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Sivanathan GT, Mallubhotla H, Suggala SV, Tholu MS. Separation of closely related monoclonal antibody charge variant impurities using poly(ethylenimine)-grafted cation-exchange chromatography resin. 3 Biotech 2022; 12:293. [PMID: 36276450 PMCID: PMC9515282 DOI: 10.1007/s13205-022-03350-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/04/2022] [Indexed: 11/28/2022] Open
Abstract
The removal of protein charge variants due to complex chemical and enzymatic modifications like glycosylation, fragmentation and deamidation presents a significant challenge in the purification of monoclonal antibodies (mAb) and complicates downstream processing. These protein modifications occur either in vivo or during fermentation and downstream processing. The presence of charge variants can lead to diminished biological activity, differences in pharmacokinetics, pharmacodynamics, stability and efficacy. Therefore, these different product variants should be appropriately controlled for the consistency of product quality and to ensure patient safety. This investigation focuses on the development of a chromatography step for the removal of the charge variants from a recombinant single-chain variable antibody fragment (scFv-Fc-Ab). Poly(ethyleneimine)-grafted cation-exchange resins (Poly CSX and Poly ABX) were evaluated and compared to traditional macroporous cation-exchange and tentacle cation-exchange resins. Linear salt gradient experiments were conducted to study the separation efficiency of scFv-Fc-Ab variants using different resins. A classical thermodynamic model was used to develop a mechanistic understanding of the differences in charge variant retention behaviour of different resins. High selectivity in separation of scFv-Fc-Ab charge variants is obtained in the Poly CSX resin.
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Affiliation(s)
- Ganesh T. Sivanathan
- Department of Chemical Engineering, JNTUA, Ananthapuramu, Andhra Pradesh 515002 India
- Biopharmaceutical Development, Syngene International Ltd., Bangalore, 560099 India
| | - Hanuman Mallubhotla
- Biopharmaceutical Development, Syngene International Ltd., Bangalore, 560099 India
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2
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Hui JO, Flick T, Loo JA, Campuzano IDG. Unequivocal Identification of Aspartic Acid and isoAspartic Acid by MALDI-TOF/TOF: From Peptide Standards to a Therapeutic Antibody. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1901-1909. [PMID: 33390012 DOI: 10.1021/jasms.0c00370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aspartic acid (Asp) to isoaspartic acid (isoAsp) isomerization in therapeutic monoclonal antibodies (mAbs) and other biotherapeutics is a critical quality attribute (CQA) that requires careful control and monitoring during the drug discovery and production processes. The unwanted formation of isoAsp within biotherapeutics and resultant structural changes in the peptide backbone may negatively impact the efficacy, potency, and safety of the molecule or become immunogenic, especially if the isomerization occurs within the mAb complementarity determining region (CDR). Herein we describe a MALDI-TOF/TOF mass spectrometry method that affords unequivocal identification of the presence and the exact position of the isoAsp residue(s) in peptide standards ranging in size from a tripeptide to a docosapeptide (22 residues). In general, the peptide bond immediately N-terminal to the isoAsp residue is more susceptible to MALDI-TOF/TOF fragmentation than its unmodified counterpart. In some of the peptides evaluated in this study, fragmentation of the peptide bond C-terminal to the isoAsp residue (the aspartate effect) is also enhanced when compared to the control. Relative quantification by MALDI-TOF/TOF of this chemical modification is dependent upon a successful reversed-phase HPLC (rpHPLC) separation of the control and modified peptides. This method has also been validated on a therapeutic mAb that contains a well-documented isoAsp residue in the heavy chain CDR3 after forced degradation. Moreover, we also demonstrate that higher energy C-trap dissociation of only the singly charged species, and not the multiply charged form, of the isoAsp containing peptide, separated by rpHPLC, results in LC-MS/MS fragmentation that is highly consistent to that of MALDI-TOF/TOF.
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Affiliation(s)
- John O Hui
- Amgen Research, Discovery Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Tawnya Flick
- Attribute Sciences, Pivotal, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Joseph A Loo
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Iain D G Campuzano
- Amgen Research, Discovery Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
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3
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Lee YF, Jöhnck M, Frech C. Evaluation of differences between dual salt-pH gradient elution and mono gradient elution using a thermodynamic model: Simultaneous separation of six monoclonal antibody charge and size variants on preparative-scale ion exchange chromatographic resin. Biotechnol Prog 2018; 34:973-986. [DOI: 10.1002/btpr.2626] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 02/02/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yi Feng Lee
- Institute of Biochemistry, Department of Biotechnology; University of Applied Sciences Mannheim; Mannheim Germany
| | - Matthias Jöhnck
- Department of Process Solutions, Actives & Formulation; Merck KGaA; Darmstadt Germany
| | - Christian Frech
- Institute of Biochemistry, Department of Biotechnology; University of Applied Sciences Mannheim; Mannheim Germany
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4
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Proteomics Research in Cardiovascular Medicine and Biomarker Discovery. J Am Coll Cardiol 2017; 68:2819-2830. [PMID: 28007144 DOI: 10.1016/j.jacc.2016.10.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 11/21/2022]
Abstract
Proteomics is a systems physiology discipline to address the large-scale characterization of protein species within a biological system, be it a cell, a tissue, a body biofluid, an organism, or a cohort population. Building on advances from chemical analytical platforms (e.g., mass spectrometry and other technologies), proteomics approaches have contributed powerful applications in cardiovascular biomedicine, most notably in: 1) the discovery of circulating protein biomarkers of heart diseases from plasma samples; and 2) the identification of disease mechanisms and potential therapeutic targets in cardiovascular tissues, in both preclinical models and translational studies. Contemporary proteomics investigations offer powerful means to simultaneously examine tens of thousands of proteins in various samples, and understand their molecular phenotypes in health and disease. This concise review introduces study design considerations, example applications and use cases, as well as interpretation and analysis of proteomics data in cardiovascular biomedicine.
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Alekseychyk L, Su C, Becker GW, Treuheit MJ, Razinkov VI. High-Throughput Screening and Analysis of Charge Variants of Monoclonal Antibodies in Multiple Formulations. SLAS DISCOVERY 2017; 22:1044-1052. [PMID: 28570837 DOI: 10.1177/2472555217711666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Among different biopharmaceutical products, monoclonal antibodies (mAbs) show a high level of complexity, including heterogeneity due to differences in size, hydrophobicity, charge, and so forth. Such heterogeneity can be related to both cell-based production and any of the stages of purification, storage, and delivery that the mAb is subjected to. Choosing the right formulation composition providing both physical and chemical stabilities can be a very challenging process, especially when done in the limited time frame required for a typical drug development cycle. Charge variants, a common type of heterogeneity for mAbs, are easy to detect by ion exchange, specifically cation exchange chromatography (CEX). We have developed and implemented a high-throughput CEX-based approach for the rapid screening and analysis of charge modifications in multiple formulation conditions. In this work, 96 different formulations of antistreptavidin IgG1 and IgG2 molecules were automatically prepared and analyzed after incubation at high temperature. Design of experiment and statistical analysis tools have been utilized to determine the major formulation factors responsible for chemical stability of antibodies. Regression models were constructed to find the optimal formulation conditions. The methodology can be applied to different stages of preformulation and formulation development of mAbs.
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Affiliation(s)
| | - Cheng Su
- 2 Biostatistics, Amgen Inc., San Francisco, CA, USA
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Rea JC, Freistadt BS, McDonald D, Farnan D, Wang YJ. Capillary ion-exchange chromatography with nanogram sensitivity for the analysis of monoclonal antibodies. J Chromatogr A 2015; 1424:77-85. [PMID: 26596872 DOI: 10.1016/j.chroma.2015.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/27/2015] [Accepted: 11/01/2015] [Indexed: 02/04/2023]
Abstract
Ion-exchange chromatography (IEC) is widely used for profiling the charge heterogeneity of proteins, including monoclonal antibodies (mAbs). Despite good resolving power and robustness, ionic strength-based ion-exchange separations are generally product specific and can be time consuming to develop. In addition, conventional analytical scale ion-exchange separations require tens of micrograms of mAbs for each injection, amounts that are often unavailable in sample-limited applications. We report the development of a capillary IEC (c-IEC) methodology for the analysis of nanogram amounts of mAb charge variants. Several key modifications were made to a commercially available liquid chromatography system to perform c-IEC for charge variant analysis of mAbs with nanogram sensitivity. We demonstrate the method for multiple monoclonal antibodies, including antibody fragments, on different columns from different manufacturers. Relative standard deviations of <10% were achieved for relative peak areas of main peak, acidic and basic regions, which are common regions of interest for quantifying monoclonal antibody charge variants using IEC. The results herein demonstrate the excellent sensitivity of this c-IEC characterization method, which can be used for analyzing charge variants in sample-limited applications, such as early-stage candidate screening and in vivo studies.
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Affiliation(s)
- Jennifer C Rea
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Benny S Freistadt
- Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA 94080, USA
| | - Daniel McDonald
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Dell Farnan
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yajun Jennifer Wang
- Protein Analytical Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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7
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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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8
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Razinkov VI, Treuheit MJ, Becker GW. Accelerated formulation development of monoclonal antibodies (mAbs) and mAb-based modalities: review of methods and tools. ACTA ACUST UNITED AC 2015; 20:468-83. [PMID: 25576149 DOI: 10.1177/1087057114565593] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
More therapeutic monoclonal antibodies and antibody-based modalities are in development today than ever before, and a faster and more accurate drug discovery process will ensure that the number of candidates coming to the biopharmaceutical pipeline will increase in the future. The process of drug product development and, specifically, formulation development is a critical bottleneck on the way from candidate selection to fully commercialized medicines. This article reviews the latest advances in methods of formulation screening, which allow not only the high-throughput selection of the most suitable formulation but also the prediction of stability properties under manufacturing and long-term storage conditions. We describe how the combination of automation technologies and high-throughput assays creates the opportunity to streamline the formulation development process starting from early preformulation screening through to commercial formulation development. The application of quality by design (QbD) concepts and modern statistical tools are also shown here to be very effective in accelerated formulation development of both typical antibodies and complex modalities derived from them.
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Brückner C, Imhof D, Scriba GK. Capillary electrophoretic study of the degradation pathways and kinetics of the aspartyl model tetrapeptide Gly-Phe-Asp-GlyOH in alkaline solution. J Pharm Biomed Anal 2013; 76:96-103. [DOI: 10.1016/j.jpba.2012.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Revised: 12/08/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
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10
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Chatterjee T, Pal A, Chakravarty D, Dey S, Saha RP, Chakrabarti P. Protein l-isoaspartyl-O-methyltransferase of Vibrio cholerae: interaction with cofactors and effect of osmolytes on unfolding. Biochimie 2012; 95:912-21. [PMID: 23274130 DOI: 10.1016/j.biochi.2012.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 12/13/2012] [Indexed: 10/27/2022]
Abstract
Protein l-isoaspartyl-O-methyltransferase (PIMT) is an ubiquitous enzyme widely distributed in cells and plays a role in the repair of deamidated and isomerized proteins. In this study, we show that this enzyme is present in cytosolic extract of Vibrio cholerae, an enteric pathogenic Gram-negative bacterium and is enzymatically active. Additionally, we focus on the detailed biophysical characterization of the recombinant PIMT from V. cholerae to gain insight into its structure, stability and the cofactor binding. The equilibrium denaturation of PIMT has been studied using tryptophan fluorescence and CD spectroscopy. The far- and near-UV CD, as well as fluorescence experiments reveal the presence of a non-native intermediate in the folding pathway. Binding of the hydrophobic fluorescent probe, bis-ANS, to the intermediate occurs with high affinity because of the exposure of the hydrophobic clusters during the unfolding process. The existence of the probable intermediate has also been confirmed from limited tryptic digestion and DLS experiments. The protein shows higher binding affinity for AdoHcy, in comparison to AdoMet, and the binding increases the midpoint of thermal unfolding by 6 and 5 °C, respectively. Modeling and molecular dynamics simulations also support the higher stability of the protein in presence of AdoHcy.
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Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India.
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11
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Saravanaperumal SA, Pediconi D, Renieri C, La Terza A. Skipping of exons by premature termination of transcription and alternative splicing within intron-5 of the sheep SCF gene: a novel splice variant. PLoS One 2012; 7:e38657. [PMID: 22719917 PMCID: PMC3376141 DOI: 10.1371/journal.pone.0038657] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Accepted: 05/08/2012] [Indexed: 11/23/2022] Open
Abstract
Stem cell factor (SCF) is a growth factor, essential for haemopoiesis, mast cell development and melanogenesis. In the hematopoietic microenvironment (HM), SCF is produced either as a membrane-bound (-) or soluble (+) forms. Skin expression of SCF stimulates melanocyte migration, proliferation, differentiation, and survival. We report for the first time, a novel mRNA splice variant of SCF from the skin of white merino sheep via cloning and sequencing. Reverse transcriptase (RT)-PCR and molecular prediction revealed two different cDNA products of SCF. Full-length cDNA libraries were enriched by the method of rapid amplification of cDNA ends (RACE-PCR). Nucleotide sequencing and molecular prediction revealed that the primary 1519 base pair (bp) cDNA encodes a precursor protein of 274 amino acids (aa), commonly known as 'soluble' isoform. In contrast, the shorter (835 and/or 725 bp) cDNA was found to be a 'novel' mRNA splice variant. It contains an open reading frame (ORF) corresponding to a truncated protein of 181 aa (vs 245 aa) with an unique C-terminus lacking the primary proteolytic segment (28 aa) right after the D(175)G site which is necessary to produce 'soluble' form of SCF. This alternative splice (AS) variant was explained by the complete nucleotide sequencing of splice junction covering exon 5-intron (5)-exon 6 (948 bp) with a premature termination codon (PTC) whereby exons 6 to 9/10 are skipped (Cassette Exon, CE 6-9/10). We also demonstrated that the Northern blot analysis at transcript level is mediated via an intron-5 splicing event. Our data refine the structure of SCF gene; clarify the presence (+) and/or absence (-) of primary proteolytic-cleavage site specific SCF splice variants. This work provides a basis for understanding the functional role and regulation of SCF in hair follicle melanogenesis in sheep beyond what was known in mice, humans and other mammals.
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Affiliation(s)
| | - Dario Pediconi
- School of Environmental Sciences, University of Camerino, via Gentile III da Varano, Camerino (MC), Italy
| | - Carlo Renieri
- School of Environmental Sciences, University of Camerino, via Gentile III da Varano, Camerino (MC), Italy
| | - Antonietta La Terza
- School of Environmental Sciences, University of Camerino, via Gentile III da Varano, Camerino (MC), Italy
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12
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Eon-Duval A, Broly H, Gleixner R. Quality attributes of recombinant therapeutic proteins: An assessment of impact on safety and efficacy as part of a quality by design development approach. Biotechnol Prog 2012; 28:608-22. [DOI: 10.1002/btpr.1548] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 03/26/2012] [Indexed: 12/12/2022]
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13
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Indeykina MI, Popov IA, Kozin SA, Kononikhin AS, Kharybin ON, Tsvetkov PO, Makarov AA, Nikolaev EN. Capabilities of MS for Analytical Quantitative Determination of the Ratio of α- and βAsp7 Isoforms of the Amyloid-β Peptide in Binary Mixtures. Anal Chem 2011; 83:3205-10. [DOI: 10.1021/ac103213j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria I. Indeykina
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Igor A. Popov
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Alexey S. Kononikhin
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Oleg N. Kharybin
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Philippe O. Tsvetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Evgenij N. Nikolaev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
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Adsorption of deamidated antibody variants on macroporous and dextran-grafted cation exchangers: I. Adsorption equilibrium. J Chromatogr A 2011; 1218:1519-29. [DOI: 10.1016/j.chroma.2011.01.049] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 01/13/2011] [Accepted: 01/17/2011] [Indexed: 11/22/2022]
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15
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Rao S, Pohl C. Reversible interference of Fe3+ with monoclonal antibody analysis in cation exchange columns. Anal Biochem 2011; 409:293-5. [DOI: 10.1016/j.ab.2010.10.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 10/19/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]
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16
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Rapid analysis of charge variants of monoclonal antibodies with capillary zone electrophoresis in dynamically coated fused-silica capillary. J Sep Sci 2011; 34:548-55. [DOI: 10.1002/jssc.201000719] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/03/2010] [Accepted: 12/06/2010] [Indexed: 11/07/2022]
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17
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Rea JC, Moreno GT, Lou Y, Farnan D. Validation of a pH gradient-based ion-exchange chromatography method for high-resolution monoclonal antibody charge variant separations. J Pharm Biomed Anal 2011; 54:317-23. [DOI: 10.1016/j.jpba.2010.08.030] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 08/11/2010] [Accepted: 08/21/2010] [Indexed: 10/19/2022]
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18
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Desfougères Y, Jardin J, Lechevalier V, Pezennec S, Nau F. Succinimidyl residue formation in hen egg-white lysozyme favors the formation of intermolecular covalent bonds without affecting its tertiary structure. Biomacromolecules 2010; 12:156-66. [PMID: 21166442 DOI: 10.1021/bm101089g] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protein chemical degradations occur naturally into living cells as soon as proteins have been synthesized. Among these modifications, deamidation of asparagine or glutamine residues has been extensively studied, whereas the intermediate state, a succinimide derivative, was poorly investigated because of the difficulty of isolating those transient species. We used an indirect method, a limited thermal treatment in the dry state at acidic pH, to produce stable cyclic imide residues in hen lysozyme molecules, enabling us to examine the structural and functional properties of so modified proteins. Five cyclic imide rings have been located at sites directly accessible to solvent and did not lead to any changes in secondary or tertiary structures. However, they altered the catalytic properties of lysozyme and significantly decreased the intrinsic stability of the molecules. Moreover, dimerization occurred during the treatment, and this phenomenon was proportional to the extent of chemical degradation. We propose that succinimide formation could be responsible for covalent bond formation under specific physicochemical conditions that could be found in vivo.
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Affiliation(s)
- Yann Desfougères
- Agrocampus Ouest and INRA, UMR1253 STLO, F-35042 Rennes, France.
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19
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Noguchi S. Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B. Biopolymers 2010; 93:1003-10. [PMID: 20623666 DOI: 10.1002/bip.21514] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Under physiological conditions, the deamidation and isomerization of asparagine to isoaspartate (isoAsp) proceeds nonenzymatically via succinimide. Although a large number of proteins have been reported to contain isoAsp, information concerning the three-dimensional structure of proteins containing isoaspartate is still limited. We have crystallized isoAsp containing Ustilago sphaerogena ribonuclease U2B, and determined the crystal structure at 1.32 Å resolution. The structure revealed that the formation of isoAsp32 induces a single turn unfolding of the α-helix from Asp29 to Asp34, and the region from Asp29 to Arg35 forms a U-shaped loop structure. The electron density map shows that isoAsp32 retained the L-configuration at the C(α) atom. IsoAsp32 is in gauche conformation about a C(α)--C(β) bond, and the polypeptide chain bends by ∼90° at isoAsp32. IsoAsp32 protrudes from the surface of the protein, and the abnormal β-peptide bond in the main-chain and α-carboxylate in the side-chain is fully exposed. The structure suggests that the deamidation of the Asn and the isoAsp formation in proteins could confer immunogenicity.
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Affiliation(s)
- Shuji Noguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo 113-0033, Japan.
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20
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Kim J, Jones L, Taylor L, Kannan G, Jackson F, Lau H, Latypov RF, Bailey B. Characterization of a unique IgG1 mAb CEX profile by limited Lys-C proteolysis/CEX separation coupled with mass spectrometry and structural analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:1973-81. [DOI: 10.1016/j.jchromb.2010.05.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 04/28/2010] [Accepted: 05/20/2010] [Indexed: 11/29/2022]
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21
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Chan WYK, Chan TWD, O'Connor PB. Electron transfer dissociation with supplemental activation to differentiate aspartic and isoaspartic residues in doubly charged peptide cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1012-5. [PMID: 20304674 PMCID: PMC3114307 DOI: 10.1016/j.jasms.2010.02.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 05/11/2023]
Abstract
Electron-transfer dissociation (ETD) with supplemental activation of the doubly charged deamidated tryptic digested peptide ions allows differentiation of isoaspartic acid and aspartic acid residues using the c + 57 or z*-57 peaks. The diagnostic peak clearly localizes and characterizes the isoaspartic acid residue. Supplemental activation in ETD of the doubly charged peptide ions involves resonant excitation of the charge reduced precursor radical cations and leads to further dissociation, including extra backbone cleavages and secondary fragmentation. Supplemental activation is essential to obtain a high quality ETD spectrum (especially for doubly charged peptide ions) with sequence information. Unfortunately, the low-resolution of the ion trap mass spectrometer makes detection of the diagnostic peak, [M-60], for the aspartic acid residue difficult due to interference with side-chain loss from arginine and glutamic acid residues.
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Affiliation(s)
- Wai Yi Kelly Chan
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
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22
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Farnan D, Moreno GT. Multiproduct High-Resolution Monoclonal Antibody Charge Variant Separations by pH Gradient Ion-Exchange Chromatography. Anal Chem 2009; 81:8846-57. [DOI: 10.1021/ac901408j] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dell Farnan
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080
| | - G. Tony Moreno
- Protein Analytical Chemistry, Genentech, 1 DNA Way, South San Francisco, California 94080
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Tsvetkov FO, Makarov AA, Archakov AI, Kozin SA. Effect of isomerization of aspartate-7 on the binding of copper (II) ion by the β-amyloid peptide. Biophysics (Nagoya-shi) 2009. [DOI: 10.1134/s0006350909020018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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24
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Abstract
The removal of product variants that form during downstream processing remains a challenge in the purification of recombinant therapeutic proteins. We examined the feasibility of separating variants with slightly different net charge using high-performance membrane ultrafiltration. A myoglobin variant was formed by reaction of the lysine epsilon-amino group with succinic anhydride. Sieving data were obtained over a range of solution conditions using commercial polyethersulfone ultrafiltration membranes. Maximum selectivity of about 7-fold was obtained at very low conductivity due to the strong electrostatic repulsion of the more negatively charged variant. Protein separations were performed by diafiltration. A two-stage process generated solutions of the normal myoglobin (in the permeate) and the charge variant (in the retentate), both at greater than 9-fold purification and 90% yield. These results provide the first demonstration that membrane systems can be used to separate proteins that differ by only a single charged amino acid residue.
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Affiliation(s)
- Mareia Frost Ebersold
- Department of Chemical Engineering, University of Delaware, Newark, Delaware 19716, USA
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25
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Zhang Y, Martinez T, Woodruff B, Goetze A, Bailey R, Pettit D, Balland A. Hydrophobic interaction chromatography of soluble interleukin I receptor type II to reveal chemical degradations resulting in loss of potency. Anal Chem 2008; 80:7022-8. [PMID: 18707131 DOI: 10.1021/ac800928z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A hydrophobic interaction chromatography method was developed to analyze recombinant soluble Interleukin 1 receptor type II (sIL-1R type II) drug substance and assess the stability of the drug under accelerated degradation studies. HIC resolved the degraded molecules into three peaks. A combination of several analytical techniques, including cyanogen bromide cleavage, reversed-phase chromatography, mass spectrometry, and N-terminal sequencing, were used to identify the origins of these peaks. We found that accelerated degradation resulted from three different events, deamidation and isomerization at asparagine 317 (Asn317), C-terminal cleavage, and aggregation. The iso-aspartate 317 (iso-Asp317)-containing species were shown to elute in HIC peak I and the Asp317-containing species in HIC peak II, respectively. Deamidation-isomerization to iso-Asp317, but not deamidation to Asp317, resulted in altered retention time on HIC companied by loss of potency, presumably by introducing a significant conformational change. CNBr C-terminal analysis showed that the inactive HIC peak I consisted of sIL-1R type II with "large" C-terminal truncations of 13 or 14 amino acids, whereas the active HIC peak II contained C-terminally full length and "small" C-terminal clips of two amino acids. Molecular modeling indicates that the short loop D317-S320, in the third domain of IL-1R type II, has a crucial impact on the stability of the molecule.
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Affiliation(s)
- Yuling Zhang
- Department of Analytical and Formulation Sciences, Amgen Inc. 1201 Amgen Court West, Seattle, Washington 98119, USA.
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26
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Jenkins N, Murphy L, Tyther R. Post-translational modifications of recombinant proteins: significance for biopharmaceuticals. Mol Biotechnol 2008; 39:113-8. [PMID: 18327554 DOI: 10.1007/s12033-008-9049-4] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The production of recombinant therapeutic proteins is one of the fastest growing sectors of the pharmaceutical industry, particularly monoclonal antibodies and Fc-fusion proteins. Currently, mammalian cells are the dominant production system for these proteins because they can perform complex post-translational modifications that are often required for efficient secretion, drug efficacy, and stability. These protein modifications include misfolding and aggregation, oxidation of methionine, deamidation of asparagine and glutamine, variable glycosylation, and proteolysis. Such modifications not only pose challenges for accurate and consistent bioprocessing, but also may have consequences for the patient in that incorrect modifications and aggregation can lead to an immune response to the therapeutic protein. This mini-review describes examples analytical and preventative advances in the fields of protein oxidation, deamidation, misfolding and aggregation (glycosylation is covered in other articles in this issue). The feasibility of partially replacing traditional analytical methods such as peptide mapping with high-throughput screens and their use in clone and media selection are evaluated. This review also discusses how further technical advances could improve the manufacturability, potency, and safety of biotherapeutics.
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Affiliation(s)
- Nigel Jenkins
- National Institute for Bioprocessing Research and Training (NIBRT), Engineering Building, University College Dublin, Belfield, Dublin 4, Ireland.
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27
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Chapter 16 Analysis of Deamidation in Proteins. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/s0166-526x(08)00216-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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28
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Yuzawa S, Opatowsky Y, Zhang Z, Mandiyan V, Lax I, Schlessinger J. Structural basis for activation of the receptor tyrosine kinase KIT by stem cell factor. Cell 2007; 130:323-34. [PMID: 17662946 DOI: 10.1016/j.cell.2007.05.055] [Citation(s) in RCA: 248] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2007] [Revised: 04/25/2007] [Accepted: 05/22/2007] [Indexed: 01/15/2023]
Abstract
Stem Cell Factor (SCF) initiates its multiple cellular responses by binding to the ectodomain of KIT, resulting in tyrosine kinase activation. We describe the crystal structure of the entire ectodomain of KIT before and after SCF stimulation. The structures show that KIT dimerization is driven by SCF binding whose sole role is to bring two KIT molecules together. Receptor dimerization is followed by conformational changes that enable lateral interactions between membrane proximal Ig-like domains D4 and D5 of two KIT molecules. Experiments with cultured cells show that KIT activation is compromised by point mutations in amino acids critical for D4-D4 interaction. Moreover, a variety of oncogenic mutations are mapped to the D5-D5 interface. Since key hallmarks of KIT structures, ligand-induced receptor dimerization, and the critical residues in the D4-D4 interface, are conserved in other receptors, the mechanism of KIT stimulation unveiled in this report may apply for other receptor activation.
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Affiliation(s)
- Satoru Yuzawa
- Department of Pharmacology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA
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29
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Liu H, Chen X, Focia PJ, He X. Structural basis for stem cell factor-KIT signaling and activation of class III receptor tyrosine kinases. EMBO J 2007; 26:891-901. [PMID: 17255936 PMCID: PMC1794399 DOI: 10.1038/sj.emboj.7601545] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Accepted: 12/15/2006] [Indexed: 11/08/2022] Open
Abstract
Stem cell factor (SCF) binds to and activates the KIT receptor, a class III receptor tyrosine kinase (RTK), to stimulate diverse processes including melanogenesis, gametogenesis and hematopoeisis. Dysregulation of KIT activation is associated with many cancers. We report a 2.5 A crystal structure of the functional core of SCF bound to the extracellular ligand-binding domains of KIT. The structure reveals a 'wrapping' SCF-recognition mode by KIT, in which KIT adopts a bent conformation to facilitate each of its first three immunoglobulin (Ig)-like domains to interact with SCF. Three surface epitopes on SCF, an extended loop, the B and C helices, and the N-terminal segment, contact distinct KIT domains, with two of the epitopes undergoing large conformational changes upon receptor binding. The SCF/KIT complex reveals a unique RTK dimerization assembly, and a novel recognition mode between four-helix bundle cytokines and Ig-family receptors. It serves as a framework for understanding the activation mechanisms of class III RTKs.
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Affiliation(s)
- Heli Liu
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xiaoyan Chen
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pamela J Focia
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Xiaolin He
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Searle 8-417, 303 E Chicago Ave, Chicago, IL 60611, USA. Tel.: +1 312 503 8030; Fax: +1 312 503 5349; E-mail:
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30
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Cournoyer JJ, Lin C, Bowman MJ, O'Connor PB. Quantitating the relative abundance of isoaspartyl residues in deamidated proteins by electron capture dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:48-56. [PMID: 16997569 DOI: 10.1016/j.jasms.2006.08.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2006] [Revised: 08/16/2006] [Accepted: 08/16/2006] [Indexed: 05/11/2023]
Abstract
Relative quantitation of aspartyl and isoaspartyl residue mixtures from asparagine deamidation is demonstrated using electron capture dissociation without prior HPLC separation. The method utilizes the linear relationship found between the relative abundance of the isoaspartyl diagnostic ion, z(n)-57, and % isoaspartyl content based on the ECD spectra of known isoaspartyl/aspartyl mixtures of synthetic peptides. The observed linearity appears to be sequence independent because the relationship exists despite sequence variations and changes in backbone fragment abundances when isoaspartyl and aspartyl residues are interchanged. Furthermore, a new method to calculate the relative abundances of isomer from protein deamidation without synthetic peptides is proposed and tested using a linear peptide released by protein digestion that contains the deamidation site. The proteolytic peptide can be rapidly aged to the expected 3:1 (isoaspartyl:aspartyl) mixture to generate a two-point calibration standard for ECD analysis. The procedure can then be used to determine the relative abundance of deamidation products from in vivo or in vitro protein aging experiments.
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Affiliation(s)
- Jason J Cournoyer
- Department of Chemistry, Boston University, Boston, Massachusetts, USA
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31
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O'Connor CM. 13 Protein L-isoaspartyl, D-aspartyl O-methyltransferases: Catalysts for protein repair. Enzymes 2006; 24:385-433. [PMID: 26718047 DOI: 10.1016/s1874-6047(06)80015-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
Protein L-isoaspartyl, D-aspartyl O-methyltransferases (PIMTs) are ancient enzymes distributed through all phylogenetic domains. PIMTs catalyze the methylation of L-isoaspartyl, and to a lesser extent D-aspartyl, residues arising from the spontaneous deamidation and isomerization of protein asparaginyl and aspartyl residues. PIMTs catalyze the methylation of isoaspartyl residues in a large number of primary sequence configurations, which accounts for the broad specificity of the enzyme for protein substrates both in vitro and in vivo. PIMT-catalyzed methylation of isoaspartyl substrates initiates the repair of the polypeptide backbone in its damaged substrates by a spontaneous mechanism that involves a succinimidyl intermediate. The repair process catalyzed by PEVITs is not completely efficient, however, leaving open the possibility that unidentified enzymatic activities cooperate with PIMT in the repair process. Structurally, PIMTs are members of the class I family of AdoMet-dependent methyltransferases. PIMTs have a unique topological arrangement of strands in the central β sheet that provides a signature for this class of enzymes. The regulation and physiological significance of PIMT has been studied in several model organisms. PIMTs are constitutively synthesized by cells, but they can be upregulated in response to conditions that are potentially damaging to protein structures, or when proteins are stored for prolonged periods of time. Disruption of PIMT genes in bacteria and simple eukaryotes produces subtle phenotypes that are apparent only under stress. Loss of PIMT function in transgenic mice leads to fatalepilepsy, suggesting that PIMT function is particularly important to neurons in mammals.
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Affiliation(s)
- Clare M O'Connor
- Biology Department Boston College 140 Commonwealth Avenue Chestnut Hill, MA 02467, USA
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32
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Vitali R, Clarke S. Improved rotorod performance and hyperactivity in mice deficient in a protein repair methyltransferase. Behav Brain Res 2004; 153:129-41. [PMID: 15219714 DOI: 10.1016/j.bbr.2003.11.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2003] [Revised: 11/17/2003] [Accepted: 11/17/2003] [Indexed: 11/18/2022]
Abstract
The protein L-isoaspartate (D-aspartate)-O-methyltransferase participates in the repair of age-induced protein damage by initiating the conversion of abnormal aspartyl residues within proteins to normal L-aspartyl residues. Previous studies have shown that mice deficient in the gene encoding this enzyme (Pcmt1-/-) accumulate damaged proteins, have altered levels of brain S-adenosylmethionine (AdoMet) and S-adenosylhomocysteine (AdoHcy), and suffer from epileptic seizures that result in death at an average age of about 42 days. In this study, we found that the behavior of Pcmt1-/- mice is abnormal in comparison to their wild-type (Pcmt1+/+) and heterozygous (Pcmt1+/-) littermates in two standard quantitative behavioral assays - the accelerating rotorod and the open-field test. On the accelerating rotorod, we found Pcmt1-/- mice actually perform significantly better than their heterozygous and wild-type littermates, a situation that has only been infrequently described in the literature and has not been described to date for epilepsy-prone mice. The Pcmt1-/- mice show, however, hyperactivity in the open-field test that becomes more pronounced with age, with a partial habituation with time in the chamber. Additionally, these mice demonstrate a strong thigmotaxic movement pattern. We present evidence that these phenotypes are not related to the alterations of the AdoMet/AdoHcy ratio in the brain and thus may be a function of the accumulation of damaged proteins. These results implicate a role for this enzyme in motor coordination and cerebellum development and suggest the importance of the function of the repair methyltransferase in hippocampal-dependent spatial learning.
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Affiliation(s)
- Ryan Vitali
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569, USA
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33
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Zhang W, Czupryn JMJ, Boyle PT, Amari J. Characterization of asparagine deamidation and aspartate isomerization in recombinant human interleukin-11. Pharm Res 2003; 19:1223-31. [PMID: 12240950 DOI: 10.1023/a:1019814713428] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
UNLABELLED PURPOSE; The aim of this study was to investigate asparagine (Asn) deamidation and aspartate (Asp) isomerization and to measure the content of isoaspartate (isoAsp) in recombinant human interleukin-11 (rhIL-11). METHODS The rhIL-11 control and heat stressed samples were characterized with trypsin and endoproteinase Asp-N peptide mapping, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), reversed-phase high performance liquid chromatography (RP-HPLC), electrospray ionization mass spectrometry (ESI MS) and capillary electrophoresis (CE). The total isoAsp content and bioactivity were also assessed. RESULTS Stress of rhIL11 at 30 degrees C for 6 weeks in liquid resulted in significant isomerization of Asp45 and Asp47. Isomerization of Asp51 and deamidation of Asn49 were also detected at low levels. The stressed rhIL-11 molecule contained 0.3 mol of isoAsp per mol of protein, compared to only 0.007 mol/mol of protein in the control. CONCLUSIONS Asp and Asn residues, located in a loop structure of rhIL-11, undergo isoAsp formation under stressed conditions.
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Affiliation(s)
- Wei Zhang
- Wyeth BioPharma, Genetics Institute Campus, Andover, Massachusetts 01810, USA.
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34
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Karty JA, Ireland MME, Brun YV, Reilly JP. Artifacts and unassigned masses encountered in peptide mass mapping. J Chromatogr B Analyt Technol Biomed Life Sci 2002; 782:363-83. [PMID: 12458019 DOI: 10.1016/s1570-0232(02)00550-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In peptide mass mapping of isolated proteins, a significant number of the observed mass spectral peaks are often uninterpreted. These peaks derive from a number of sources: errors in the genome that give rise to incorrect peptide mass predictions, undocumented post-translational modifications, sample handling-induced modifications, contaminants in the sample, non-standard protein cleavage sites, and non-protein components of the sample. In a study of the stalk organelle of Caulobacter crescentus, roughly one-third (782/2215) of all observed masses could not be assigned to the proteins identified in the gel spots (Karty et al., J. Proteome Res., 1 (2002) 325). By interpreting these masses, this work illuminates a number of phenomena that may arise in the course of peptide mass mapping of electrophoretically separated proteins and presents results from a number of related studies.
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Affiliation(s)
- Jonathan A Karty
- Department of Chemistry, Indiana University, Bloomington 47405, USA
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35
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Meyer JD, Ho B, Manning MC. Effects of conformation on the chemical stability of pharmaceutically relevant polypeptides. PHARMACEUTICAL BIOTECHNOLOGY 2002; 13:85-107. [PMID: 11987755 DOI: 10.1007/978-1-4615-0557-0_4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Control of chemical instability in protein pharmaceuticals continues to be a critical issue in developing stable formulations. While the effects of pH, buffer composition, ionic strength and temperature remain the most effective methods for controlling hydrolysis and oxidation reactions, it appears that conformational control may also be important. Addition of excipients to maintain native structure and reduce the propensity of the protein to denature and/or aggregate is already a central theme in stabilizing proteins (Arakawa et al., 1993). The same additives have now been found to slow both deamidation and oxidation, whether in solution or in the solid state. What is emerging is an additional approach for producing protein pharmaceuticals that maintain native structure and activity during long-term storage.
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Affiliation(s)
- Jeffrey D Meyer
- Center for Pharmaceutical Biotechnology, Department of Pharmaceutical Sciences, School of Pharmacy, University of Colorado Health Sciences Center, Denver, CO 80262, USA
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36
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Abstract
At acidic pH, Asp67 and beta-Asp67 (beta-Asp: isoaspartic acid residue) derivatives of RNase A, obtained by selective deamidation of the parent enzyme, spontaneously produces a new derivative containing an aminosuccinyl residue (Asu). The overall secondary structure of the protein chain does not change as a consequence of this substitution, while the catalytic activity on RNA is reduced to about 25%. The pH dependence of the first-order rate constants for the Asu formation has a bell-shaped profile, the maximum being close to the pK(a) of the aspartic acid side chains. Moreover, the values of the rate constants are of the same magnitude of those measured for Asp-containing peptides whose sequence mimics the Asu formation site of the enzyme. This feature indicates that Asp67 and beta-Asp67 residues in the deamidated RNase A derivatives are sited in a region flexible enough to permit the cyclization of the carboxylic side chain to succinimide ring. These results are discussed at the light on to the three-dimensional structure and the thermodynamic stability of the aspartic acid derivatives of RNase A.
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Affiliation(s)
- S Capasso
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy.
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37
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Abstract
Nonenzymatic deamidation of peptides and proteins represents an important degradation reaction occurring in vitro in the course of isolation or storage and in vivo during development and/or aging of cells. This review first presents a synopsis of the influence of structure on deamidation reaction proceeding via a five-membered succinimide intermediate, followed by an outline of procedures for separation and detection of deamidated forms. Selected examples for in vitro and in vivo deamidation are reviewed including the possible biological consequences of this protein degradation. Finally, the reaction of protein methyltransferase with L-isoaspartyl- and D-aspartyl residues and its possible role in protein repair is elucidated.
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Affiliation(s)
- H Lindner
- Institute of Medical Chemistry and Biochemistry, University of Innsbruck, Fritz-Preglstrasse 3, A-6020 Innsbruck, Austria.
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38
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Jiang X, Gurel O, Mendiaz EA, Stearns GW, Clogston CL, Lu HS, Osslund TD, Syed RS, Langley KE, Hendrickson WA. Structure of the active core of human stem cell factor and analysis of binding to its receptor kit. EMBO J 2000; 19:3192-203. [PMID: 10880433 PMCID: PMC313947 DOI: 10.1093/emboj/19.13.3192] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/1998] [Revised: 05/09/2000] [Accepted: 05/11/2000] [Indexed: 11/12/2022] Open
Abstract
Stem cell factor (SCF) is an early-acting hematopoietic cytokine that elicits multiple biological effects. SCF is dimeric and occurs in soluble and membrane-bound forms. It transduces signals by ligand- mediated dimerization of its receptor, Kit, which is a receptor tyrosine kinase related to the receptors for platelet-derived growth factor (PDGF), macrophage colony-stimulating factor, Flt-3 ligand and vascular endothelial growth factor (VEGF). All of these have extracellular ligand-binding portions composed of immunoglobulin-like repeats. We have determined the crystal structure of selenomethionyl soluble human SCF at 2.2 A resolution by multiwavelength anomalous diffraction phasing. SCF has the characteristic helical cytokine topology, but the structure is unique apart from core portions. The SCF dimer has a symmetric 'head-to-head' association. Using various prior observations, we have located potential Kit-binding sites on the SCF dimer. A superimposition of this dimer onto VEGF in its complex with the receptor Flt-1 places the binding sites on SCF in positions of topographical and electrostatic complementarity with the Kit counterparts of Flt-1, and a similar model can be made for the complex of PDGF with its receptor.
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Affiliation(s)
- X Jiang
- Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, Columbia University, New York, NY 10032, USA
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39
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Savvides SN, Boone T, Andrew Karplus P. Flt3 ligand structure and unexpected commonalities of helical bundles and cystine knots. NATURE STRUCTURAL BIOLOGY 2000; 7:486-91. [PMID: 10881197 DOI: 10.1038/75896] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Human Flt3 ligand (Flt3L) stimulates early hematopoiesis by activating a type III tyrosine kinase receptor on primitive bone marrow stem cells. The crystal structure of soluble Flt3L reveals that it is a homodimer of two short chain alpha-helical bundles. Comparisons of structure-function relationships of Flt3L with the homologous hematopoietic cytokines macrophage colony stimulating factor (MCSF) and stem cell factor (SCF) suggest that they have a common receptor binding mode that is distinct from the paradigm derived from the complex of growth hormone with its receptor. Furthermore, we identify recognition features common to all helical and cystine-knot protein ligands that activate type III tyrosine kinase receptors, and the closely related type V tyrosine kinase receptors.
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Affiliation(s)
- S N Savvides
- Program in Biophysics, Cornell University, Ithaca, NY 14853, USA
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40
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Sarioglu H, Lottspeich F, Walk T, Jung G, Eckerskorn C. Deamidation as a widespread phenomenon in two-dimensional polyacrylamide gel electrophoresis of human blood plasma proteins. Electrophoresis 2000; 21:2209-18. [PMID: 10892731 DOI: 10.1002/1522-2683(20000601)21:11<2209::aid-elps2209>3.0.co;2-t] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The human plasma protein patterns obtained by two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) is a good model system for post-translational modifications because of the existence of several "ladders" of protein spots [Anderson, N. L., Anderson, N. G., Electrophoresis 1991, 12, 883-906], so-called "trains" of spots. Our investigation of several proteins, amongst others beta2-microglobulin and the haptoglobin chains, found the differences in isoelectric points (p/) to be due to deamidation of asparagines. After enzymatic cleavage with endopeptidases in the 2-D polyacrylamide gel, the asparagine and deamidated asparagine containing peptides were separated and quantified by reversed-phase HPLC. In order to separate these peptides, a neutral pH system was established and, as a result, the differences in hydrophobicity of asparagine-containing and deamidated asparagine-containing peptides increased. But how do deamidated asparagines contribute to the observed spot pattern? One spot in the 2-D gel consists of a mixture of protein species with the same number of deamidated asparagines but on different sequence position sites. The difference between the spots in the "ladder" is a growing number of negative charges introduced in the protein by an increasing number of deamidated asparagines. As a consequence, the mass difference between two spots is exactly 1 Da, which is shown in this paper for intact protein masses and the corresponding deamidated peptides.
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Affiliation(s)
- H Sarioglu
- Department for Protein Analytics, Max-Planck-Institut for Biochemistry, Martinsried, Germany.
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41
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Vassileva-Atanassova A, Niwa T, Mironova R, Ivanov I. Mass-spectral analysis of human interferon-gamma and chloramphenicol acetyltransferase I produced in two Escherichia coli strains. J Biotechnol 2000; 78:61-7. [PMID: 10702911 DOI: 10.1016/s0168-1656(99)00236-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recombinant human interferon-gamma and chloramphenicol acetyltransferase I were isolated from two Escherichia coli strains, E. coli LE329 and E. coli XL1-blue and characterized by electrospray ionization mass spectrometry (ESI-MS). The ESI-MS analysis showed higher masses in comparison with the theoretically calculated for both proteins as well as unexpected molecular heterogeneity. The ESI-MS spectral patterns of the proteins depended on the host strain used and were more heterogenous for the proteins isolated from E. coli LE392. One of the proteins (human interferon-gamma obtained from E. coli XL1-blue) was further subjected to BrCN cleavage. The ESI-MS analysis of the polypeptide mixture revealed shift in the molecular mass for two peptides including the last 26 amino acids of the human interferon-gamma molecule.
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42
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di Salvo ML, Delle Fratte S, Maras B, Bossa F, Wright HT, Schirch V. Deamidation of asparagine residues in a recombinant serine hydroxymethyltransferase. Arch Biochem Biophys 1999; 372:271-9. [PMID: 10600164 DOI: 10.1006/abbi.1999.1512] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Serine hydroxymethyltransferase purified from rabbit liver cytosol has at least two Asn residues (Asn(5) and Asn(220)) that are 67 and 30% deamidated, respectively. Asn(5) is deamidated equally to Asp and isoAsp, while Asn(220) is deamidated only to isoAsp. To determine the effect of these Asn deamidations on enzyme activity and stability a recombinant rabbit liver cytosolic serine hydroxymethyltransferase was expressed in Escherichia coli over a 5-h period. About 90% of the recombinant enzyme could be isolated with the two Asn residues in a nondeamidated form. Compared with the enzyme isolated from liver the recombinant enzyme had a 35% increase in catalytic activity but exhibited no significant changes in either affinity for substrates or stability. Introduction of Asp residues for either Asn(5) or Asn(220) did not significantly alter activity or stability of the mutant forms. In vitro incubation of the recombinant enzyme at 37 degrees C and pH 7.3 resulted in the rapid deamidation of Asn(5) to both Asp and isoAsp with a t(1/2) of 50-70 h, which is comparable to the rate found with small flexible peptides containing the same sequence. The t(1/2) for deamidation of Asn(220) was at least 200 h. This residue may become deamidated only after some unfolding of the enzyme. The rates for deamidation of Asn(5) and Asn(220) are consistent with the structural environment of the two Asn residues in the native enzyme. There are also at least two additional deamidation events that occur during prolonged incubation of the recombinant enzyme.
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Affiliation(s)
- M L di Salvo
- Department of Biochemistry, The Institute for Structural Biology and Drug Discovery, Virginia Comonwealth University, Richmond, Virginia, 23219, USA
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