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Zhou Y, Wang Y. Direct deamidation analysis of intact adeno-associated virus serotype 9 capsid proteins using reversed-phase liquid chromatography. Anal Biochem 2023; 668:115099. [PMID: 36871622 DOI: 10.1016/j.ab.2023.115099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Recombinant adeno-associated viral (AAV) vectors have taken center stage as gene delivery vehicles for gene therapy. Asparagine deamidation of AAV capsid proteins has been reported to reduce vector stability and potency of AAV gene therapy products. Deamidation of asparagine residue is a common post-translational modification of proteins that is detected and quantified by liquid chromatography-tandem mass spectrometry (LC-MS)-based peptide mapping. However, artificial deamidation can be spontaneously induced during sample preparation for peptide mapping prior to LC-MS analysis. We have developed an optimized sample preparation method to reduce and minimize deamidation artifacts induced during sample preparation for peptide mapping, which typically takes several hours to complete. To shorten turnaround time of deamidation results and to avoid artificial deamidation, we developed orthogonal RPLC-MS and RPLC-fluorescence detection methods for direct deamidation analysis at the intact AAV9 capsid protein level to routinely support downstream purification, formulation development, and stability testing. Similar trends of increasing deamidation of AAV9 capsid proteins in stability samples were observed at the intact protein level and peptide level, indicating that the developed direct deamidation analysis of intact AAV9 capsid proteins is comparable to the peptide mapping-based deamidation analysis and both methods are suitable for deamidation monitoring of AAV9 capsid proteins.
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Affiliation(s)
- Yu Zhou
- Analytical Development & Operation, Novartis Pharmaceuticals, 10210 Campus Point Drive, SanDiego, CA92121, USA.
| | - Yueju Wang
- Analytical Development & Operation, Novartis Pharmaceuticals, 10210 Campus Point Drive, SanDiego, CA92121, USA
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2
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Kacen A, Javitt A, Kramer MP, Morgenstern D, Tsaban T, Shmueli MD, Teo GC, da Veiga Leprevost F, Barnea E, Yu F, Admon A, Eisenbach L, Samuels Y, Schueler-Furman O, Levin Y, Nesvizhskii AI, Merbl Y. Post-translational modifications reshape the antigenic landscape of the MHC I immunopeptidome in tumors. Nat Biotechnol 2023; 41:239-251. [PMID: 36203013 PMCID: PMC11197725 DOI: 10.1038/s41587-022-01464-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 08/09/2022] [Indexed: 11/08/2022]
Abstract
Post-translational modification (PTM) of antigens provides an additional source of specificities targeted by immune responses to tumors or pathogens, but identifying antigen PTMs and assessing their role in shaping the immunopeptidome is challenging. Here we describe the Protein Modification Integrated Search Engine (PROMISE), an antigen discovery pipeline that enables the analysis of 29 different PTM combinations from multiple clinical cohorts and cell lines. We expanded the antigen landscape, uncovering human leukocyte antigen class I binding motifs defined by specific PTMs with haplotype-specific binding preferences and revealing disease-specific modified targets, including thousands of new cancer-specific antigens that can be shared between patients and across cancer types. Furthermore, we uncovered a subset of modified peptides that are specific to cancer tissue and driven by post-translational changes that occurred in the tumor proteome. Our findings highlight principles of PTM-driven antigenicity, which may have broad implications for T cell-mediated therapies in cancer and beyond.
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Affiliation(s)
- Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Aaron Javitt
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Matthias P Kramer
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - David Morgenstern
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Tomer Tsaban
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Eilon Barnea
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Arie Admon
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lea Eisenbach
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
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3
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Bickel F, Griaud F, Kern W, Kroener F, Gritsch M, Dayer J, Barteau S, Denefeld B, Kao-Scharf CY, Lang M, Slupska-Muanza I, Schmidt C, Berg M, Sigg J, Boado L, Chelius D. Restoring the biological activity of crizanlizumab at physiological conditions through a pH-dependent aspartic acid isomerization reaction. MAbs 2023; 15:2151075. [PMID: 36519228 PMCID: PMC9762811 DOI: 10.1080/19420862.2022.2151075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In this study, we report the isomerization of an aspartic acid residue in the complementarity-determining region (CDR) of crizanlizumab as a major degradation pathway. The succinimide intermediate and iso-aspartic acid degradation products were successfully isolated by ion exchange chromatography for characterization. The isomerization site was identified at a DG motif in the CDR by peptide mapping. The biological characterization of the isolated variants showed that the succinimide variant exhibited a loss in target binding and biological activity compared to the aspartic acid and iso-aspartic acid variants of the molecule. The influence of pH on this isomerization reaction was investigated using capillary zone electrophoresis. Below pH 6.3, the succinimide formation was predominant, whereas at pH values above 6.3, iso-aspartic acid was formed and the initial amounts of succinimide dropped to levels even lower than those observed in the starting material. Importantly, while the succinimide accumulated at long-term storage conditions of 2 to 8°C at pH values below 6.3, a complete hydrolysis of succinimide was observed at physiological conditions (pH 7.4, 37°C), resulting in full recovery of the biological activity. In this study, we demonstrate that the critical quality attribute succinimide with reduced potency has little or no impact on the efficacy of crizanlizumab due to the full recovery of the biological activity within a few hours under physiological conditions.
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Affiliation(s)
- Fabian Bickel
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - François Griaud
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Wolfram Kern
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Frieder Kroener
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Manuela Gritsch
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Jérôme Dayer
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Samuel Barteau
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Blandine Denefeld
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Chi-Ya Kao-Scharf
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Manuel Lang
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Izabela Slupska-Muanza
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Carla Schmidt
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Matthias Berg
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Jürgen Sigg
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Lina Boado
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
| | - Dirk Chelius
- Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland,CONTACT Dirk Chelius Analytical Development, Technical Research and Development Biologics, Novartis Pharma AG, Basel, Switzerland
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4
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Liu B, Huang L, Xu R, Fan H, Wang Y. An Improved Isotope Labelling Method for Quantifying Deamidated Cobratide Using High-Resolution Quadrupole-Orbitrap Mass Spectrometry. Molecules 2022; 27:molecules27196154. [PMID: 36234709 PMCID: PMC9572859 DOI: 10.3390/molecules27196154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Protein deamidation can severely alter the physicochemical characteristics and biological functions of protein therapeutics. Cobratide is a non-addictive analgesic with wide clinical acceptance. However, the Asn residue at position 48 from the N-terminus of the cobratide amino acid sequence (N48) tends to degrade during purification, storage, and transport. This characteristic could severely affect the drug safety and clinical efficacy of cobratide. Traditional methods for quantitating deamidation reported in previous research are characterised by low efficiency and accuracy; the quality control of cobratide via this method is limited. Herein, we developed an improved 18O-labelling method based on the detection of a unique peptide (i.e., the protein fragment of cobratide containing the N48 deamidation hotspot after enzymolysis) using an Orbitrap high-resolution mass spectrometer to quantify deamidated cobratide. The limits of detection and quantification of this method reached 0.02 and 0.025 μM, respectively, and inter- and intra-day precision values of the method were <3%. The accuracy of the 18O-labelling strategy was validated by using samples containing synthesised peptides with a known ratio of deamidation impurities and also by comparing the final total deamidation results with our previously developed capillary electrophoresis method. The recoveries for deamidation (Asp), deamidation isomerisation (iso-Asp), and total deamidation were 101.52 ± 1.17, 102.42 ± 1.82, and 103.55 ± 1.07, respectively. The robustness of the method was confirmed by verifying the chromatographic parameters. Our results demonstrate the applicability of the 18O-labelling strategy for detecting protein deamidation and lay a robust foundation for protein therapeutics studies and drug quality consistency evaluations.
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Affiliation(s)
- Bo Liu
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
| | - Lu Huang
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
| | - Rongrong Xu
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
| | - Huihong Fan
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
- Correspondence:
| | - Yue Wang
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
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5
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Muroski JM, Fu JY, Nguyen HH, Wofford NQ, Mouttaki H, James KL, McInerney MJ, Gunsalus RP, Loo JA, Ogorzalek Loo RR. The Acyl-Proteome of Syntrophus aciditrophicus Reveals Metabolic Relationships in Benzoate Degradation. Mol Cell Proteomics 2022; 21:100215. [PMID: 35189333 PMCID: PMC8942843 DOI: 10.1016/j.mcpro.2022.100215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 11/08/2022] Open
Abstract
Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate, and H2 that are utilized by methanogens and other hydrogen-consuming microbes. S. aciditrophicus benzoate degradation proceeds by a multistep pathway with many intermediate reactive acyl-coenzyme A species (RACS) that can potentially Nε-acylate lysine residues. Herein, we describe the identification and characterization of acyl-lysine modifications that correspond to RACS in the benzoate degradation pathway. The amounts of modified peptides are sufficient to analyze the post-translational modifications without antibody enrichment, enabling a range of acylations located, presumably, on the most extensively acylated proteins throughout the proteome to be studied. Seven types of acyl modifications were identified, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway including 3-hydroxypimeloylation, a modification first identified in this system. Indeed, benzoate-degrading enzymes are heavily represented among the acylated proteins. A total of 125 sites were identified in 60 proteins. Functional deacylase enzymes are present in the proteome, indicating a potential regulatory system/mechanism by which S. aciditrophicus modulates acylation. Uniquely, Nε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility that post-translational modifications modulate benzoate degradation in this and potentially other, syntrophic bacteria. Our results outline candidates for further study of how acylations impact syntrophic consortia.
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Affiliation(s)
- John M Muroski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Janine Y Fu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | | | - Neil Q Wofford
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Housna Mouttaki
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Kimberly L James
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Michael J McInerney
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, USA; UCLA-DOE Institute, University of California, Los Angeles, California, USA; UCLA Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA; UCLA-DOE Institute, University of California, Los Angeles, California, USA; UCLA Molecular Biology Institute, University of California, Los Angeles, California, USA; Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA; UCLA-DOE Institute, University of California, Los Angeles, California, USA; UCLA Molecular Biology Institute, University of California, Los Angeles, California, USA.
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6
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Zakharova NV, Kononikhin AS, Indeykina MI, Bugrova AE, Strelnikova P, Pekov S, Kozin SA, Popov IA, Mitkevich V, Makarov AA, Nikolaev EN. Mass spectrometric studies of the variety of beta-amyloid proteoforms in Alzheimer's disease. MASS SPECTROMETRY REVIEWS 2022:e21775. [PMID: 35347731 DOI: 10.1002/mas.21775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
This review covers the results of the application of mass spectrometric (MS) techniques to study the diversity of beta-amyloid (Aβ) peptides in human samples. Since Aβ is an important hallmark of Alzheimer's disease (AD), which is a socially significant neurodegenerative disorder of the elderly worldwide, analysis of its endogenous variations is of particular importance for elucidating the pathogenesis of AD, predicting increased risks of the disease onset, and developing effective therapy. MS approaches have no alternative for the study of complex samples, including a wide variety of Aβ proteoforms, differing in length and modifications. Approaches based on matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography with electrospray ionization tandem MS are most common in Aβ studies. However, Aβ forms with isomerized and/or racemized Asp and Ser residues require the use of special methods for separation and extra sensitive and selective methods for detection. Overall, this review summarizes current knowledge of Aβ species found in human brain, cerebrospinal fluid, and blood plasma; focuses on application of different MS approaches for Aβ studies; and considers the potential of MS techniques for further studies of Aβ-peptides.
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Affiliation(s)
- Natalia V Zakharova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kononikhin
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria I Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Polina Strelnikova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stanislav Pekov
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor A Popov
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- N.N. Semenov Federal Center of Chemical Physics, V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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7
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Duivelshof BL, Murisier A, Camperi J, Fekete S, Beck A, Guillarme D, D'Atri V. Therapeutic Fc-fusion proteins: Current analytical strategies. J Sep Sci 2020; 44:35-62. [PMID: 32914936 DOI: 10.1002/jssc.202000765] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/27/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Fc-Fusion proteins represent a successful class of biopharmaceutical products, with already 13 drugs approved in the European Union and United States as well as three biosimilar versions of etanercept. Fc-Fusion products combine tailored pharmacological properties of biological ligands, together with multiple functions of the fragment crystallizable domain of immunoglobulins. There is a great diversity in terms of possible biological ligands, including the extracellular domains of natural receptors, functionally active peptides, recombinant enzymes, and genetically engineered binding constructs acting as cytokine traps. Due to their highly diverse structures, the analytical characterization of Fc-Fusion proteins is far more complex than that of monoclonal antibodies and requires the use and development of additional product-specific methods over conventional generic/platform methods. This can be explained, for example, by the presence of numerous sialic acids, leading to high diversity in terms of isoelectric points and complex glycosylation profiles including multiple N- and O-linked glycosylation sites. In this review, we highlight the wide range of analytical strategies used to fully characterize Fc-fusion proteins. We also present case studies on the structural assessment of all commercially available Fc-fusion proteins, based on the features and critical quality attributes of their ligand-binding domains.
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Affiliation(s)
- Bastiaan L Duivelshof
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Amarande Murisier
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Julien Camperi
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Alain Beck
- IRPF - Centre d'Immunologie Pierre-Fabre (CIPF), Saint-Julien-en-Genevois, France
| | - Davy Guillarme
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
| | - Valentina D'Atri
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland.,Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, Geneva, Switzerland
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8
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Wang S, Liu AP, Li N. An 18O-Labeling Assisted LC-MS Method for Accurate Quantitation of Unprocessed C-Terminal Lysine in Therapeutic Monoclonal Antibodies. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1587-1592. [PMID: 32515589 DOI: 10.1021/jasms.0c00149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unprocessed C-terminal lysine (C-term Lys) is one of the most common causes for the formation of basic variants in therapeutic monoclonal antibodies (mAbs). Although the C-term Lys variants are routinely quantified by a LC-MS-based peptide mapping method using the relative MS responses from both C-terminal peptides (with and without Lys), this approach often leads to overestimation of Lys-containing peptide due to the intrinsic difference in ionization efficiency. Herein, we report an 18O-labeling assisted LC-MS method, which takes advantage of the carboxypeptidase B-catalyzed Lys removal and 18O-labeling to achieve improved accuracy of C-term Lys quantitation. The fidelity of this method was first demonstrated using synthetic peptide mixture standards that mimic a wide range of C-term Lys levels. Finally, the newly developed method was applied in a case study where C-term Lys variants in mAb samples manufactured from different processes were accurately quantified and compared. This new method provides a valuable solution for studies where accurate C-term Lys levels are needed to assist decision-making and root-cause investigation.
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Affiliation(s)
- Shunhai Wang
- Analytical Chemistry Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Anita P Liu
- Analytical Chemistry Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
| | - Ning Li
- Analytical Chemistry Group, Regeneron Pharmaceuticals, Inc., 777 Old Saw Mill River Road, Tarrytown, New York 10591-6707, United States
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9
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From proof of concept to the routine use of an automated and robust multi-dimensional liquid chromatography mass spectrometry workflow applied for the charge variant characterization of therapeutic antibodies. J Chromatogr A 2020; 1615:460740. [DOI: 10.1016/j.chroma.2019.460740] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/26/2019] [Indexed: 11/24/2022]
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10
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Sankaran PK, Kabadi PG, Honnappa CG, Subbarao M, Pai HV, Adhikary L, Palanivelu DV. Identification and quantification of product-related quality attributes in bio-therapeutic monoclonal antibody via a simple, and robust cation-exchange HPLC method compatible with direct online detection of UV and native ESI-QTOF-MS analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1102-1103:83-95. [PMID: 30380467 DOI: 10.1016/j.jchromb.2018.10.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/14/2018] [Accepted: 10/19/2018] [Indexed: 02/03/2023]
Abstract
Modern analytical ion-exchange chromatography is one of the conventional tools used for assessment of product-related quality attributes in bio-therapeutic monoclonal antibodies (mAbs). Here, we present an approach to resolve, identify, and quantify product-related substances of therapeutic mAb at its intact molecular level by cation exchange (CIEX) HPLC coupled directly to electrospray ionization - quadrupole time of flight mass spectrometry (ESI-QTOF-MS). This method utilizes pH gradient elution mode comprised of ammonium formate buffer components, and a weak cation exchange column as stationary phase. Furthermore, ion-mobility mass spectrometry (IM-MS) provided additional insights on its higher order structure. Also, orthogonal assays such as conventional CIEX-HPLC, high resolution capillary isoelectric focusing, peptide mapping, spectroscopic, and fluorescence methods were used considerably to support the findings. Additionally, an in vitro assay was included to assess the associated impact on Fc mediated function. Overall, the developed method with simultaneous detection of UV peak area percentage at 280 nm and native ESI-MS is found to be a rapid and robust analytical tool for direct assessment of structural and purity attributes, process optimization, product development, and to decipher the relevant role of micro-variants on quality, stability, and clinical outcomes.
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Affiliation(s)
- Praveen Kallamvalliillam Sankaran
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India.
| | - Pradeep G Kabadi
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India
| | - Chethan Gejjalagere Honnappa
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India
| | - Malini Subbarao
- Bioassay Development Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India
| | - Harish V Pai
- Bioassay Development Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India
| | - Laxmi Adhikary
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India
| | - Dinesh V Palanivelu
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore 560099, India
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11
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Giles AR, Sims JJ, Turner KB, Govindasamy L, Alvira MR, Lock M, Wilson JM. Deamidation of Amino Acids on the Surface of Adeno-Associated Virus Capsids Leads to Charge Heterogeneity and Altered Vector Function. Mol Ther 2018; 26:2848-2862. [PMID: 30343890 DOI: 10.1016/j.ymthe.2018.09.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 09/10/2018] [Accepted: 09/13/2018] [Indexed: 12/19/2022] Open
Abstract
Post-translational modification of the adeno-associated virus capsids is a poorly understood factor in the development of these viral vectors into pharmaceutical products. Here we report the extensive capsid deamidation of adeno-associated virus serotype 8 and seven other diverse adeno-associated virus serotypes, with supporting evidence from structural, biochemical, and mass spectrometry approaches. The extent of deamidation at each site depended on the vector's age and multiple primary-sequence and three-dimensional structural factors. However, the extent of deamidation was largely independent of the vector recovery and purification conditions. We demonstrate the potential for deamidation to impact transduction activity and, moreover, correlate an early time point loss in vector activity to rapidly progressing spontaneous deamidation at several adeno-associated virus 8 asparagines. We explore mutational strategies that stabilize side-chain amides, improving vector transduction and reducing the lot-to-lot molecular variability that presents a key concern in biologics manufacturing. This study illuminates a previously unknown aspect of adeno-associated virus capsid heterogeneity and highlights its importance in the development of these vectors for gene therapy.
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Affiliation(s)
- April R Giles
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Joshua J Sims
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kevin B Turner
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lakshmanan Govindasamy
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mauricio R Alvira
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Martin Lock
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James M Wilson
- Gene Therapy Program, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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12
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Jansson ET. Strategies for analysis of isomeric peptides. J Sep Sci 2017; 41:385-397. [PMID: 28922569 DOI: 10.1002/jssc.201700852] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023]
Abstract
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion-mobility spectrometry.
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Affiliation(s)
- Erik T Jansson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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13
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Beyer B, Schuster M, Jungbauer A, Lingg N. Microheterogeneity of Recombinant Antibodies: Analytics and Functional Impact. Biotechnol J 2017; 13. [PMID: 28862393 DOI: 10.1002/biot.201700476] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 08/08/2017] [Indexed: 02/04/2023]
Abstract
Antibodies are typical examples of biopharmaceuticals which are composed of numerous, almost infinite numbers of potential molecular entities called variants or isoforms, which constitute the microheterogeneity of these molecules. These variants are generated during biosynthesis by so-called posttranslational modification, during purification or upon storage. The variants differ in biological properties such as pharmacodynamic properties, for example, Antibody Dependent Cellular Cytotoxicity, complement activation, and pharmacokinetic properties, for example, serum half-life and safety. Recent progress in analytical technologies such as various modes of liquid chromatography and mass spectrometry has helped to elucidate the structure of a lot of these variants and their biological properties. In this review the most important modifications (glycosylation, terminal modifications, amino acid side chain modifications, glycation, disulfide bond variants and aggregation) are reviewed and an attempt is made to give an overview on the biological properties, for which the reports are often contradictory. Even though there is a deep understanding of cellular and molecular mechanism of antibody modification and their consequences, the clinical proof of the effects observed in vitro and in vivo is still not fully rendered. For some modifications such as core-fucosylation of the N-glycan and aggregation the effects are clear and should be monitored, but with others such as C-terminal lysine clipping the reports are contradictory. As a consequence it seems too early to tell if any modification can be safely ignored.
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Affiliation(s)
- Beate Beyer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | | | - Alois Jungbauer
- Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Nico Lingg
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
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14
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Regl C, Wohlschlager T, Holzmann J, Huber CG. A Generic HPLC Method for Absolute Quantification of Oxidation in Monoclonal Antibodies and Fc-Fusion Proteins Using UV and MS Detection. Anal Chem 2017; 89:8391-8398. [DOI: 10.1021/acs.analchem.7b01755] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christof Regl
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Therese Wohlschlager
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
| | - Johann Holzmann
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Technical
Development
Biosimilars, Physicochemical Characterization Kundl, Novartis BTDM,
Sandoz GmbH, Biochemiestrasse 10, 6250 Kundl, Austria
| | - Christian G. Huber
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunner Strasse 34, 5020 Salzburg, Austria
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15
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Wang H, Shu Q, Frieden C, Gross ML. Deamidation Slows Curli Amyloid-Protein Aggregation. Biochemistry 2017; 56:2865-2872. [PMID: 28497950 DOI: 10.1021/acs.biochem.7b00241] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonenzymatic deamidation of asparagine and glutamine in peptides and proteins is a frequent modification both in vivo and in vitro. The biological effect is not completely understood, but it is often associated with protein degradation and loss of biological function. Here we describe the deamidation of CsgA, the major protein subunit of curli, which are important proteinaceous components of biofilms. CsgA has a high content of Asn and Gln, a feature seen in a few proteins that self-aggregate. We have implemented an approach to monitor deamidation rapidly by following the globally centroid mass shift, providing guidance for studies at the residue level. From the global mass measurement, we identified, using LC-MS/MS, extensive deamidation of several Asn residues and discovered three "Asn-Gly" sites to be the hottest spots for deamidation. The fibrillization of deamidated CsgA was measured using thioflavin T (ThT) fluorescence, circular dichroism (CD), and a previously reported hydrogen-deuterium exchange (HDX) platform. Deamidated proteins exhibit a longer lag phase and lower final ThT fluorescence, strongly suggesting slower and less amyloid fibril formation. CD spectra show that extensively deamidated CsgA remains unstructured and loses its ability to form amyloids. Mass-spectrometry-based HDX also shows that deamidated CsgA aggregates more slowly than wild-type CsgA. Taken together, the results show that deamidation of CsgA slows its fibrillization and disrupts its function, suggesting an opportunity to modulate CsgA fibrillization and affect curli and biofilm formation.
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Affiliation(s)
- Hanliu Wang
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Qin Shu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
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16
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Lee J, Wen B, Carter EA, Combes V, Grau GER, Lay PA. Infrared spectroscopic characterization of monocytic microvesicles (microparticles) released upon lipopolysaccharide stimulation. FASEB J 2017; 31:2817-2827. [PMID: 28314769 DOI: 10.1096/fj.201601272r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Accepted: 02/26/2017] [Indexed: 12/28/2022]
Abstract
Microvesicles (MVs) are involved in cell-cell interactions, including disease pathogenesis. Nondestructive Fourier-transform infrared (FTIR) spectra from MVs were assessed as a technique to provide new biochemical insights into a LPS-induced monocyte model of septic shock. FTIR spectroscopy provided a quick method to investigate relative differences in biomolecular content of different MV populations that was complementary to traditional semiquantitative omics approaches, with which it is difficult to provide information on relative changes between classes (proteins, lipids, nucleic acids, carbohydrates) or protein conformations. Time-dependent changes were detected in biomolecular contents of MVs and in the monocytes from which they were released. Differences in phosphatidylcholine and phosphatidylserine contents were observed in MVs released under stimulation, and higher relative concentrations of RNA and α-helical structured proteins were present in stimulated MVs compared with MVs from resting cells. FTIR spectra of stimulated monocytes displayed changes that were consistent with those observed in the corresponding MVs they released. LPS-stimulated monocytes had reduced concentrations of nucleic acids, α-helical structured proteins, and phosphatidylcholine compared with resting monocytes but had an increase in total lipids. FTIR spectra of MV biomolecular content will be important in shedding new light on the mechanisms of MVs and the different roles they play in physiology and disease pathogenesis.-Lee, J., Wen, B., Carter, E. A., Combes, V., Grau, G. E. R., Lay, P. A. Infrared spectroscopic characterization of monocytic microvesicles (microparticles) released upon lipopolysaccharide stimulation.
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Affiliation(s)
- Joonsup Lee
- School of Chemistry and Vibrational Spectroscopy Core Facility, The University of Sydney, Sydney, New South Wales, Australia
| | - Beryl Wen
- Vascular Immunopathology Unit, Bosch Institute-School of Medical Sciences, and
| | - Elizabeth A Carter
- School of Chemistry and Vibrational Spectroscopy Core Facility, The University of Sydney, Sydney, New South Wales, Australia
| | - Valery Combes
- Vascular Immunopathology Unit, Bosch Institute-School of Medical Sciences, and.,Faculty of Science, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Georges E R Grau
- Vascular Immunopathology Unit, Bosch Institute-School of Medical Sciences, and.,Australian Institute of Nanoscale Science and Technology (AINST), The University of Sydney, Sydney, New South Wales, Australia
| | - Peter A Lay
- School of Chemistry and Vibrational Spectroscopy Core Facility, The University of Sydney, Sydney, New South Wales, Australia; .,Australian Institute of Nanoscale Science and Technology (AINST), The University of Sydney, Sydney, New South Wales, Australia
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17
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Chen Y, Kim MT, Zheng L, Deperalta G, Jacobson F. Structural Characterization of Cross-Linked Species in Trastuzumab Emtansine (Kadcyla). Bioconjug Chem 2016; 27:2037-47. [DOI: 10.1021/acs.bioconjchem.6b00316] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yan Chen
- Department of Protein Analytical
Chemistry, Genentech, Inc., 1 DNA way, South San Francisco, California 94080-4990, United States
| | - Michael T. Kim
- Department of Protein Analytical
Chemistry, Genentech, Inc., 1 DNA way, South San Francisco, California 94080-4990, United States
| | - Laura Zheng
- Department of Protein Analytical
Chemistry, Genentech, Inc., 1 DNA way, South San Francisco, California 94080-4990, United States
| | - Galahad Deperalta
- Department of Protein Analytical
Chemistry, Genentech, Inc., 1 DNA way, South San Francisco, California 94080-4990, United States
| | - Fred Jacobson
- Department of Protein Analytical
Chemistry, Genentech, Inc., 1 DNA way, South San Francisco, California 94080-4990, United States
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18
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Butts CT, Zhang X, Kelly JE, Roskamp KW, Unhelkar MH, Freites JA, Tahir S, Martin RW. Sequence comparison, molecular modeling, and network analysis predict structural diversity in cysteine proteases from the Cape sundew, Drosera capensis. Comput Struct Biotechnol J 2016; 14:271-82. [PMID: 27471585 PMCID: PMC4949590 DOI: 10.1016/j.csbj.2016.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/11/2016] [Accepted: 05/17/2016] [Indexed: 01/02/2023] Open
Abstract
Carnivorous plants represent a so far underexploited reservoir of novel proteases with potentially useful activities. Here we investigate 44 cysteine proteases from the Cape sundew, Drosera capensis, predicted from genomic DNA sequences. D. capensis has a large number of cysteine protease genes; analysis of their sequences reveals homologs of known plant proteases, some of which are predicted to have novel properties. Many functionally significant sequence and structural features are observed, including targeting signals and occluding loops. Several of the proteases contain a new type of granulin domain. Although active site residues are conserved, the sequence identity of these proteases to known proteins is moderate to low; therefore, comparative modeling with all-atom refinement and subsequent atomistic MD-simulation is used to predict their 3D structures. The structure prediction data, as well as analysis of protein structure networks, suggest multifarious variations on the papain-like cysteine protease structural theme. This in silico methodology provides a general framework for investigating a large pool of sequences that are potentially useful for biotechnology applications, enabling informed choices about which proteins to investigate in the laboratory. 44 new cysteine proteases from the carnivorous plant Drosera capensis are described. Structure prediction and molecular dynamics simulation predict overall folds similar to papain. Functionally significant sequence and structural features are observed, including targeting signals and occluding loops. Several of the proteases contain a new type of granulin domain. Protein structure networks reveal global differences in interactions among chemical groups.
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Affiliation(s)
- Carter T Butts
- Department of Sociology, UC Irvine, USA; Department of Sociology, UC Irvine, USA; Department of Electrical Engineering and Computer Science, UC Irvine, USA
| | | | | | | | | | | | | | - Rachel W Martin
- Department of Chemistry, UC Irvine, USA; Department of Molecular Biology & Biochemistry, UC Irvine, Irvine, CA, 92697 USA
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19
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Resemann A, Jabs W, Wiechmann A, Wagner E, Colas O, Evers W, Belau E, Vorwerg L, Evans C, Beck A, Suckau D. Full validation of therapeutic antibody sequences by middle-up mass measurements and middle-down protein sequencing. MAbs 2016; 8:318-30. [PMID: 26760197 PMCID: PMC4966597 DOI: 10.1080/19420862.2015.1128607] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The regulatory bodies request full sequence data assessment both for innovator and biosimilar monoclonal antibodies (mAbs). Full sequence coverage is typically used to verify the integrity of the analytical data obtained following the combination of multiple LC-MS/MS datasets from orthogonal protease digests (so called “bottom-up” approaches). Top-down or middle-down mass spectrometric approaches have the potential to minimize artifacts, reduce overall analysis time and provide orthogonality to this traditional approach. In this work we report a new combined approach involving middle-up LC-QTOF and middle-down LC-MALDI in-source decay (ISD) mass spectrometry. This was applied to cetuximab, panitumumab and natalizumab, selected as representative US Food and Drug Administration- and European Medicines Agency-approved mAbs. The goal was to unambiguously confirm their reference sequences and examine the general applicability of this approach. Furthermore, a new measure for assessing the integrity and validity of results from middle-down approaches is introduced – the “Sequence Validation Percentage.” Full sequence data assessment of the 3 antibodies was achieved enabling all 3 sequences to be fully validated by a combination of middle-up molecular weight determination and middle-down protein sequencing. Three errors in the reference amino acid sequence of natalizumab, causing a cumulative mass shift of only −2 Da in the natalizumab Fd domain, were corrected as a result of this work.
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Affiliation(s)
- Anja Resemann
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Wolfgang Jabs
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Anja Wiechmann
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Elsa Wagner
- b Centre d'Immunologie Pierre , St Julien-en-Genevois, France
| | - Olivier Colas
- b Centre d'Immunologie Pierre , St Julien-en-Genevois, France
| | - Waltraud Evers
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Eckhard Belau
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | - Lars Vorwerg
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
| | | | - Alain Beck
- b Centre d'Immunologie Pierre , St Julien-en-Genevois, France
| | - Detlev Suckau
- a Bruker Daltonics GmbH , Fahrenheitstr. 4, Bremen , Germany
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20
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Mildly acidic conditions eliminate deamidation artifact during proteolysis: digestion with endoprotease Glu-C at pH 4.5. Amino Acids 2016; 48:1059-1067. [PMID: 26748652 DOI: 10.1007/s00726-015-2166-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Common yet often overlooked, deamidation of peptidyl asparagine (Asn or N) generates aspartic acid (Asp or D) or isoaspartic acid (isoAsp or isoD). Being a spontaneous, non-enzymatic protein post-translational modification, deamidation artifact can be easily introduced during sample preparation, especially proteolysis where higher-order structures are removed. This artifact not only complicates the analysis of bona fide deamidation but also affects a wide range of chemical and enzymatic processes; for instance, the newly generated Asp and isoAsp residues may block or introduce new proteolytic sites, and also convert one Asn peptide into multiple species that affect quantification. While the neutral to mildly basic conditions for common proteolysis favor deamidation, mildly acidic conditions markedly slow down the process. Unlike other commonly used endoproteases, Glu-C remains active under mildly acid conditions. As such, as demonstrated herein, deamidation artifact during proteolysis was effectively eliminated by simply performing Glu-C digestion at pH 4.5 in ammonium acetate, a volatile buffer that is compatible with mass spectrometry. Moreover, nearly identical sequence specificity was observed at both pH's (8.0 for ammonium bicarbonate), rendering Glu-C as effective at pH 4.5. In summary, this method is generally applicable for protein analysis as it requires minimal sample preparation and uses the readily available Glu-C protease.
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21
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Kori Y, Patel R, Neill A, Liu H. A conventional procedure to reduce Asn deamidation artifacts during trypsin peptide mapping. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1009-1010:107-13. [DOI: 10.1016/j.jchromb.2015.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/12/2022]
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22
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Bush DR, Zang L, Belov AM, Ivanov AR, Karger BL. High Resolution CZE-MS Quantitative Characterization of Intact Biopharmaceutical Proteins: Proteoforms of Interferon-β1. Anal Chem 2015; 88:1138-46. [DOI: 10.1021/acs.analchem.5b03218] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- David R. Bush
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Li Zang
- Analytical
Development Department, Biogen, Cambridge, Massachusetts 02142, United States
| | - Arseniy M. Belov
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Alexander R. Ivanov
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Barry L. Karger
- Barnett
Institute, Northeastern University, 360 Huntington Ave, Boston, Massachusetts 02115, United States
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23
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Wu Y, Li L. Sample normalization methods in quantitative metabolomics. J Chromatogr A 2015; 1430:80-95. [PMID: 26763302 DOI: 10.1016/j.chroma.2015.12.007] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/30/2015] [Accepted: 12/02/2015] [Indexed: 12/31/2022]
Abstract
To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts.
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Affiliation(s)
- Yiman Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G2G2, Canada.
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24
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Forstenlehner IC, Holzmann J, Toll H, Huber CG. Site-Specific Characterization and Absolute Quantification of Pegfilgrastim Oxidation by Top-Down High-Performance Liquid Chromatography–Mass Spectrometry. Anal Chem 2015; 87:9336-43. [DOI: 10.1021/acs.analchem.5b02029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ines C. Forstenlehner
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
| | - Johann Holzmann
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
- Analytical
Characterization Biopharmaceuticals, Sandoz GmbH, Biochemiestrasse
10, 6250 Kundl, Austria
| | - Hansjörg Toll
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
- Analytical
Characterization Biopharmaceuticals, Sandoz GmbH, Biochemiestrasse
10, 6250 Kundl, Austria
| | - Christian G. Huber
- Christian
Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
- Department
of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020 Salzburg, Austria
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25
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Kvitvang HFN, Bruheim P. Fast filtration sampling protocol for mammalian suspension cells tailored for phosphometabolome profiling by capillary ion chromatography - tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 998-999:45-9. [PMID: 26151192 DOI: 10.1016/j.jchromb.2015.06.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 11/16/2022]
Abstract
Capillary ion chromatography (capIC) is the premium separation technology for low molecular phosphometabolites and nucleotides in biological extracts. Removal of excessive amounts of salt during sample preparation stages is a prerequisite to enable high quality capIC separation in combination with reproducible and sensitive MS detection. Existing sampling protocols for mammalian cells used for GC-MS and LC-MS metabolic profiling can therefore not be directly applied to capIC separations. Here, the development of a fast filtration sampling protocol for mammalian suspension cells tailored for quantitative profiling of the phosphometabolome on capIC-MS/MS is presented. The whole procedure from sampling the culture to transfer of filter to quenching and extraction solution takes less than 10s. To prevent leakage it is critical that a low vacuum pressure is applied, and satisfactorily reproducibility was only obtained by usage of a vacuum pressure controlling device. A vacuum of 60mbar was optimal for filtration of multiple myeloma Jjn-3 cell cultures through 5μm polyvinylidene (PVDF) filters. A quick deionized water (DI-water) rinse step prior to extraction was tested, and significantly higher metabolite yields were obtained during capIC-MS/MS analyses in this extract compared to extracts prepared by saline and reduced saline (25%) washing steps only. In addition, chromatographic performance was dramatically improved. Thus, it was verified that a quick DI-water rinse is tolerated by the cells and can be included as the final stage during filtration. Over 30 metabolites were quantitated in JJN-3 cell extracts by using the optimized sampling protocol with subsequent capIC-MS/MS analysis, and up to 2 million cells can be used in a single filtration step for the chosen filter and vacuum pressure. The technical set-up is also highly advantageous for microbial metabolome filtration protocols after optimization of vacuum pressure and washing solutions, and the reduced salt content of the extract will also improve the quality of LC-MS analysis due to lower salt adduct ion formation.
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Affiliation(s)
- Hans F N Kvitvang
- Department of Biotechnology, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology, NTNU Norwegian University of Science and Technology, Trondheim, Norway.
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Bults P, van de Merbel NC, Bischoff R. Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays. Expert Rev Proteomics 2015; 12:355-74. [DOI: 10.1586/14789450.2015.1050384] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Levery SB, Steentoft C, Halim A, Narimatsu Y, Clausen H, Vakhrushev SY. Advances in mass spectrometry driven O-glycoproteomics. Biochim Biophys Acta Gen Subj 2014; 1850:33-42. [PMID: 25284204 DOI: 10.1016/j.bbagen.2014.09.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Global analyses of proteins and their modifications by mass spectrometry are essential tools in cell biology and biomedical research. Analyses of glycoproteins represent particular challenges and we are only at the beginnings of the glycoproteomic era. Some of the challenges have been overcome with N-glycoproteins and proteome-wide analysis of N-glycosylation sites is accomplishable today but only by sacrificing information of structures at individual glycosites. More recently advances in analysis of O-glycoproteins have been made and proteome-wide analysis of O-glycosylation sites is becoming available as well. SCOPE OF REVIEW Here we discuss the challenges of analysis of O-glycans and new O-glycoproteomics strategies focusing on O-GalNAc and O-Man glycoproteomes. MAJOR CONCLUSIONS A variety of strategies are now available for proteome-wide analysis of O-glycosylation sites enabling functional studies. However, further developments are still needed for complete analysis of glycan structures at individual sites for both N- and O-glycoproteomics strategies. GENERAL SIGNIFICANCE The advances in O-glycoproteomics have led to identification of new biological functions of O-glycosylation and a new understanding of the importance of where O-glycans are positioned on proteins.
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Affiliation(s)
- Steven B Levery
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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Klaene JJ, Ni W, Alfaro JF, Zhou ZS. Detection and quantitation of succinimide in intact protein via hydrazine trapping and chemical derivatization. J Pharm Sci 2014; 103:3033-42. [PMID: 25043726 DOI: 10.1002/jps.24074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/01/2014] [Accepted: 06/04/2014] [Indexed: 12/19/2022]
Abstract
The formation of aspartyl succinimide is a common post-translational modification of protein pharmaceuticals under acidic conditions. We present a method to detect and quantitate succinimide in intact protein via hydrazine trapping and chemical derivatization. Succinimide, which is labile under typical analytical conditions, is first trapped with hydrazine to form stable hydrazide and can be directly analyzed by mass spectrometry. The resulting aspartyl hydrazide can be selectively derivatized by various tags, such as fluorescent rhodamine sulfonyl chloride that absorbs strongly in the visible region (570 nm). Our tagging strategy allows the labeled protein to be analyzed by orthogonal methods, including HPLC-UV-Vis, liquid chromatography mass spectrometry (LC-MS), and SDS-PAGE coupled with fluorescence imaging. A unique advantage of our method is that variants containing succinimide, after derivatization, can be readily resolved via either affinity enrichment or chromatographic separation. This allows further investigation of individual factors in a complex protein mixture that affect succinimide formation. Some additional advantages are imparted by fluorescence labeling including the facile detection of the intact protein without proteolytic digestion to peptides; and high sensitivity, for example, without optimization, 0.41% succinimide was readily detected. As such, our method should be useful for rapid screening, optimization of formulation conditions, and related processes relevant to protein pharmaceuticals.
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Affiliation(s)
- Joshua J Klaene
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
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Vilhauer L, Jervis J, Ray WK, Helm RF. The exo-proteome and exo-metabolome of Nostoc punctiforme (Cyanobacteria) in the presence and absence of nitrate. Arch Microbiol 2014; 196:357-67. [PMID: 24643449 DOI: 10.1007/s00203-014-0974-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 02/27/2014] [Indexed: 01/04/2023]
Abstract
The ability of nitrogen-fixing filamentous Cyanobacteria to adapt to multiple environments comes in part from assessing and responding to external stimuli, an event that is initiated in the extracellular milieu. While it is known that these organisms produce numerous extracellular substances, little work has been done to characterize both the metabolites and proteins present under standard laboratory growth conditions. We have assessed the extracellular milieu of Nostoc punctiforme when grown in liquid culture in the presence and absence of a nitrogen source (nitrate). The extracellular proteins identified were enriched in integrin β-propellor domains and calcium-binding sites with sequences unique to N. punctiforme, supporting a role for extracellular proteins in modulating species-specific recognition and behavior processes. Extracellular proteases are present and active under both conditions, with the cells grown with nitrate having a higher activity when normalized to chlorophyll levels. The released metabolites are enriched in peptidoglycan-derived tetrasaccharides, with higher levels in nitrate-free media.
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Affiliation(s)
- Laura Vilhauer
- Department of Biochemistry, Virginia Tech, 143 Life Sciences 1, Blacksburg, VA, 24061-0910, USA
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Sandra K, Vandenheede I, Sandra P. Modern chromatographic and mass spectrometric techniques for protein biopharmaceutical characterization. J Chromatogr A 2014; 1335:81-103. [DOI: 10.1016/j.chroma.2013.11.057] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Revised: 11/27/2013] [Accepted: 11/29/2013] [Indexed: 10/25/2022]
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Lee DY, Chang GD. Methylglyoxal in cells elicits a negative feedback loop entailing transglutaminase 2 and glyoxalase 1. Redox Biol 2014; 2:196-205. [PMID: 24494193 PMCID: PMC3909781 DOI: 10.1016/j.redox.2013.12.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 12/27/2013] [Accepted: 12/27/2013] [Indexed: 01/13/2023] Open
Abstract
Glyoxalase 1 (GlxI) is the key enzyme that converts the highly reactive α-oxo-aldehydes into the corresponding α-hydroxy acids using l-glutathione as a cofactor. In our preliminary data, GlxI was identified as a substrate of transglutaminase 2 (TG2), a ubiquitous enzyme with multiple functions. According to the catalytic properties of TG2, protein cross-linking, polyamine conjugation, and/or deamidation are potential post-translational modifications. In this article, we have demonstrated that TG2 catalyzes either polyamine conjugation or deamidation to GlxI depending on the presence of polyamines or not. Deamidation leads to activation of GlxI while polyamine conjugation results in activation of GlxI as well as stabilization of GlxI against denaturation treatment. In cultured HeLa cells, methylglyoxal challenge causes increase in intracellular levels of reactive oxygen species (ROS) and calcium leading to TG2 activation and subsequent transamidation and activation of GlxI. The inhibition of TG2 significantly weakens the cell resistance to the methylglyoxal challenge. Thus, GlxI is a novel substrate of TG2 and is activated by TG2 in vitro and in cellulo. Exposure to methylglyoxal elicits a negative feedback loop entailing ROS, calcium, TG2 and GlxI, thus leading to attenuation of the increase in the methylglyoxal level. The results imply that cancer cells highly express TG2 or GlxI can endure the oxidative stress derived from higher glycolytic flux and may gain extra growth advantage from the aerobic glycolysis. We have demonstrated novel modifications of glyoxalase I by transglutaminase 2. The modifications mediated by transglutaminse 2 modulate the glyoxalase I activities. Methylglyoxal treatment in cells induces increases in the levels of endogenous reactive oxygen species and activation transglutaminase 2 and glyoxalase I. Cells dispose the accumulated intracellular methylglyoxal by a negative feedback loop consisting of reactive oxygen species, calcium, transglutaminase 2 and glyoxalase I.
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Affiliation(s)
- Der-Yen Lee
- Graduate Institute of Biochemical Sciences, Technology Commons, Center for Systems Biology, National Taiwan University, No.1, Section 4, Roosevelt Road, Taipei 106, Taiwan
- Technology Commons, Center for Systems Biology, National Taiwan University, No.1, Section 4, Roosevelt Road, Taipei 106, Taiwan
| | - Geen-Dong Chang
- Graduate Institute of Biochemical Sciences, Technology Commons, Center for Systems Biology, National Taiwan University, No.1, Section 4, Roosevelt Road, Taipei 106, Taiwan
- Center for Systems Biology, National Taiwan University, No.1, Section 4, Roosevelt Road, Taipei 106, Taiwan
- Correspondence to: Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei 106, Taiwan. Tel.: +886 2 3366 4071; fax: +886 2 2363 5038.
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Silva LP, Lorenzi PL, Purwaha P, Yong V, Hawke DH, Weinstein JN. Measurement of DNA concentration as a normalization strategy for metabolomic data from adherent cell lines. Anal Chem 2013; 85:9536-42. [PMID: 24011029 PMCID: PMC3868625 DOI: 10.1021/ac401559v] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Metabolomics is a rapidly advancing field, and much of our understanding of the subject has come from research on cell lines. However, the results and interpretation of such studies depend on appropriate normalization of the data; ineffective or poorly chosen normalization methods can lead to frankly erroneous conclusions. That is a recurrent challenge because robust, reliable methods for normalization of data from cells have not been established. In this study, we have compared several methods for normalization of metabolomic data from cell extracts. Total protein concentration, cell count, and DNA concentration exhibited strong linear correlations with seeded cell number, but DNA concentration was found to be the most generally useful method for the following reasons: (1) DNA concentration showed the greatest consistency across a range of cell numbers; (2) DNA concentration was the closest to proportional with cell number; (3) DNA samples could be collected from the same dish as the metabolites; and (4) cell lines that grew in clumps were difficult to count accurately. We therefore conclude that DNA concentration is a widely applicable method for normalizing metabolomic data from adherent cell lines.
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Affiliation(s)
- Leslie P. Silva
- Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX, 77030, United States
| | - Philip L. Lorenzi
- Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX, 77030, United States
| | - Preeti Purwaha
- Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX, 77030, United States
| | - Valeda Yong
- Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX, 77030, United States
| | - David H. Hawke
- Department of Pathology, University of Texas MD Anderson Cancer Center, 7435 Fannin St., Houston, TX, 77054, United States
| | - John N. Weinstein
- Department of Bioinformatics & Computational Biology, University of Texas MD Anderson Cancer Center, 1400 Pressler St., Houston, TX, 77030, United States
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Shi Y, Rhodes NR, Abdolvahabi A, Kohn T, Cook NP, Marti AA, Shaw BF. Deamidation of asparagine to aspartate destabilizes Cu, Zn superoxide dismutase, accelerates fibrillization, and mirrors ALS-linked mutations. J Am Chem Soc 2013; 135:15897-908. [PMID: 24066782 DOI: 10.1021/ja407801x] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The reactivity of asparagine residues in Cu, Zn superoxide dismutase (SOD1) to deamidate to aspartate remains uncharacterized; its occurrence in SOD1 has not been investigated, and the biophysical effects of deamidation on SOD1 are unknown. Deamidation is, nonetheless, chemically equivalent to Asn-to-Asp missense mutations in SOD1 that cause amyotrophic lateral sclerosis (ALS). This study utilized computational methods to identify three asparagine residues in wild-type (WT) SOD1 (i.e., N26, N131, and N139) that are predicted to undergo significant deamidation (i.e., to >20%) on time scales comparable to the long lifetime (>1 year) of SOD1 in large motor neurons. Site-directed mutagenesis was used to successively substitute these asparagines with aspartate (to mimic deamidation) according to their predicted deamidation rate, yielding: N26D, N26D/N131D, and N26D/N131D/N139D SOD1. Differential scanning calorimetry demonstrated that the thermostability of N26D/N131D/N139D SOD1 is lower than WT SOD1 by ~2-8 °C (depending upon the state of metalation) and <3 °C lower than the ALS mutant N139D SOD1. The triply deamidated analog also aggregated into amyloid fibrils faster than WT SOD1 by ~2-fold (p < 0.008**) and at a rate identical to ALS mutant N139D SOD1 (p > 0.2). A total of 534 separate amyloid assays were performed to generate statistically significant comparisons of aggregation rates among WT and N/D SOD1 proteins. Capillary electrophoresis and mass spectrometry demonstrated that ~23% of N26 is deamidated to aspartate (iso-aspartate was undetectable) in a preparation of WT human SOD1 (isolated from erythrocytes) that has been used for decades by researchers as an analytical standard. The deamidation of asparagine--an analytically elusive, sub-Dalton modification--represents a plausible and overlooked mechanism by which WT SOD1 is converted to a neurotoxic isoform that has a similar structure, instability, and aggregation propensity as ALS mutant N139D SOD1.
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Affiliation(s)
- Yunhua Shi
- Department of Chemistry and Biochemistry, Baylor University , Waco, Texas 76706, United States
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Yang H, Lowenson JD, Clarke S, Zubarev RA. Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice. J Proteome Res 2013; 12:4566-76. [PMID: 23947766 DOI: 10.1021/pr400688r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein l-isoaspartyl methyltransferase (PIMT) repairs the isoaspartyl residues (isoAsp) that originate from asparagine deamidation and aspartic acid (Asp) isomerization to Asp residues. Deletion of the gene encoding PIMT in mice (Pcmt1) leads to isoAsp accumulation in all tissues measured, especially in the brain. These PIMT-knockout (PIMT-KO) mice have perturbed glutamate metabolism and die prematurely of epileptic seizures. To elucidate the role of PIMT further, brain proteomes of PIMT-KO mice and controls were analyzed. The isoAsp levels from two of the detected 67 isoAsp sites (residue 98 from calmodulin and 68 from glyceraldehyde-3-phosphate dehydrogenase) were quantified and found to be significantly increased in PIMT-KO mice (p < 0.01). Additionally, the abundance of at least 151 out of the 1017 quantified proteins was found to be altered in PIMT-KO mouse brains. Gene ontology analysis revealed that many down-regulated proteins are involved in cellular amino acid biosynthesis. For example, the serine synthesis pathway was suppressed, possibly leading to reduced serine production in PIMT-KO mice. Additionally, the abundances of enzymes in the glutamate-glutamine cycle were altered toward the accumulation of glutamate. These findings support the involvement of PIMT in glutamate metabolism and suggest that the absence of PIMT also affects other processes involving amino acid synthesis and metabolism.
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Affiliation(s)
- Hongqian Yang
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Scheeles väg 2, SE-17 177 Stockholm, Sweden
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Dai S, Ni W, Patananan AN, Clarke SG, Karger BL, Zhou ZS. Integrated proteomic analysis of major isoaspartyl-containing proteins in the urine of wild type and protein L-isoaspartate O-methyltransferase-deficient mice. Anal Chem 2013; 85:2423-30. [PMID: 23327623 DOI: 10.1021/ac303428h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The formation of isoaspartyl residues (isoAsp or isoD) via either aspartyl isomerization or asparaginyl deamidation alters protein structure and potentially biological function. This is a spontaneous and nonenzymatic process, ubiquitous both in vivo and in nonbiological systems, such as in protein pharmaceuticals. In almost all organisms, protein L-isoaspartate O-methyltransferase (PIMT, EC2.1.1.77) recognizes and initiates the conversion of isoAsp back to aspartic acid. Additionally, alternative proteolytic and excretion pathways to metabolize isoaspartyl-containing proteins have been proposed but not fully explored, largely due to the analytical challenges for detecting isoAsp. We report here the relative quantitation and site profiling of isoAsp in urinary proteins from wild type and PIMT-deficient mice, representing products from excretion pathways. First, using a biochemical approach, we found that the total isoaspartyl level of proteins in urine of PIMT-deficient male mice was elevated. Subsequently, the major isoaspartyl protein species in urine from these mice were identified as major urinary proteins (MUPs) by shotgun proteomics. To enhance the sensitivity of isoAsp detection, a targeted proteomic approach using electron transfer dissociation-selected reaction monitoring (ETD-SRM) was developed to investigate isoAsp sites in MUPs. A total of 38 putative isoAsp modification sites in MUPs were investigated, with five derived from the deamidation of asparagine that were confirmed to contribute to the elevated isoAsp levels. Our findings lend experimental evidence for the hypothesized excretion pathway for isoAsp proteins. Additionally, the developed method opens up the possibility to explore processing mechanisms of isoaspartyl proteins at the molecular level, such as the fate of protein pharmaceuticals in circulation.
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Affiliation(s)
- Shujia Dai
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston Massachusetts 02115, United States
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36
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Quantitation of asparagine deamidation by isotope labeling and liquid chromatography coupled with mass spectrometry analysis. Anal Biochem 2013; 432:16-22. [DOI: 10.1016/j.ab.2012.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 09/17/2012] [Indexed: 12/20/2022]
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Zybailov BL, Glazko GV, Jaiswal M, Raney KD. Large Scale Chemical Cross-linking Mass Spectrometry Perspectives. ACTA ACUST UNITED AC 2013; 6:001. [PMID: 25045217 PMCID: PMC4101816 DOI: 10.4172/jpb.s2-001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The spectacular heterogeneity of a complex protein mixture from biological samples becomes even more difficult to tackle when one’s attention is shifted towards different protein complex topologies, transient interactions, or localization of PPIs. Meticulous protein-by-protein affinity pull-downs and yeast-two-hybrid screens are the two approaches currently used to decipher proteome-wide interaction networks. Another method is to employ chemical cross-linking, which gives not only identities of interactors, but could also provide information on the sites of interactions and interaction interfaces. Despite significant advances in mass spectrometry instrumentation over the last decade, mapping Protein-Protein Interactions (PPIs) using chemical cross-linking remains time consuming and requires substantial expertise, even in the simplest of systems. While robust methodologies and software exist for the analysis of binary PPIs and also for the single protein structure refinement using cross-linking-derived constraints, undertaking a proteome-wide cross-linking study is highly complex. Difficulties include i) identifying cross-linkers of the right length and selectivity that could capture interactions of interest; ii) enrichment of the cross-linked species; iii) identification and validation of the cross-linked peptides and cross-linked sites. In this review we examine existing literature aimed at the large-scale protein cross-linking and discuss possible paths for improvement. We also discuss short-length cross-linkers of broad specificity such as formaldehyde and diazirine-based photo-cross-linkers. These cross-linkers could potentially capture many types of interactions, without strict requirement for a particular amino-acid to be present at a given protein-protein interface. How these shortlength, broad specificity cross-linkers be applied to proteome-wide studies? We will suggest specific advances in methodology, instrumentation and software that are needed to make such a leap.
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Affiliation(s)
- Boris L Zybailov
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mihir Jaiswal
- UALR/UAMS Joint Bioinformatics Program, University of Arkansas Little Rock, Little Rock, AR, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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