase of the glycation sites and the degree of substitution per peptide (DSP) value determined by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). Ultrasound pretreatment at 400 W showed the most significantly enhanced glycation extent. Besides, the results suggested FTICR-MS could provide insights into the glycation at molecular level, which was conducive to the understanding of the mechanism of the reduction in the IgG and IgE binding of β-Lg. Therefore, ultrasound pretreatment combined with dry-state glycation may be a promising method for β-Lg hyposensitization.
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Affiliation(s)
- Wenhua Yang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang, Jiangxi 330047, China
| | - Zongcai Tu
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang, Jiangxi 330047, China
- College of Life Science, Jiangxi Normal University , Nanchang, Jiangxi 330022, China
| | - Hui Wang
- State Key Laboratory of Food Science and Technology, Nanchang University , Nanchang, Jiangxi 330047, China
| | - Lu Zhang
- College of Life Science, Jiangxi Normal University , Nanchang, Jiangxi 330022, China
| | - Shengsheng Xu
- Department of Chemistry, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States
| | - Chendi Niu
- Department of Chemistry, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States
| | - Honglin Yao
- Department of Chemistry, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst , Amherst, Massachusetts 01003, United States
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Xu S, Kaltashov IA. Overcoming the Hydrolytic Lability of a Reaction Intermediate in Production of Protein/Drug Conjugates: Conjugation of an Acyclic Nucleoside Phosphonate to a Model Carrier Protein. Mol Pharm 2017; 14:2843-2851. [DOI: 10.1021/acs.molpharmaceut.7b00410] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shengsheng Xu
- Department of Chemistry, University of Massachusetts−Amherst, Amherst, Massachusetts 01003, United States
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts−Amherst, Amherst, Massachusetts 01003, United States
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44
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Minsky BB, Dubin PL, Kaltashov IA. Electrostatic Forces as Dominant Interactions Between Proteins and Polyanions: an ESI MS Study of Fibroblast Growth Factor Binding to Heparin Oligomers. J Am Soc Mass Spectrom 2017; 28:758-767. [PMID: 28211013 PMCID: PMC5808462 DOI: 10.1007/s13361-017-1596-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Revised: 12/26/2016] [Accepted: 01/04/2017] [Indexed: 05/24/2023]
Abstract
The interactions between fibroblast growth factors (FGFs) and their receptors (FGFRs) are facilitated by heparan sulfate (HS) and heparin (Hp), highly sulfated biological polyelectrolytes. The molecular basis of FGF interactions with these polyelectrolytes is highly complex due to the structural heterogeneity of HS/Hp, and many details still remain elusive, especially the significance of charge density and minimal chain length of HS/Hp in growth factor recognition and multimerization. In this work, we use electrospray ionization mass spectrometry (ESI MS) to investigate the association of relatively homogeneous oligoheparins (octamer, dp8, and decamer, dp10) with acidic fibroblast growth factor (FGF-1). This growth factor forms 1:1, 2:1, and 3:1 protein/heparinoid complexes with both dp8 and dp10, and the fraction of bound protein is highly dependent on protein/heparinoid molar ratio. Multimeric complexes are preferentially formed on the highly sulfated Hp oligomers. Although a variety of oligomers appear to be binding-competent, there is a strong correlation between the affinity and the overall level of sulfation (the highest charge density polyanions binding FGF most strongly via multivalent interactions). These results show that the interactions between FGF-1 and Hp oligomers are primarily directed by electrostatics, and also demonstrate the power of ESI MS as a tool to study multiple binding equilibria between proteins and structurally heterogeneous polyanions. Graphical Abstract ᅟ.
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Affiliation(s)
- Burcu Baykal Minsky
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Paul L Dubin
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA.
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Affiliation(s)
- Nicolau Beckmann
- Musculoskeletal Diseases Department, Imaging and Histology Group, Novartis Institutes for BioMedical Research Basel, Switzerland
| | - Igor A Kaltashov
- Chemistry Department, University of Massachusetts Amherst, MA, USA
| | - Albert D Windhorst
- Department of Radiology and Nuclear Medicine, VU University Medical Center Amsterdam, Netherlands
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Xu S, Kaltashov IA. Evaluation of Gallium as a Tracer of Exogenous Hemoglobin-Haptoglobin Complexes for Targeted Drug Delivery Applications. J Am Soc Mass Spectrom 2016; 27:2025-2032. [PMID: 27619921 DOI: 10.1007/s13361-016-1484-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
Haptoglobin (Hp) is a plasma glycoprotein that generates significant interest in the drug delivery community because of its potential for delivery of antiretroviral medicines with high selectivity to macrophages and monocytes, the latent reservoirs of human immunodeficiency virus. As is the case with other therapies that exploit transport networks for targeted drug delivery, the success of the design and optimization of Hp-based therapies will critically depend on the ability to accurately localize and quantitate Hp-drug conjugates on the varying and unpredictable background of endogenous proteins having identical structure. In this work, we introduce a new strategy for detecting and quantitating exogenous Hp and Hp-based drugs with high sensitivity in complex biological samples using gallium as a tracer of this protein and inductively coupled plasma mass spectrometry (ICP MS) as a method of detection. Metal label is introduced by reconstituting hemoglobin (Hb) with gallium(III)-protoporphyrin IX followed by its complexation with Hp. Formation of the Hp/Hb assembly and its stability are evaluated with native electrospray ionization mass spectrometry. Both stable isotopes of Ga give rise to an abundant signal in ICP MS of a human plasma sample spiked with the metal-labeled Hp/Hb complex. The metal label signal exceeds the spectral interferences' contributions by more than an order of magnitude even with the concentration of the exogenous protein below 10 nM, the level that is more than adequate for the planned pharmacokinetic studies of Hp-based therapeutics. Graphical Abstract ᅟ.
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Affiliation(s)
- Shengsheng Xu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.
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Fatunmbi O, Abzalimov RR, Savinov SN, Gershenson A, Kaltashov IA. Interactions of Haptoglobin with Monomeric Globin Species: Insights from Molecular Modeling and Native Electrospray Ionization Mass Spectrometry. Biochemistry 2016; 55:1918-28. [DOI: 10.1021/acs.biochem.5b00807] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ololade Fatunmbi
- Department of Chemistry and ‡Department of
Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Rinat R. Abzalimov
- Department of Chemistry and ‡Department of
Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Sergey N. Savinov
- Department of Chemistry and ‡Department of
Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Anne Gershenson
- Department of Chemistry and ‡Department of
Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Igor A. Kaltashov
- Department of Chemistry and ‡Department of
Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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Pawlowski JW, Kellicker N, Bobst CE, Kaltashov IA. Assessing the iron delivery efficacy of transferrin in clinical samples by native electrospray ionization mass spectrometry. Analyst 2016; 141:853-61. [PMID: 26646585 PMCID: PMC4727994 DOI: 10.1039/c5an02159f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Serum transferrin is a key player in iron homeostasis, and its ability to deliver iron to cells via the endosomal pathway critically depends on the presence of carbonate that binds this protein synergistically with ferric ion. Oxalate is another ubiquitous anionic species that can act as a synergistic anion, and in fact its interaction with transferrin is notably stronger compared to carbonate, preventing the protein from releasing the metal in the endosomal environment. While this raises concerns that high oxalate levels in plasma may interfere with iron delivery to tissues, concentration of free oxalate in blood appears to be a poor predictor of impeded availability of iron, as previous studies showed that it cannot displace carbonate from ferro-transferrin on a physiologically relevant time scale under the conditions mimicing plasma. In this work we present a new method that allows different forms of ferro-transferrin (carbonate- vs. oxalate-bound) to be distinguished from each other by removing this protein from plasma without altering the composition of the protein/metal/synergistic anion complexes, and determining their accurate masses using native electrospray ionization mass spectrometry (ESI MS). The new method has been validated using a mixture of recombinant proteins, followed by its application to the analysis of clinical samples of human plasma, demonstrating that native ESI MS can be used in clinical analysis.
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Affiliation(s)
- Jake W Pawlowski
- University of Massachusetts-Amherst, Department of Chemistry, 240 Thatcher Drive, Life Sciences Laboratories N369, Amherst, MA 01003, USA.
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Zhao H, Wang S, Nguyen SN, Elci SG, Kaltashov IA. Evaluation of Nonferrous Metals as Potential In Vivo Tracers of Transferrin-Based Therapeutics. J Am Soc Mass Spectrom 2016; 27:211-9. [PMID: 26392277 PMCID: PMC4724545 DOI: 10.1007/s13361-015-1267-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 09/02/2015] [Accepted: 09/04/2015] [Indexed: 05/10/2023]
Abstract
Transferrin (Tf) is a promising candidate for targeted drug delivery. While development of such products is impossible without the ability to monitor biodistribution of Tf-drug conjugates in tissues and reliable measurements of their levels in blood and other biological fluids, the presence of very abundant endogenous Tf presents a significant impediment to such efforts. Several noncognate metals have been evaluated in this work as possible tracers of exogenous transferrin in complex biological matrices using inductively coupled plasma mass spectrometry (ICP MS) as a detection tool. Placing Ni(II) on a His-tag of recombinant Tf resulted in formation of a marginally stable protein-metal complex, which readily transfers the metal to ubiquitous physiological scavengers, such as serum albumin. An alternative strategy targeted iron-binding pockets of Tf, where cognate Fe(III) was replaced by metal ions known to bind this protein. Both Ga(III) and In(III) were evaluated, with the latter being vastly superior as a tracer (stronger binding to Tf unaffected by the presence of metal scavengers and the retained ability to associate with Tf receptor). Spiking serum with indium-loaded Tf followed by ICP MS detection demonstrated that protein quantities as low as 0.04 nM can be readily detected in animal blood. Combining laser ablation with ICP MS detection allows distribution of exogenous Tf to be mapped within animal tissue cross-sections with spatial resolution exceeding 100 μm. The method can be readily extended to a range of other therapeutics where metalloproteins are used as either carriers or payloads. Graphical Abstract ᅟ.
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Affiliation(s)
- Hanwei Zhao
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Shunhai Wang
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Son N Nguyen
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - S Gokhan Elci
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, 01003, USA.
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50
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Zhao Y, Abzalimov RR, Kaltashov IA. Interactions of Intact Unfractionated Heparin with Its Client Proteins Can Be Probed Directly Using Native Electrospray Ionization Mass Spectrometry. Anal Chem 2016; 88:1711-8. [DOI: 10.1021/acs.analchem.5b03792] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yunlong Zhao
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Rinat R. Abzalimov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Igor A. Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
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