1
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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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Montioli R, Campagnari R, Fasoli S, Fagagnini A, Caloiu A, Smania M, Menegazzi M, Gotte G. RNase A Domain-Swapped Dimers Produced Through Different Methods: Structure-Catalytic Properties and Antitumor Activity. Life (Basel) 2021; 11:life11020168. [PMID: 33669993 PMCID: PMC7926746 DOI: 10.3390/life11020168] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/16/2022] Open
Abstract
Upon oligomerization, RNase A can acquire important properties, such as cytotoxicity against leukemic cells. When lyophilized from 40% acetic acid solutions, the enzyme self-associates through the so-called three-dimensional domain swapping (3D-DS) mechanism involving both N- and/or C-terminals. The same species are formed if the enzyme is subjected to thermal incubation in various solvents, especially in 40% ethanol. We evaluated here if significant structural modifications might occur in RNase A N- or C-swapped dimers and/or in the residual monomer(s), as a function of the oligomerization protocol applied. We detected that the monomer activity vs. ss-RNA was partly affected by both protocols, although the protein does not suffer spectroscopic alterations. Instead, the two N-swapped dimers showed differences in the fluorescence emission spectra but almost identical enzymatic activities, while the C-swapped dimers displayed slightly different activities vs. both ss- or ds-RNA substrates together with not negligible fluorescence emission alterations within each other. Besides these results, we also discuss the reasons justifying the different relative enzymatic activities displayed by the N-dimers and C-dimers. Last, similarly with data previously registered in a mouse model, we found that both dimeric species significantly decrease human melanoma A375 cell viability, while only N-dimers reduce human melanoma MeWo cell growth.
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Affiliation(s)
- Riccardo Montioli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Rachele Campagnari
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Sabrina Fasoli
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Andrea Fagagnini
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Andra Caloiu
- Department of Microbiology and Virology, Wexham Park Hospital, Wexham Road, Slough SL24HL, Berkshire, UK;
| | - Marcello Smania
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
| | - Marta Menegazzi
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
- Correspondence: (M.M.); (G.G.); Tel.: +39-045-8027168 (M.M.); +39-045-8027694 (G.G.)
| | - Giovanni Gotte
- Department of Neuroscience, Biomedicine, and Movement Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie, 8, I-37134 Verona, Italy; (R.M.); (R.C.); (S.F.); (A.F.); (M.S.)
- Correspondence: (M.M.); (G.G.); Tel.: +39-045-8027168 (M.M.); +39-045-8027694 (G.G.)
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3
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Gotte G, Menegazzi M. Biological Activities of Secretory RNases: Focus on Their Oligomerization to Design Antitumor Drugs. Front Immunol 2019; 10:2626. [PMID: 31849926 PMCID: PMC6901985 DOI: 10.3389/fimmu.2019.02626] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022] Open
Abstract
Ribonucleases (RNases) are a large number of enzymes gathered into different bacterial or eukaryotic superfamilies. Bovine pancreatic RNase A, bovine seminal BS-RNase, human pancreatic RNase 1, angiogenin (RNase 5), and amphibian onconase belong to the pancreatic type superfamily, while binase and barnase are in the bacterial RNase N1/T1 family. In physiological conditions, most RNases secreted in the extracellular space counteract the undesired effects of extracellular RNAs and become protective against infections. Instead, if they enter the cell, RNases can digest intracellular RNAs, becoming cytotoxic and having advantageous effects against malignant cells. Their biological activities have been investigated either in vitro, toward a number of different cancer cell lines, or in some cases in vivo to test their potential therapeutic use. However, immunogenicity or other undesired effects have sometimes been associated with their action. Nevertheless, the use of RNases in therapy remains an appealing strategy against some still incurable tumors, such as mesothelioma, melanoma, or pancreatic cancer. The RNase inhibitor (RI) present inside almost all cells is the most efficacious sentry to counteract the ribonucleolytic action against intracellular RNAs because it forms a tight, irreversible and enzymatically inactive complex with many monomeric RNases. Therefore, dimerization or multimerization could represent a useful strategy for RNases to exert a remarkable cytotoxic activity by evading the interaction with RI by steric hindrance. Indeed, the majority of the mentioned RNases can hetero-dimerize with antibody derivatives, or even homo-dimerize or multimerize, spontaneously or artificially. This can occur through weak interactions or upon introducing covalent bonds. Immuno-RNases, in particular, are fusion proteins representing promising drugs by combining high target specificity with easy delivery in tumors. The results concerning the biological features of many RNases reported in the literature are described and discussed in this review. Furthermore, the activities displayed by some RNases forming oligomeric complexes, the mechanisms driving toward these supramolecular structures, and the biological rebounds connected are analyzed. These aspects are offered with the perspective to suggest possible efficacious therapeutic applications for RNases oligomeric derivatives that could contemporarily lack, or strongly reduce, immunogenicity and other undesired side-effects.
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Affiliation(s)
- Giovanni Gotte
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Marta Menegazzi
- Biological Chemistry Section, Department of Neuroscience, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
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4
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Development of a capillary zone electrophoresis method to quantify E. coli l-asparaginase and its acidic variants. Talanta 2018; 182:83-91. [DOI: 10.1016/j.talanta.2018.01.048] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/14/2018] [Accepted: 01/17/2018] [Indexed: 11/18/2022]
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5
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Vergara A, Caterino M, Merlino A. Raman-markers of X-ray radiation damage of proteins. Int J Biol Macromol 2018; 111:1194-1205. [PMID: 29374529 DOI: 10.1016/j.ijbiomac.2018.01.135] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/10/2018] [Accepted: 01/19/2018] [Indexed: 12/25/2022]
Abstract
Despite their high relevance, the mechanisms of X-ray radiation damage on protein structure yet have to be completely established. Here, we used Raman microspectrophotometry to follow X-ray-induced chemical modifications on the structure of the model protein bovine pancreatic ribonuclease (RNase A). The combination of dose-dependent Raman spectra and ultrahigh resolution (eight structures solved using data collected between 0.85 and 1.17 Å resolution on the same single crystal) allowed direct observation of several radiation damage events, including covalent bond breakages and formation of radicals. Our results are relevant for analytical photodamage detection and provide implications for a detailed understanding of the mechanisms of photoproduct formation.
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Affiliation(s)
- Alessandro Vergara
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy; CEINGE Biotecnologie Avanzate Scarl, Via G. Salvatore, Napoli, Italy
| | - Marco Caterino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy
| | - Antonello Merlino
- Department of Chemical Sciences, University of Naples "Federico II", Via Cinthia, Naples I-80126, Italy.
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6
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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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7
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Fagagnini A, Montioli R, Caloiu A, Ribó M, Laurents DV, Gotte G. Extensive deamidation of RNase A inhibits its oligomerization through 3D domain swapping. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:76-87. [PMID: 27783927 DOI: 10.1016/j.bbapap.2016.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/03/2016] [Accepted: 10/20/2016] [Indexed: 12/27/2022]
Abstract
Bovine pancreatic ribonuclease A (RNase A) is the monomeric prototype of the so-called secretory 'pancreatic-type' RNase super-family. Like the naturally domain-swapped dimeric bovine seminal variant, BS-RNase, and its glycosylated RNase B isoform, RNase A forms N- and C-terminal 3D domain-swapped oligomers after lyophilization from acid solutions, or if subjected to thermal denaturation at high protein concentration. All mentioned RNases can undergo deamidation at Asn67, forming Asp or isoAsp derivatives that modify the protein net charge and consequently its enzymatic activity. In addition, deamidation slightly affects RNase B self-association through the 3D domain swapping (3D-DS) mechanism. We report here the influence of extensive deamidation on RNase A tendency to oligomerize through 3D-DS. In particular, deamidation of Asn67 alone slightly decreases the propensity of the protein to oligomerize, with the Asp derivative being less affected than the isoAsp one. Contrarily, the additional Asp and/or isoAsp conversion of residues other than N67 almost nullifies RNase A oligomerization capability. In addition, Gln deamidation, although less kinetically favorable, may affect RNase A self-association. Using 2D and 3D NMR we identified the Asn/Gln residues most prone to undergo deamidation. Together with CD spectroscopy, NMR also indicates that poly-deamidated RNase A generally maintains its native tertiary structure. Again, we investigated in silico the effect of the residues undergoing deamidation on RNase A dimers structures. Finally, the effect of deamidation on RNase A oligomerization is discussed in comparison with studies on deamidation-prone proteins involved in amyloid formation.
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Affiliation(s)
- Andrea Fagagnini
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Riccardo Montioli
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Andra Caloiu
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
| | - Marc Ribó
- Laboratori d'Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Universitat de Girona, 17071, y Institut d'Investigació Biomèdica de Girona Josep Trueta, (IdIBGi), Girona, Spain
| | - Douglas V Laurents
- Instituto de Quimica Fisica "Rocasolano" (C.S.I.C.), Serrano 119, E-28006 Madrid, Spain
| | - Giovanni Gotte
- Dipartimento di Neuroscienze, Biomedicina e del Movimento, Sezione di Chimica Biologica, Università degli Studi di Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
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8
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Chen B, Peng Y, Valeja SG, Xiu L, Alpert AJ, Ge Y. Online Hydrophobic Interaction Chromatography-Mass Spectrometry for Top-Down Proteomics. Anal Chem 2016; 88:1885-91. [PMID: 26729044 DOI: 10.1021/acs.analchem.5b04285] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent progress in top-down proteomics has led to a demand for mass spectrometry (MS)-compatible chromatography techniques to separate intact proteins using volatile mobile phases. Conventional hydrophobic interaction chromatography (HIC) provides high-resolution separation of proteins under nondenaturing conditions but requires high concentrations of nonvolatile salts. Herein, we introduce a series of more-hydrophobic HIC materials that can retain proteins using MS-compatible concentrations of ammonium acetate. The new HIC materials appear to function as a hybrid form of conventional HIC and reverse phase chromatography. The function of the salt seems to be preserving protein structure rather than promoting retention. Online HIC-MS is feasible for both qualitative and quantitative analysis. This is demonstrated with standard proteins and a complex cell lysate. The mass spectra of proteins from the online HIC-MS exhibit low charge-state distributions, consistent with those commonly observed in native MS. Furthermore, HIC-MS can chromatographically separate proteoforms differing by minor modifications. Hence, this new HIC-MS combination is promising for top-down proteomics.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Santosh G Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Lichen Xiu
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Andrew J Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States.,PolyLC, Inc., 9151 Rumsey Rd., Suite 180, Columbia, Maryland, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin, United States
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9
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Yu X, Sargaeva NP, Thompson CJ, Costello CE, Lin C. In-Source Decay Characterization of Isoaspartate and β-Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:101-109. [PMID: 26644780 PMCID: PMC4669973 DOI: 10.1016/j.ijms.2015.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Deamidation and the subsequent formation of isoaspartic acid (isoAsp) are common modifications of asparagine (Asn) residues in proteins. Differentiation of isoAsp and Asp residues is a challenging task owing to their similar chemical properties and identical molecular mass. Recent studies showed that they can be differentiated using electron capture dissociation (ECD) which generates diagnostic fragments c'+57 and z•-57 specific to the isoAsp residue. However, the ECD approach is only applicable towards multiply charged precursor ions and generally does not work for β-amino acids other than isoAsp. In this study, the potential of in-source decay (ISD) in characterization of isoAsp and other β-amino acids was explored. For isoAsp-containing peptides, ISD with a conventional hydrogen-donating matrix produced ECD-like, c'+57 and z•-57 diagnostic ions, even for singly charged precursor ions. For other β-amino acids, a hydrogen-accepting matrix was used to induce formation of site-specific a-14 ions from a synthetic β-analogue of substance P. These results indicated that ISD can be broadly applied for β-peptide characterization.
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Affiliation(s)
- Xiang Yu
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | | | - Catherine E. Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
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10
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Furman JL, Chiu M, Hunter MJ. Early engineering approaches to improve peptide developability and manufacturability. AAPS JOURNAL 2014; 17:111-20. [PMID: 25338742 DOI: 10.1208/s12248-014-9681-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/02/2014] [Indexed: 02/08/2023]
Abstract
Downstream success in Pharmaceutical Development requires thoughtful molecule design early in the lifetime of any potential therapeutic. Most therapeutic monoclonal antibodies are quite similar with respect to their developability properties. However, the properties of therapeutic peptides tend to be as diverse as the molecules themselves. Analysis of the primary sequence reveals sites of potential adverse posttranslational modifications including asparagine deamidation, aspartic acid isomerization, methionine, tryptophan, and cysteine oxidation and, potentially, chemical and proteolytic degradation liabilities that can impact the developability and manufacturability of a potential therapeutic peptide. Assessing these liabilities, both biophysically and functionally, early in a molecule's lifetime can drive a more effective path forward in the drug discovery process. In addition to these potential liabilities, more complex peptides that contain multiple disulfide bonds can pose particular challenges with respect to production and manufacturability. Approaches to reducing the disulfide bond complexity of these peptides are often explored with mixed success. Proteolytic degradation is a major contributor to decreased half-life and efficacy. Addressing this aspect of peptide stability early in the discovery process increases downstream success. We will address aspects of peptide sequence analysis, molecule complexity, developability analysis, and manufacturing routes that drive the decision making processes during peptide therapeutic development.
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Affiliation(s)
- Jennifer L Furman
- Janssen Research & Development, LLC, 3210 Merryfield Row, San Diego, California, 92121, USA
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11
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Ion-pair reversed-phase high performance liquid chromatography method for the quantification of isoaspartic acid in a monoclonal antibody. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 955-956:26-33. [PMID: 24631807 DOI: 10.1016/j.jchromb.2014.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/22/2014] [Accepted: 02/02/2014] [Indexed: 11/22/2022]
Abstract
Isomerization of aspartic acid residues is one of the major causes of chemical degradation during the shelf life of biological pharmaceuticals. Monoclonal antibody biopharmaceuticals are typically stored at mildly acidic pH conditions, which can lead to the isomerization reaction. The mechanism of this non-enzymatic chemical reaction has been studied in great detail. However, the identification and quantification of the isomerization sites in a given protein still remains a challenge. We developed an ion-pair reversed-phase HPLC method for the separation of an intact monoclonal antibody variant containing a single isoaspartic acid residue from its native counterpart. We identified and characterized the isomerization site using ion-pair reversed-phase HPLC mass spectrometry methods of the reduced and alkylated antibody and the enzymatically cleaved antibody. Lys-C followed by Asp-N digestion of the antibody was used for the identification of the isomerization site. Electron transfer dissociation (ETD) mass spectrometry was used to confirm the isomerization site at a DY motif at an aspartic acid residue in the CDR-H3 region of the antibody. Tyrosine at the C-terminus of an aspartic acid residue is typically not regarded as a hot spot for isomerization. Our findings suggest that it is not possible to predict isomerization sites in proteins with confidence and all aspartic acid residues located in the CDR regions of antibodies must be considered as potential isomerization site due to the solvent exposure or the flexibility of these regions of the molecule. Additionally, the effect of the pH on the isomerization rate was evaluated using the ion-pair reversed-phase HPLC method, showing that at a lower pH the isomerization rate is faster. Storage at 25°C for 6 months resulted in an increase of the amount of isoaspartic acid to 6.6% at pH 5.4, 6.0% at pH 5.8, and 5.6% at pH 6.2.
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12
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Characterization of deamidation at Asn138 in L-chain of recombinant humanized Fab expressed from Pichia pastoris. J Biochem 2013; 154:333-40. [DOI: 10.1093/jb/mvt061] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Jha SK, Deepalakshmi PD, Udgaonkar JB. Characterization of deamidation of barstar using electrospray ionization quadrupole time-of-flight mass spectrometry, which stabilizes an equilibrium unfolding intermediate. Protein Sci 2012; 21:633-46. [PMID: 22431291 DOI: 10.1002/pro.2047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 02/01/2012] [Accepted: 02/13/2012] [Indexed: 11/09/2022]
Abstract
Deamidation of asparaginyl residues is a common posttranslational modification in proteins and has been studied extensively because of its important biological effects, such as those on enzymatic activity, protein folding, and proteolytic degradation. However, characterization of the sites of deamidation of a protein has been a difficult analytical problem. In this study, mass spectrometry has been used as an analytical tool to characterize the deamidation of barstar, an RNAse inhibitor. Upon incubation of the protein at alkaline pH for 5 h, intact mass analysis of barstar, using electrospray ionization quadrupole time-of-flight mass spectrometry (ESI QToF MS), indicated an increase in the mass of +2 Da, suggesting possible deamidation of the protein. The sites of deamidation have been identified using the conventional bottom-up approach using a capillary liquid chromatography connected on line to an ESI QToF mass spectrometer and top down approach by direct infusion of the intact protein and fragmenting inside MS. These chemical modifications are shown to lead to stabilization of an unfolding intermediate, which can be observed in equilibrium unfolding studies.
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Affiliation(s)
- Santosh Kumar Jha
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore 560065, India
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14
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Zhang J, Katta V. Identification of Asp isomerization in proteins by ¹⁸O labeling and tandem mass spectrometry. Methods Mol Biol 2012; 899:365-377. [PMID: 22735965 DOI: 10.1007/978-1-61779-921-1_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Isomerization of aspartic acid (Asp) to isoaspartic acid (isoAsp) via succinimide intermediate is a common route of degradation for proteins that can affect their structural integrity. As Asp/isoAsp is isobaric in mass, it is difficult to identify the site of modification by LC-MS/MS peptide mapping. Here, we describe an approach to label the Asp residue involved in isomerization at the protein level by hydrolyzing the succinimide intermediate in H₂¹⁸O. Tryptic digestion of this labeled protein will result in peptides containing the site of isomerization being 2 Da heavier than the ¹⁶O-containing counterparts, due to ¹⁸O incorporation during the hydrolysis process. Comparison of tandem mass spectra of isomerized peptides with and without ¹⁸O incorporation allows easy identification of the Asp residue involved. This method proved to be especially useful in identifying the sites when isomerization occurs in Asp-Asp motifs.
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Affiliation(s)
- Jennifer Zhang
- Protein Analytical Chemistry, Genentech Inc, South San Francisco, CA, USA.
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15
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Sargaeva NP, Lin C, O’Connor PB. Differentiating N-terminal aspartic and isoaspartic acid residues in peptides. Anal Chem 2011; 83:6675-82. [PMID: 21736361 PMCID: PMC3165085 DOI: 10.1021/ac201223d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Formation of isoaspartic acid (isoAsp) is a common modification of aspartic acid (Asp) or asparagine (Asn) residue in proteins. Differentiation of isoAsp and Asp residues is a challenging task owing to their similar properties and identical molecular mass. It was recently shown that they can be differentiated using ion-electron or ion-ion interaction fragmentation methods (ExD) because these methods provide diagnostic fragments c + 57 and z(•) - 57 specific to the isoAsp residue. To date, however, the presence of such fragments has not been explored on peptides with an N-terminal isoAsp residue. To address this question, several N-terminal isoAsp-containing peptides were analyzed using ExD methods alone or combined with chromatography. A diagnostic fragment [M + 2H - 74](+•) was observed for the doubly charged precursor ions with N-terminal isoAsp residues. For some peptides, identification of the N-terminal isoAsp residue was challenging because of the low diagnostic ion peak intensity and the presence of interfering peaks. Supplemental activation was used to improve diagnostic ion detection. Further, N-terminal acetylation was offered as a means to overcome the interference problem by shifting the diagnostic fragment peak to [M + 2H - 116](+•).
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Affiliation(s)
- Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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16
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Chen X, Tolley HD, Lee ML. Monolithic capillary columns synthesized from a single phosphate-containing dimethacrylate monomer for cation-exchange chromatography of peptides and proteins. J Chromatogr A 2011; 1218:4322-31. [DOI: 10.1016/j.chroma.2011.04.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/22/2011] [Accepted: 04/24/2011] [Indexed: 10/18/2022]
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17
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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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18
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Kameoka D, Ueda T, Imoto T. Effect of the Conformational Stability of the CH2 Domain on the Aggregation and Peptide Cleavage of a Humanized IgG. Appl Biochem Biotechnol 2011; 164:642-54. [DOI: 10.1007/s12010-011-9164-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Accepted: 01/10/2011] [Indexed: 12/01/2022]
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19
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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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20
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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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21
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Zhang J, Yip H, Katta V. Identification of isomerization and racemization of aspartate in the Asp-Asp motifs of a therapeutic protein. Anal Biochem 2010; 410:234-43. [PMID: 21130067 DOI: 10.1016/j.ab.2010.11.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Revised: 11/22/2010] [Accepted: 11/26/2010] [Indexed: 11/18/2022]
Abstract
A thermally stressed Fab molecule showed a significant increase of basic variants in imaged capillary isoelectric focusing (iCIEF) analysis. Mass analyses of the reduced protein found an increase in -18Da species from both light chain and heavy chain. A tryptic peptide map identified two isoAsp-containing peptides, both containing Asp-Asp motifs and located in complementarity-determining regions (CDRs) of light chains and heavy chains, respectively. The approaches of hydrolyzing succinimide in H(2)(18)O followed by tryptic digestion were used to label and identify the sites of isomerization. This method enabled identification of the isomerization site by comparing the MS/MS spectra of isomerized peptides with and without (18)O incorporation. The light chain peptide L2 VTITCITSTDID(12)DDMNWYQQKPGK underwent simultaneous isomerization and recemization at residue Asp-12 after thermal stress as evidenced by the coinjection of synthetic peptide L2 with l-Asp-12, l-isoAsp-12, d-Asp-12, and d-isoAsp-12, respectively. A thermal stress study of the synthetic peptide (l-)L2 showed that the isomerization and racemization did not occur, indicating that the Asp degradation in this Asp-Asp motif is more related to the protein conformation than the primary sequence. Another isomerization site was identified as Asp-24 in the heavy chain peptide H5 QAPGQGLEWMGWINTYTGETTYAD(24)DFK. No other isomerizations were detected in CDR peptides containing either Asp-Ser or Asp-Thr motifs.
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Affiliation(s)
- Jennifer Zhang
- Protein Analytical Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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22
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Abstract
Following isolation and purification, it is often necessary to store proteins and peptides for extended periods of time before performing detailed biophysical, enzymatic, and structural proteomics. Therefore, it is essential that the pure target protein maintain its original biological (or functional) behavior over an extended period of storage which may range from weeks to years. Protein pharmaceuticals must remain viable following extensive shipping and storage, and they must remain devoid of all possible inactivation processes. The shelf life of a protein depends on both the intrinsic nature of the protein and the storage conditions. Proteins (especially enzymes) must be stored at an appropriate temperature and pH range and frequently in the presence of concentrated (approximately 1 M) glycerol, sucrose, or a similar substance, for the proteins to retain activity and prevent aggregation. This article discusses the major causes of protein inactivation and describes a range of measures that can be adopted to maintain the stability and solubility of proteins.
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23
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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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24
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Vlasak J, Bussat MC, Wang S, Wagner-Rousset E, Schaefer M, Klinguer-Hamour C, Kirchmeier M, Corvaïa N, Ionescu R, Beck A. Identification and characterization of asparagine deamidation in the light chain CDR1 of a humanized IgG1 antibody. Anal Biochem 2009; 392:145-54. [DOI: 10.1016/j.ab.2009.05.043] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 05/28/2009] [Accepted: 05/28/2009] [Indexed: 10/20/2022]
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25
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López-Alonso JP, Diez-García F, Font J, Ribó M, Vilanova M, Scholtz JM, González C, Vottariello F, Gotte G, Libonati M, Laurents DV. Carbodiimide EDC Induces Cross-Links That Stabilize RNase A C-Dimer against Dissociation: EDC Adducts Can Affect Protein Net Charge, Conformation, and Activity. Bioconjug Chem 2009; 20:1459-73. [DOI: 10.1021/bc9001486] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Jorge P. López-Alonso
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Fernando Diez-García
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Josep Font
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Marc Ribó
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Maria Vilanova
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - J. Martin Scholtz
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Carlos González
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Francesca Vottariello
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Giovanni Gotte
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Massimo Libonati
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
| | - Douglas V. Laurents
- Instituto de Química Física “Rocasolano” (C.S.I.C.), Serrano 119, E-28006, Madrid, Spain, Dipartimento di Scienze Morfologico-Biomediche, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134, Verona, Italy, Laboratori d’Enginyeria de Proteïnes, Departament de Biología, Facultad de Ciències, Universitat de Girona, Campus Montilivi, 17071 Girona, Spain, and Department of Medical Biochemistry, Texas A&M University School of Medicine, College
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26
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Valliere-Douglass J, Wallace A, Balland A. Separation of populations of antibody variants by fine tuning of hydrophobic-interaction chromatography operating conditions. J Chromatogr A 2008; 1214:81-9. [DOI: 10.1016/j.chroma.2008.10.078] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2008] [Revised: 10/09/2008] [Accepted: 10/13/2008] [Indexed: 10/21/2022]
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27
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Development of a comprehensive multidimensional liquid chromatography system with tandem mass spectrometry detection for detailed characterization of recombinant proteins. J Chromatogr A 2008; 1189:183-95. [DOI: 10.1016/j.chroma.2007.11.031] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/12/2007] [Accepted: 11/09/2007] [Indexed: 11/21/2022]
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28
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Ferreri C, Chatgilialoglu C, Torreggiani A, Salzano AM, Renzone G, Scaloni A. The Reductive Desulfurization of Met and Cys Residues in Bovine RNase A Is Associated with trans Lipids Formation in a Mimetic Model of Biological Membranes. J Proteome Res 2008; 7:2007-15. [DOI: 10.1021/pr700691x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Carla Ferreri
- ISOF, Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy, and Proteomics & Mass Spectrometry Laboratory, ISPAAM, Consiglio Nazionale delle Ricerche, via Argine 1085, 80147 Napoli, Italy
| | - Chryssostomos Chatgilialoglu
- ISOF, Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy, and Proteomics & Mass Spectrometry Laboratory, ISPAAM, Consiglio Nazionale delle Ricerche, via Argine 1085, 80147 Napoli, Italy
| | - Armida Torreggiani
- ISOF, Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy, and Proteomics & Mass Spectrometry Laboratory, ISPAAM, Consiglio Nazionale delle Ricerche, via Argine 1085, 80147 Napoli, Italy
| | - Anna Maria Salzano
- ISOF, Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy, and Proteomics & Mass Spectrometry Laboratory, ISPAAM, Consiglio Nazionale delle Ricerche, via Argine 1085, 80147 Napoli, Italy
| | - Giovanni Renzone
- ISOF, Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy, and Proteomics & Mass Spectrometry Laboratory, ISPAAM, Consiglio Nazionale delle Ricerche, via Argine 1085, 80147 Napoli, Italy
| | - Andrea Scaloni
- ISOF, Consiglio Nazionale delle Ricerche, via P. Gobetti 101, 40129 Bologna, Italy, and Proteomics & Mass Spectrometry Laboratory, ISPAAM, Consiglio Nazionale delle Ricerche, via Argine 1085, 80147 Napoli, Italy
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29
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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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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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DeLuna A, Quezada H, Gómez-Puyou A, González A. Asparaginyl deamidation in two glutamate dehydrogenase isoenzymes from Saccharomyces cerevisiae. Biochem Biophys Res Commun 2005; 328:1083-90. [PMID: 15707988 DOI: 10.1016/j.bbrc.2005.01.057] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Indexed: 11/21/2022]
Abstract
The non-enzymatic deamidation of asparaginyl residues is a major source of spontaneous damage of several proteins under physiological conditions. In many cases, deamidation and isoaspartyl formation alters the biological activity or stability of the native polypeptide. Rates of deamidation of particular residues depend on many factors including protein structure and solvent exposure. Here, we investigated the spontaneous deamidation of the two NADP-glutamate dehydrogenase isoenzymes from Saccharomyces cerevisiae, which have different kinetic properties and are differentially expressed in this yeast. Our results show that Asn54, present in Gdh3p but missing in the GDH1-encoded homologue, is readily deamidated in vitro under alkaline conditions. Relative to the native enzyme, deamidated Gdh3p shows reduced protein stability. The different deamidation rates of the two isoenzymes could explain to some extent, the relative in vivo instability of the allosteric Gdh3p enzyme, compared to that of Gdh1p. It is thus possible that spontaneous asparaginyl modification could play a role in the metabolic regulation of ammonium assimilation and glutamate biosynthesis.
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Affiliation(s)
- Alexander DeLuna
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Apartado Postal 70-242, 04510 México DF, Mexico.
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32
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Volkin DB, Sanyal G, Burke CJ, Middaugh CR. Preformulation studies as an essential guide to formulation development and manufacture of protein pharmaceuticals. PHARMACEUTICAL BIOTECHNOLOGY 2004; 14:1-46. [PMID: 12189723 DOI: 10.1007/978-1-4615-0549-5_1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- David B Volkin
- Department of Vaccine Pharmaceutical Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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33
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Gotte G, Libonati M, Laurents DV. Glycosylation and specific deamidation of ribonuclease B affect the formation of three-dimensional domain-swapped oligomers. J Biol Chem 2003; 278:46241-51. [PMID: 12966091 DOI: 10.1074/jbc.m308470200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
RNase A oligomerizes via the three-dimensional domain-swapping mechanism to form a variety of oligomers, including two dimers. One, called the N-dimer, forms by swapping of the N termini of the protein; the other, called the C-dimer, forms by swapping of the C termini. RNase B is identical in protein sequence and conformation to RNase A, but its Asn34 bears an oligosaccharide chain that might affect oligomerization. The ability of RNase B to oligomerize under two sets of conditions has been examined. The amount of oligomers formed via lyophilization was somewhat lower for RNase B than RNase A, and RNase B oligomerized more rapidly in 40% ethanol solution at high temperature than RNase A. The ratio of the N-dimer to C-dimer formed increased with the size of the carbohydrate chain under both sets of conditions. These results suggest that the oligosaccharide chain either favors productive collisions or stabilizes the oligomers, especially the N-dimer. Endoglycosidase H treatment of RNase B partially restored RNase A-like oligomerization. Derivatives of RNase A conjugated at the amine groups to polyethylene glycol chains showed a greatly reduced capacity for oligomerization, suggesting that oligomerization can be impeded sterically. Commercial preparations of RNase B eluted as two main peaks by cation exchange chromatography. Using chromatography, mass spectroscopy, and two-dimensional NMR, the major peak was identified as RNase B selectively deamidated at Asn67. This deamidated protein showed a >4 degrees C drop in thermal stability, disruption of the native structure of residues 67-69, and a decreased ability to oligomerize compared with unmodified RNase B.
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Affiliation(s)
- Giovanni Gotte
- Dipartimento di Scienze Neurologiche e della Visione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Strada Le Grazie 8, I-37134 Verona, Italy
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34
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Jozic D, Kaiser JT, Huber R, Bode W, Maskos K. X-ray structure of isoaspartyl dipeptidase from E.coli: a dinuclear zinc peptidase evolved from amidohydrolases. J Mol Biol 2003; 332:243-56. [PMID: 12946361 DOI: 10.1016/s0022-2836(03)00845-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
L-aspartyl and L-asparaginyl residues in proteins spontaneously undergo intra-residue rearrangements forming isoaspartyl/beta-aspartyl residues linked through their side-chain beta-carboxyl group with the following amino acid. In order to avoid accumulation of isoaspartyl dipeptides left over from protein degradation, some bacteria have developed specialized isoaspartyl/beta-aspartyl zinc dipeptidases sequentially unrelated to other peptidases, which also poorly degrade alpha-aspartyl dipeptides. We have expressed and crystallized the 390 amino acid residue isoaspartyl dipeptidase (IadA) from E.coli, and have determined its crystal structure in the absence and presence of the phosphinic inhibitor Asp-Psi[PO(2)CH(2)]-LeuOH. This structure reveals an octameric particle of 422 symmetry, with each polypeptide chain organized in a (alphabeta)(8) TIM-like barrel catalytic domain attached to a U-shaped beta-sandwich domain. At the C termini of the beta-strands of the beta-barrel, the two catalytic zinc ions are surrounded by four His, a bridging carbamylated Lys and an Asp residue, which seems to act as a proton shuttle. A large beta-hairpin loop protruding from the (alphabeta)(8) barrel is disordered in the free peptidase, but forms a flap that stoppers the barrel entrance to the active center upon binding of the dipeptide mimic. This isoaspartyl dipeptidase shows strong topological homology with the alpha-subunit of the binickel-containing ureases, the dinuclear zinc dihydroorotases, hydantoinases and phosphotriesterases, and the mononuclear adenosine and cytosine deaminases, which all are catalyzing hydrolytic reactions at carbon or phosphorous centers. Thus, nature has adapted an existing fold with catalytic tools suitable for hydrolysis of amide bonds to the binding requirements of a peptidase.
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Affiliation(s)
- Daniela Jozic
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany
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35
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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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36
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Cloos PAC, Christgau S. Non-enzymatic covalent modifications of proteins: mechanisms, physiological consequences and clinical applications. Matrix Biol 2002; 21:39-52. [PMID: 11827791 DOI: 10.1016/s0945-053x(01)00188-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Given the complexity of the biosynthetic machinery and the delicate chemical composition of proteins, it is remarkable that cells manage to produce and maintain normally functioning proteins under most conditions. However, it is now well known that proteins are susceptible to various non-enzymatic covalent modifications (NECM) under physiological conditions. Such modifications can be of no or little importance to the protein or they can be absolutely detrimental. Often NECM are difficult to study due to the complex and technically demanding methods required to identify many of these modifications. Thus, the role of NECM has not yet been adequately resolved but recent research has allowed a better understanding of such modifications. The present review outlines the various forms of NECM that involve covalent modifications of proteins, and discusses their relevance, biological impact and potential applications in the study of protein turnover and diagnosis of disease.
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Affiliation(s)
- Paul A C Cloos
- Nordic Bioscience A/S, Herlev Hovedgade 207, DK-2730 Herlev, Denmark.
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37
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Chatani E, Hayashi R. Functional and structural roles of constituent amino acid residues of bovine pancreatic ribonuclease A. J Biosci Bioeng 2001. [DOI: 10.1016/s1389-1723(01)80208-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Capasso S, Di Cerbo P. Kinetic and thermodynamic control of the relative yield of the deamidation of asparagine and isomerization of aspartic acid residues. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 2000; 56:382-7. [PMID: 11152297 DOI: 10.1034/j.1399-3011.2000.00778.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Selective deamidation of Asn67 of RNase A to beta-Asp67 and Asp67 residues at neutral pH initially produces greater amounts of the beta-Asp derivative. As the reaction proceeds the relative concentration of [Asp67]-RNase A increases and, at equilibrium, becomes predominant. Such a discrepancy between the kinetic and thermodynamic control on reaction products is discussed in light of information from X-ray three-dimensional analysis and the lower thermodynamic stability of the beta-Asp derivative relative to the parent enzyme.
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Affiliation(s)
- S Capasso
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy.
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39
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Orrù S, Vitagliano L, Esposito L, Mazzarella L, Marino G, Ruoppolo M. Effect of deamidation on folding of ribonuclease A. Protein Sci 2000; 9:2577-82. [PMID: 11206080 PMCID: PMC2144509 DOI: 10.1110/ps.9.12.2577] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The folding of ribonuclease A (RNase A) has been extensively studied by characterizing the disulfide containing intermediates using different experimental conditions and analytical techniques. So far, some aspects still remain unclear such as the role of the loop 65-72 in the folding pathway. We have studied the oxidative folding of a RNase A derivative containing at position 67 the substitution Asn --> isoAsp where the local structure of the loop 65-72 has been modified keeping intact the C65-C72 disulfide bond. By comparing the folding behavior of this mutant to that of the wild-type protein, we found that the deamidation significantly decreases the folding rate and alters the folding pathway of RNase A. Results presented here shed light on the role of the 65-72 region in the folding process of RNase A and also clarifies the effect of the deamidation on the folding/unfolding processes. On a more general ground, this study represents the first characterization of the intermediates produced along the folding of a deamidated protein.
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Affiliation(s)
- S Orrù
- Dipartimento di Chimica, Università degli Studi di Salerno, Italy
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40
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Skinner MM, Puvathingal JM, Walter RL, Friedman AM. Crystal structure of protein isoaspartyl methyltransferase: a catalyst for protein repair. Structure 2000; 8:1189-201. [PMID: 11080641 DOI: 10.1016/s0969-2126(00)00522-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation. RESULTS We have determined the first structure of a PIMT from crystals of the T. maritima enzyme complexed to S-adenosyl-L-homocysteine (AdoHcy) and refined it to 1.8 A resolution. Although PIMT forms one structural unit, the protein can be divided functionally into three subdomains. The central subdomain closely resembles other S-adenosyl-L-methionine-dependent methyltransferases but bears a striking alteration of topological connectivity, which is not shared by any other member of this family. Rather than arranged as a mixed beta sheet with topology 6 upward arrow7 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow, the central sheet of PIMT is reorganized to 7 upward arrow6 downward arrow5 upward arrow4 upward arrow1 upward arrow2 upward arrow3 upward arrow. AdoHcy is largely buried between the N-terminal and central subdomains by a conserved and largely hydrophobic loop on one rim of the binding cleft, and a conserved Ser/Thr-rich beta strand on the other. The Ser/Thr-rich strand may provide hydrogen bonds for specific interactions with isoaspartyl substrates. The side chain of Ile-206, a conserved residue, crosses the cleft, restricting access to the donor methyl group to a deep well, the putative isoaspartyl methyl acceptor site. CONCLUSIONS The structure of PIMT reveals a unique modification of the methyltransferase fold along with a site for specific recognition of isoaspartyl substrates. The sequence conservation among PIMTs suggests that the current structure should prove a reliable model for understanding the repair of isoaspartyl damage in all organisms.
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Affiliation(s)
- M M Skinner
- Department of Biological Sciences, Purdue University , West Lafayette, IN 47907, USA
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41
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Bai L, Burman S, Gledhill L. Development of ion exchange chromatography methods for monoclonal antibodies. J Pharm Biomed Anal 2000; 22:605-11. [PMID: 10766377 DOI: 10.1016/s0731-7085(00)00236-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- L Bai
- Analytical Sciences Department, SmithKline Beecham Pharmaceuticals, King of Prussia, PA 19406, USA.
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42
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Esposito L, Vitagliano L, Sica F, Sorrentino G, Zagari A, Mazzarella L. The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. J Mol Biol 2000; 297:713-32. [PMID: 10731423 DOI: 10.1006/jmbi.2000.3597] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.101 for all observed reflections in the resolution range 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 A resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C(alpha)-H(alpha).O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation.
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Affiliation(s)
- L Esposito
- Centro di Studio di Biocristallografia, CNR and Dipartimento di Chimica Università di Napoli "Federico II", Via Mezzocannone 4 I-80134, Napoli, Italy
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43
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Abstract
The effect of lysine residues on the deamidation reaction of the asparagine side chain has been studied on the peptide and on its lysine-acetylated derivative in a wide range of pH values. The amino acid sequence of these peptides is similar to the local sequence flanking the labile Asn-67 in RNAse A. The experimental data show that Lys influences both the deamidation rate and the relative yield of the two reaction products, i.e., the aspartic acid and beta-aspartic acid containing peptide. These effects are pH dependent and can be rationalized based on the mechanism previously proposed for the deamidation reaction via succinimide derivative.
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Affiliation(s)
- S Capasso
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Italy.
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44
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Sorrentino S, Barone R, Bucci E, Gotte G, Russo N, Libonati M, D'Alessio G. The two dimeric forms of RNase A. FEBS Lett 2000; 466:35-9. [PMID: 10648807 DOI: 10.1016/s0014-5793(99)01742-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In 1965 Fruchter and Crestfield (J. Biol. Chem. 240, 2868-3874) observed that dimeric RNase A prepared by lyophilization from acetic acid could be separated into two forms. Surprisingly, no other structural or functional differences could be detected between the two forms. In 1998 a structure for dimeric RNase A was determined by X-ray crystallography by Liu et al. (Proc. Natl. Acad. Sci. USA 95, 3437-3442). We found that the two forms of dimeric RNase A have indeed different structural and functional properties, and suggest that the dimer whose structure was investigated by Liu and coworkers may be identified with the lesser form of dimeric RNase A.
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Affiliation(s)
- S Sorrentino
- Dipartimento di Chimica Organica e Biologica, Università di Napoli Federico II, Via Mezzocannone 16, 80134, Naples, Italy
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45
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Capasso S, Salvadori S. Effect of the three-dimensional structure on the deamidation reaction of ribonuclease A. THE JOURNAL OF PEPTIDE RESEARCH : OFFICIAL JOURNAL OF THE AMERICAN PEPTIDE SOCIETY 1999; 54:377-82. [PMID: 10563503 DOI: 10.1034/j.1399-3011.1999.00111.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Kinetic data on the deamidation reaction of Asn67 in RNase A and of Asn3 in the two peptides Ac-Cys-Lys-Asn-Gly-Gln-Thr-Asn-Cys-NH2 and Ac-Cys(Me)-Lys-Asn-Gly-Gln-Thr-Asn-Cys(Me)-NH2, whose sequences are similar to that of the deamidation site in the enzyme, have been determined in a wide range of pH and buffer concentrations. The values of the observed rate constant (k) for the enzyme are markedly lower than those for the peptides. However, the k dependence on pH and buffers is similar for all three substrates, indicating a similar reaction mechanism. The lower k-values for the enzyme have been quantitatively related to the thermal stability and the three-dimensional structure of the enzyme.
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Affiliation(s)
- S Capasso
- Dipatimento di Scienze Ambientali, Seconda Università di Napoli, Caserta, Centro di Studio di Biocristallografia, CNR, Italy.
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46
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Gotte G, Bertoldi M, Libonati M. Structural versatility of bovine ribonuclease A. Distinct conformers of trimeric and tetrameric aggregates of the enzyme. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 265:680-7. [PMID: 10504400 DOI: 10.1046/j.1432-1327.1999.00761.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Lyophilization of bovine ribonuclease A (RNase A; Sigma, type XII-A) from 40% acetic acid solutions leads to the formation of approximately 14 aggregated species that can be separated by ion-exchange chromatography. Several aggregates were identified, including two variously deamidated dimeric subspecies, two distinct trimeric and two distinct tetrameric RNase A conformers, besides the two forms of dimer characterized previously [Gotte, G. & Libonati, M. (1998) Two different forms of aggregated dimers of ribonuclease A. Biochim. Biophys. Acta 1386, 106-112]. We also have possible evidence for the existence of two forms of pentameric RNase A. The two forms of trimers and tetramers are characterized by: (a) slightly different gel filtration patterns; (b) different retention times in ion-exchange chromatography; and (c) different mobilities in cathodic gel electrophoresis under nondenaturing conditions. Therefore, they appear to have distinct structural organizations responsible for a different availability of their positively charged amino acid residues. All RNase A oligomers, in particular the two distinct trimeric and tetrameric conformers, degrade poly(A).poly(U), viral double-stranded RNA and polyadenylate with a catalytic efficiency that is in general higher for the more basic species. On the contrary, the activity of the RNase A oligomers, from dimer to pentamer, on yeast RNA and poly(C) (Kunitz assay) is lower than that of monomeric RNase A.
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Affiliation(s)
- G Gotte
- Dipartimento di Scienze Neurologiche e della Visione, Sezione di Chimica Biologica, Facoltà di Medicina e Chirurgia, Università di Verona, Italy
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47
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Cox GA, Johnson RB, Cook JA, Wakulchik M, Johnson MG, Villarreal EC, Wang QM. Identification and characterization of human rhinovirus-14 3C protease deamidation isoform. J Biol Chem 1999; 274:13211-6. [PMID: 10224078 DOI: 10.1074/jbc.274.19.13211] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A purified recombinant human rhinovirus-14 3C protease preparation contained only approximately 50% active enzyme as titrated using specifically designed irreversible 3C protease inhibitors. Analysis of the purified 3C protein by isoelectric focusing showed differently charged 3C isoforms that had isoelectric points (pI) of 8.3 (55%) and 9.0 (45%), with the latter one being consistent with the predicted pI of the human rhinovirus-14 3C protein. Further analysis indicated that the pI 8.3 protein was the deamidated form of 3C, and it displayed approximately 10-fold reduced cleavage activity relative to the original 3C protease sample. Peptide mapping followed by sequence analysis revealed that a single asparagine, Asn-164, was deamidated to aspartic acid in the pI 8.3 isoform. Converting Asn-164 to Asp by site-directed mutagenesis resulted in a mutated 3C protease with extremely low activity, as seen with the pI 8.3 isoform, indicating a role of Asn-164 in substrate recognition and binding. In addition, the deamidated 3C protease was found to be present in vivo, and its abundance was related to the viral replication cycle. Moreover, mutant virus carrying Asp-164 showed reduced viability in infected cells. Taken together, our data suggest that 3C protein deamidation plays a role in the regulation of its enzymatic activity.
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Affiliation(s)
- G A Cox
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
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48
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Niewmierzycka A, Clarke S. Do damaged proteins accumulate in Caenorhabditis elegans L-isoaspartate methyltransferase (pcm-1) deletion mutants? Arch Biochem Biophys 1999; 364:209-18. [PMID: 10190976 DOI: 10.1006/abbi.1999.1114] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The protein l-isoaspartate (d-aspartate) O-methyltransferase (E.C. 2. 1.1.77) can initiate the conversion of isomerized and racemized aspartyl residues to their normal l-aspartyl forms and has therefore been hypothesized to function as a repair enzyme, responsible for helping to limit the accumulation of damaged proteins in aging organisms. In this study, the effect of a disruption in the pcm-1 gene encoding the l-isoaspartyl methyltransferase was investigated in the nematode Caenorhabditis elegans. It was found that damaged proteins recognized by this enzyme accumulated to significant levels during long-term incubation of both pcm-1+ and pcm-1- nematodes in a specialized larval stage called the dauer. The l-isoaspartyl methyltransferase-deficient mutants accumulated about twice the level of damaged proteins as the control nematodes during dauer aging. The mutants also accumulated higher levels of damage when both strains were incubated at 30 degrees C for up to 3 days. However, when nonviable nematodes were removed in a Percoll separation, similar levels of damage were measured between the two strains following both dauer aging and 30 degrees C incubation. Both strains were able to effectively eliminate damaged proteins recognized by the methyltransferase after recovery from dauer. Characterization of the methyl-accepting polypeptide substrates which accumulate in aged dauers revealed that although substrates of all molecular weights are present, the majority of substrates are peptides not precipitated by acetone. These results suggest that protein degradation, rather than repair, may be the major mechanism by which C. elegans eliminates damaged proteins containing l-isoaspartyl residues.
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Affiliation(s)
- A Niewmierzycka
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, California, 90095-1569, USA
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49
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Abstract
The deamidation reactions of asparagine residues in alpha-helical and beta-turn secondary structural environments of peptides and proteins are reviewed. Both kinds of secondary structure tend to stabilize asparagine residues against deamidation, although the effects are not large. The effect of beta-sheet structures on asparagine stability is unclear, although simple considerations suggest a stabilization in this environment also.
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Affiliation(s)
- M Xie
- Department of Pharmaceutical Chemistry, Simons Laboratories of the Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047, USA
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50
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Weitzhandler M, Farnan D, Horvath J, Rohrer JS, Slingsby RW, Avdalovic N, Pohl C. Protein variant separations by cation-exchange chromatography on tentacle-type polymeric stationary phases. J Chromatogr A 1998; 828:365-72. [PMID: 9916317 DOI: 10.1016/s0021-9673(98)00521-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We developed a set of prototype cation-exchange column packings that are based on a hydrophilic coated, pellicular polymeric support with a grafted tentacular surface chemistry that is highly suited to resolving closely related protein variants. These column packings (1) afford minimal band spreading in conjunction with extremely high selectivity, (2) exhibit a very hydrophilic character and (3) have moderate loading capacity. Cytochrome c variants (bovine, horse, rabbit) were baseline-separated, as was native ribonuclease A and its two deamidation products, the Asp67 and isoAsp67 forms. Humanized monoclonal antibody variants differing in the presence of lysine at the C terminus of the heavy chains were baseline-resolved. Finally, the separation of hemoglobin variants found in a sample containing elevated levels of glycated hemoglobin was also demonstrated.
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