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Sadiki A, Liu S, Vaidya SR, Kercher EM, Lang RT, McIsaac J, Spring BQ, Auclair JR, Zhou ZS. Site-Specific Conjugation of Native Antibody: Transglutaminase-Mediated Modification of a Conserved Glutamine While Maintaining the Primary Sequence and Core Fc Glycan via Trimming with an Endoglycosidase. Bioconjug Chem 2024; 35:465-471. [PMID: 38499390 PMCID: PMC11036358 DOI: 10.1021/acs.bioconjchem.4c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 03/20/2024]
Abstract
A versatile chemo-enzymatic tool to site-specifically modify native (nonengineered) antibodies is using transglutaminase (TGase, E.C. 2.3.2.13). With various amines as cosubstrates, this enzyme converts the unsubstituted side chain amide of glutamine (Gln or Q) in peptides and proteins into substituted amides (i.e., conjugates). A pleasant surprise is that only a single conserved glutamine (Gln295) in the Fc region of IgG is modified by microbial TGase (mTGase, EC 2.3.2.13), thereby providing a highly specific and generally applicable conjugation method. However, prior to the transamidation (access to the glutamine residue by mTGase), the steric hindrance from the nearby conserved N-glycan (Asn297 in IgG1) must be reduced. In previous approaches, amidase (PNGase F, EC 3.5.1.52) was used to completely remove the N-glycan. However, PNGase F also converts a net neutral asparagine (Asn297) to a negatively charged aspartic acid (Asp297). This charge alteration may markedly change the structure, function, and immunogenicity of an IgG antibody. In contrast, in our new method presented herein, the N-glycan is trimmed by an endoglycosidase (EndoS2, EC 3.2.1.96), hence retaining both the core N-acetylglucosamine (GlcNAc) moiety and the neutral asparaginyl amide. The trimmed glycan also reduces or abolishes Fc receptor-mediated functions, which results in better imaging agents by decreasing nonspecific binding to other cells (e.g., immune cells). Moreover, the remaining core glycan allows further derivatization such as glycan remodeling and dual conjugation. Practical and robust, our method generates conjugates in near quantitative yields, and both enzymes are commercially available.
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Affiliation(s)
- Amissi Sadiki
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shanshan Liu
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Shefali R. Vaidya
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Eric M. Kercher
- Translational
Biophotonics Cluster, Department of Physics, Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ryan T. Lang
- Translational
Biophotonics Cluster, Department of Physics, Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - James McIsaac
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Bryan Q. Spring
- Translational
Biophotonics Cluster, Department of Physics, Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States
| | - Jared R. Auclair
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
| | - Zhaohui Sunny Zhou
- Department
of Chemistry and Chemical Biology, Barnett Institute of Chemical and
Biological Analysis, Northeastern University, Boston, Massachusetts 02115, United States
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2
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Yang ML, Lam TT, Kanyo J, Kang I, Zhou ZS, Clarke SG, Mamula MJ. Natural isoaspartyl protein modification of ZAP70 alters T cell responses in lupus. Autoimmunity 2023; 56:2282945. [PMID: 37994408 PMCID: PMC10897934 DOI: 10.1080/08916934.2023.2282945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/08/2023] [Indexed: 11/24/2023]
Abstract
Protein posttranslational modifications (PTMs) arise in a number of normal cellular biological pathways and in response to pathology caused by inflammation and/or infection. Indeed, a number of PTMs have been identified and linked to specific autoimmune responses and metabolic pathways. One particular PTM, termed isoaspartyl (isoAsp or isoD) modification, is among the most common spontaneous PTM occurring at physiological pH and temperature. Herein, we demonstrate that isoAsp modifications arise within the ZAP70 protein tyrosine kinase upon T-cell antigen receptor (TCR) engagement. The enzyme protein L-isoaspartate O-methyltransferase (PCMT1, or PIMT, EC 2.1.1.77) evolved to repair isoaspartyl modifications in cells. In this regard, we observe that increased levels of isoAsp modification that arise under oxidative stress are correlated with reduced PIMT activity in patients with systemic lupus erythematosus (SLE). PIMT deficiency leads to T cell hyper-proliferation and hyper-phosphorylation through ZAP70 signaling. We demonstrate that inducing the overexpression of PIMT can correct the hyper-responsive phenotype in lupus T cells. Our studies reveal a phenotypic role of isoAsp modification and phosphorylation of ZAP70 in lupus T cell autoimmunity and provide a potential therapeutic target through the repair of isoAsp modification.
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Affiliation(s)
- Mei-Ling Yang
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - TuKiet T. Lam
- Keck MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
- Department of Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, WM Keck Foundation Biotechnology Resource Laboratory, New Haven, CT, USA
| | - Insoo Kang
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Steven G. Clarke
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA, Los Angeles, CA, USA
| | - Mark J. Mamula
- Section of Rheumatology, Allergy and Immunology, Department of Internal Medicine, Yale University, New Haven, CT, USA
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Zhu Y, Wang SS, Zhou ZS, Ho M. The emergence of AntibodyPlus: the future trend of antibody-based therapeutics. Antib Ther 2022; 5:280-287. [PMID: 36299417 PMCID: PMC9590318 DOI: 10.1093/abt/tbac024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/12/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
To date, close to one hundred canonical monoclonal antibody drugs have been approved by the FDA; furthermore, a number of antibody-derived therapeutics in nontraditional formats have reached late development stages and the market, and many more are being evaluated in early-stage development. To better reflect this trend and to set up a framework for forward thinking, we herein introduce the concept of AntibodyPlus, embracing any therapeutics with an antibody component, to guide and stimulate future development of antibody therapeutics. AntibodyPlus therapeutics contain effector modules, in the form of small molecules, nucleic acids, proteins, or even cells, to enhance their therapeutic activities against cancer, virus infection and other diseases. In this short review, we discuss historic perspective and current status of therapeutic antibody development, and the scope and categories of AntibodyPlus therapeutics along with their advantages, applications, and challenges. We also present several examples that highlight their design principles, potentials, and future trends.
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Affiliation(s)
- Yong Zhu
- Consultant for biopharma companies , Anaheim, CA 92808, USA
| | - Shawn Shouye Wang
- Chinese Antibody Society , 955 Massachusetts Ave, #276, Cambridge MA, 02139, USA
- CMC Management , , 1 Cedarbrook Drive, Cranbury, NJ 08512, USA
- WuXi Biologics , , 1 Cedarbrook Drive, Cranbury, NJ 08512, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology , , Boston, MA 02115-5000, USA
- Northeastern University , , Boston, MA 02115-5000, USA
- Barnett Institute for Chemical and Biological Analysis , , Boston, MA 02115-5000, USA
- Northeastern University , , Boston, MA 02115-5000, USA
| | - Mitchell Ho
- Laboratory of Molecular Biology , Center for Cancer Research, , Bethesda, MD 20892, USA
- National Cancer Institute, National Institutes of Health , Center for Cancer Research, , Bethesda, MD 20892, USA
- Antibody Engineering Program , Center for Cancer Research, , Bethesda, MD 20892, USA
- National Cancer Institute, National Institutes of Health , Center for Cancer Research, , Bethesda, MD 20892, USA
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4
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Kobayashi A, Nobili A, Neier SC, Sadiki A, Distel R, Zhou ZS, Novina CD. Front Cover: Light‐Controllable Binary Switch Activation of CAR T Cells (ChemMedChem 12/2022). ChemMedChem 2022. [DOI: 10.1002/cmdc.202200309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Aya Kobayashi
- Department of Cancer Immunology and Virology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Broad Institute of Harvard and MIT Cambridge MA 02142 USA
| | - Alberto Nobili
- Department of Cancer Immunology and Virology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Broad Institute of Harvard and MIT Cambridge MA 02142 USA
- Dynamic Cell Therapies, Inc. 127 Western Ave. Allston MA 02134 USA
| | - Steven C. Neier
- Department of Cancer Immunology and Virology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Broad Institute of Harvard and MIT Cambridge MA 02142 USA
- Binney Street Capital Boston MA 02215 USA
| | - Amissi Sadiki
- Department of Cancer Immunology and Virology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Department of Chemistry and Chemical Biology Northeastern University Boston MA 02115 USA
- Barnett Institute of Chemical and Biological Analysis Northeastern University Boston MA 02115 USA
| | - Robert Distel
- Department of Cancer Immunology and Virology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology Northeastern University Boston MA 02115 USA
- Barnett Institute of Chemical and Biological Analysis Northeastern University Boston MA 02115 USA
| | - Carl D. Novina
- Department of Cancer Immunology and Virology Dana-Farber Cancer Institute Boston MA 02215 USA
- Department of Medicine Harvard Medical School Boston MA 02115 USA
- Broad Institute of Harvard and MIT Cambridge MA 02142 USA
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Kobayashi A, Nobili A, Neier SC, Sadiki A, Distel R, Zhou ZS, Novina CD. Light-Controllable Binary Switch Activation of CAR T Cells. ChemMedChem 2022; 17:e202100722. [PMID: 35146940 PMCID: PMC9304291 DOI: 10.1002/cmdc.202100722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/05/2022] [Indexed: 11/29/2022]
Abstract
Major challenges to chimeric antigen receptor (CAR) T cell therapies include uncontrolled immune activity, off-tumor toxicities and tumor heterogeneity. To overcome these challenges, we engineered CARs directed against small molecules. By conjugating the same small molecule to distinct tumor-targeting antibodies, we show that small molecule specific-CAR T cells can be redirected to different tumor antigens. Such binary switches allow control over the degree of CAR T cell activity and enables simultaneous targeting of multiple tumor-associated antigens. We also demonstrate that ultraviolet light-sensitive caging of small molecules blocks CAR T cell activation. Exposure to ultraviolet light, uncaged small molecules and restored CAR T cell-mediated killing. Together, our data demonstrate that a light-sensitive caging system enables an additional level of control over tumor cell killing, which could improve the therapeutic index of CAR T cell therapies.
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Affiliation(s)
- Aya Kobayashi
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteBostonMA 02215USA
- Department of MedicineHarvard Medical SchoolBostonMA 02115USA
- Broad Institute of Harvard and MITCambridgeMA 02142USA
| | - Alberto Nobili
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteBostonMA 02215USA
- Department of MedicineHarvard Medical SchoolBostonMA 02115USA
- Broad Institute of Harvard and MITCambridgeMA 02142USA
- Dynamic Cell Therapies, Inc.127 Western Ave.AllstonMA 02134USA
| | - Steven C. Neier
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteBostonMA 02215USA
- Department of MedicineHarvard Medical SchoolBostonMA 02115USA
- Broad Institute of Harvard and MITCambridgeMA 02142USA
- Binney Street CapitalBostonMA 02215USA
| | - Amissi Sadiki
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteBostonMA 02215USA
- Department of MedicineHarvard Medical SchoolBostonMA 02115USA
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMA 02115USA
- Barnett Institute of Chemical and Biological AnalysisNortheastern UniversityBostonMA 02115USA
| | - Robert Distel
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteBostonMA 02215USA
- Department of MedicineHarvard Medical SchoolBostonMA 02115USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical BiologyNortheastern UniversityBostonMA 02115USA
- Barnett Institute of Chemical and Biological AnalysisNortheastern UniversityBostonMA 02115USA
| | - Carl D. Novina
- Department of Cancer Immunology and VirologyDana-Farber Cancer InstituteBostonMA 02215USA
- Department of MedicineHarvard Medical SchoolBostonMA 02115USA
- Broad Institute of Harvard and MITCambridgeMA 02142USA
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Gabrieli T, Michaeli Y, Avraham S, Torchinsky D, Margalit S, Schütz L, Juhasz M, Coruh C, Arbib N, Zhou ZS, Law JA, Weinhold E, Ebenstein Y. Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping. Nucleic Acids Res 2022; 50:e92. [PMID: 35657088 PMCID: PMC9458417 DOI: 10.1093/nar/gkac460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/12/2022] [Accepted: 06/01/2022] [Indexed: 12/15/2022] Open
Abstract
DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in CpG context, allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. We used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased up to 2-fold by the addition of a nucleosidase, presumably by degrading the inactive by-product of the cofactor after labeling, preventing its inhibitory effect. We used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient and then performed whole-genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published bisulfite sequencing methylation maps. Although mapping resolution is limited by optical detection to 500–1000 bp, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.
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Affiliation(s)
- Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sigal Avraham
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dmitry Torchinsky
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sapir Margalit
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Leonie Schütz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Matyas Juhasz
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nissim Arbib
- Department of Obstetrics and Gynecology, Meir Hospital, Kfar Saba, Israel & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, and Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts02115, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, D-52056Aachen, Germany
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, The Center for Physics and Chemistry of Living Systems, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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Zhang Z, Chow SY, De Guzman R, Joh NH, Joubert MK, Richardson J, Shah B, Wikström M, Zhou ZS, Wypych J. A Mass Spectrometric Characterization of Light-Induced Modifications in Therapeutic Proteins. J Pharm Sci 2022; 111:1556-1564. [DOI: 10.1016/j.xphs.2022.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/04/2022] [Accepted: 02/04/2022] [Indexed: 12/15/2022]
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8
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Toole EN, Dufresne C, Ray S, Schwann AB, Sadiki A, Zhou ZS, Cook K, Ivanov AR. Correction to Rapid Highly-Efficient Digestion and Peptide Mapping of Adeno-Associated Viruses. Anal Chem 2021; 93:16734. [PMID: 34850630 DOI: 10.1021/acs.analchem.1c04871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Cunningham O, Scott M, Zhou ZS, Finlay WJJ. Polyreactivity and polyspecificity in therapeutic antibody development: risk factors for failure in preclinical and clinical development campaigns. MAbs 2021; 13:1999195. [PMID: 34780320 PMCID: PMC8726659 DOI: 10.1080/19420862.2021.1999195] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antibody-based drugs, which now represent the dominant biologic therapeutic modality, are used to modulate disparate signaling pathways across diverse disease indications. One fundamental premise that has driven this therapeutic antibody revolution is the belief that each monoclonal antibody exhibits exquisitely specific binding to a single-drug target. Herein, we review emerging evidence in antibody off-target binding and relate current key findings to the risk of failure in therapeutic development. We further summarize the current state of understanding of structural mechanisms underpining the different phenomena that may drive polyreactivity and polyspecificity, and highlight current thinking on how de-risking studies may be best implemented in the screening triage. We conclude with a summary of what we believe to be key observations in the field to date, and a call for the wider antibody research community to work together to build the tools needed to maximize our understanding in this nascent area.
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Affiliation(s)
| | - Martin Scott
- Department of Biopharm Discovery, GlaxoSmithKline Research & Development, Hertfordshire, UK
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Barnett Institute for Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts, USA
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10
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Hui Q, Zhang Q, Wang KD, Zhang J, Zheng CN, Zhou ZS. [Untargeted metabolomic analysis of serum samples from children with mycoplasma pneumonia in a hospital in Beijing]. Zhonghua Yu Fang Yi Xue Za Zhi 2021; 55:660-666. [PMID: 34034408 DOI: 10.3760/cma.j.cn112150-20210310-00237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: This study was aimed to analyze the untargeted metabolomics of serum samples from children with mycoplasma pneumonia in a hospital in Beijing. Methods: A total of 50 children with mycoplasma pneumonia as the case group were recruited from Department of Pediatrics, China-Japan Friendship Hospital in Beijing from January 2019 to February 2020, and meanwhile 50 age-and gender-matched heathy children were selected and formed the control group. 2 ml venous fasting blood samples was collected from all children. Serum metabolites were quantified by using the untargeted ultra-high performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) technique. Unsupervised principle component analysis and (orthogonal) partial least-squares-discriminant analysis were employed to identify differential metabolites between cases and controls. MBRole software was used for pathway enrichment analysis. Results: There were 27 boys and 23 girls in the case group with an average age of (6.0±3.65) years, and the control group consisted of 28 boys and 22 girls with an average age of (6.62±2.64) years. A total of 392 different metabolites were detected. Compared with the control group, 306 metabolites were decreased and 86 increased in case group. Forty-one differential metabolites with variable important in projection (VIP) values larger than 5 and P values less than 0.05 were teased out, and they mainly concentrated on phospholipid. The levels of 38 metabolites were significantly lower in the case group, yet 4 metabolites were significantly higher than that of the control group. Metabolic enrichment analysis showed that different metabolites were related to the biosynthesis of phenylalanine, tyrosine, tryptophan, unsaturated fatty acid, ammonia acyl tRNA and insulin signaling pathway, as well as the metabolism of ABC transporters. Conclusion: The serum untargeted metabolomics differed remarkably between children with mycoplasma pneumonia and healthy children.
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Affiliation(s)
- Q Hui
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100070, China Department of Pediatrics, China-Japan Friendship Hospital, Beijing 100029, China
| | - Q Zhang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100070, China
| | - K D Wang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100070, China
| | - J Zhang
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100070, China
| | - C N Zheng
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100070, China
| | - Z S Zhou
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100070, China Department of Pediatrics, China-Japan Friendship Hospital, Beijing 100029, China
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11
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Sadiki A, Vaidya SR, Abdollahi M, Bhardwaj G, Dolan ME, Turna H, Arora V, Sanjeev A, Robinson TD, Koid A, Amin A, Zhou ZS. Site-specific conjugation of native antibody. Antib Ther 2020; 3:271-284. [PMID: 33644685 PMCID: PMC7906296 DOI: 10.1093/abt/tbaa027] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Traditionally, non-specific chemical conjugations, such as acylation of amines on lysine or alkylation of thiols on cysteines, are widely used; however, they have several shortcomings. First, the lack of site-specificity results in heterogeneous products and irreproducible processes. Second, potential modifications near the complementarity-determining region may reduce binding affinity and specificity. Conversely, site-specific methods produce well-defined and more homogenous antibody conjugates, ensuring developability and clinical applications. Moreover, several recent side-by-side comparisons of site-specific and stochastic methods have demonstrated that site-specific approaches are more likely to achieve their desired properties and functions, such as increased plasma stability, less variability in dose-dependent studies (particularly at low concentrations), enhanced binding efficiency, as well as increased tumor uptake. Herein, we review several standard and practical site-specific bioconjugation methods for native antibodies, i.e., those without recombinant engineering. First, chemo-enzymatic techniques, namely transglutaminase (TGase)-mediated transamidation of a conserved glutamine residue and glycan remodeling of a conserved asparagine N-glycan (GlyCLICK), both in the Fc region. Second, chemical approaches such as selective reduction of disulfides (ThioBridge) and N-terminal amine modifications. Furthermore, we list site-specific antibody–drug conjugates in clinical trials along with the future perspectives of these site-specific methods.
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Affiliation(s)
- Amissi Sadiki
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Shefali R Vaidya
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Mina Abdollahi
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Gunjan Bhardwaj
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Michael E Dolan
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA.,Downstream Development, Biologics Process Development, Millennium Pharmaceuticals, Inc., (a wholly-owned subsidiary of Takeda Pharmaceuticals Company Limited), Cambridge, Massachusetts 02139, USA
| | - Harpreet Turna
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Varnika Arora
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Athul Sanjeev
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Timothy D Robinson
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Andrea Koid
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Aashka Amin
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University Boston, Massachusetts 02115-5000, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University Boston, Massachusetts 02115-5000, USA
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12
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Sadiki A, Kercher EM, Lu H, Lang RT, Spring BQ, Zhou ZS. Site-specific Bioconjugation and Convergent Click Chemistry Enhances Antibody-Chromophore Conjugate Binding Efficiency. Photochem Photobiol 2020; 96:596-603. [PMID: 32080860 DOI: 10.1111/php.13231] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 12/20/2019] [Indexed: 12/22/2022]
Abstract
Photosensitizer (PS)-antibody conjugates (photoimmunoconjugates, PICs) enable cancer cell-targeted photodynamic therapy (PDT). Nonspecific chemical bioconjugation is widely used to synthesize PICs but gives rise to several shortcomings. The conjugates are heterogeneous, and the process is not easily reproducible. Moreover, modifications at or near the binding sites alter both binding affinity and specificity. To overcome these limitations, we introduce convergent assembly of PICs via a chemo-enzymatic site-specific approach. First, an antibody is conjugated to a clickable handle via site-specific modification of glutamine (Gln) residues catalyzed by transglutaminase (TGase, EC 2.3.2.13). Second, the modified antibody intermediate is conjugated to a compatible chromophore via click chemistry. Utilizing cetuximab, we compared this site-specific conjugation protocol to the nonspecific chemical acylation of amines using N-hydroxysuccinimide (NHS) chemistry. Both the heavy and light chains were modified via the chemical route, whereas, only a glutamine 295 in the heavy chain was modified via chemo-enzymatic conjugation. Furthermore, a 2.3-fold increase in the number of bound antibodies per cell was observed for the site-specific compared with nonspecific method, suggesting that multiple stochastic sites of modification perturb the antibody-antigen binding. Altogether, site-specific bioconjugation leads to homogenous, reproducible and well-defined PICs, conferring higher binding efficiency and probability of clinical success.
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Affiliation(s)
- Amissi Sadiki
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA
| | - Eric M Kercher
- Translational Biophotonics Cluster, Northeastern University, Boston, MA.,Department of Physics, Northeastern University, Boston, MA
| | - Haibin Lu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA.,College of Pharmacy, Jilin University, Changchun, Jilin, China
| | - Ryan T Lang
- Translational Biophotonics Cluster, Northeastern University, Boston, MA.,Department of Physics, Northeastern University, Boston, MA
| | - Bryan Q Spring
- Translational Biophotonics Cluster, Northeastern University, Boston, MA.,Department of Physics, Northeastern University, Boston, MA.,Department of Bioengineering, Northeastern University, Boston, MA.,Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA.,Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
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13
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Moulton KR, Sadiki A, Koleva BN, Ombelets LJ, Tran TH, Liu S, Wang B, Chen H, Micheloni E, Beuning PJ, O’Doherty GA, Zhou ZS. Site-Specific Reversible Protein and Peptide Modification: Transglutaminase-Catalyzed Glutamine Conjugation and Bioorthogonal Light-Mediated Removal. Bioconjug Chem 2019; 30:1617-1621. [DOI: 10.1021/acs.bioconjchem.9b00145] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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14
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Yang L, Chumsae C, Kaplan JB, Moulton KR, Wang D, Lee DH, Zhou ZS. Detection of Alkynes via Click Chemistry with a Brominated Coumarin Azide by Simultaneous Fluorescence and Isotopic Signatures in Mass Spectrometry. Bioconjug Chem 2017; 28:2302-2309. [DOI: 10.1021/acs.bioconjchem.7b00354] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Lihua Yang
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Chris Chumsae
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Jenifer B. Kaplan
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Kevin Ryan Moulton
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Dongdong Wang
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - David H. Lee
- AbbVie Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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15
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Catcott KC, Yan J, Qu W, Wysocki VH, Zhou ZS. Cover Picture: Identifying Unknown Enzyme-Substrate Pairs from the Cellular Milieu with Native Mass Spectrometry (ChemBioChem 7/2017). Chembiochem 2017. [DOI: 10.1002/cbic.201700131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Kalli C. Catcott
- Department of Chemistry and Chemical Biology; Northeastern University; 360 Huntington Avenue Boston MA 02115 USA
| | - Jing Yan
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - Wanlu Qu
- Department of Chemistry and Chemical Biology; Northeastern University; 360 Huntington Avenue Boston MA 02115 USA
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry; The Ohio State University; 100 West 18th Avenue Columbus OH 43210 USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology; Northeastern University; 360 Huntington Avenue Boston MA 02115 USA
- Barnett Institute of Chemical and Biological Analysis; Northeastern University; 360 Huntington Avenue Boston MA 02115 USA
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16
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Catcott KC, Yan J, Qu W, Wysocki VH, Zhou ZS. Identifying Unknown Enzyme-Substrate Pairs from the Cellular Milieu with Native Mass Spectrometry. Chembiochem 2017; 18:613-617. [PMID: 28140508 DOI: 10.1002/cbic.201600634] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 01/22/2023]
Abstract
The enzyme-substrate complex is inherently transient, rendering its detection difficult. In our framework designed for bisubstrate systems-isotope-labeled, activity-based identification and tracking (IsoLAIT)-the common substrate, such as S-adenosyl-l-methionine (AdoMet) for methyltransferases, is replaced by an analogue (e.g., S-adenosyl-l-vinthionine) that, as a probe, creates a tightly bound [enzyme⋅substrate⋅probe] complex upon catalysis by thiopurine-S-methyltransferase (TPMT, EC 2.1.1.67). This persistent complex is then identified by native mass spectrometry from the cellular milieu without separation. Furthermore, the probe's isotope pattern flags even unknown substrates and enzymes. IsoLAIT is broadly applicable for other enzyme systems, particularly those catalyzing group transfer and with multiple substrates, such as glycosyltransferases and kinases.
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Affiliation(s)
- Kalli C Catcott
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Jing Yan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Wanlu Qu
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
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17
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Qu W, Catcott KC, Zhang K, Liu S, Guo JJ, Ma J, Pablo M, Glick J, Xiu Y, Kenton N, Ma X, Duclos RI, Zhou ZS. Capturing Unknown Substrates via in Situ Formation of Tightly Bound Bisubstrate Adducts: S-Adenosyl-vinthionine as a Functional Probe for AdoMet-Dependent Methyltransferases. J Am Chem Soc 2016; 138:2877-80. [DOI: 10.1021/jacs.5b05950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Kun Zhang
- School
of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | | | | | - Jisheng Ma
- School
of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325035, China
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18
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Chen HS, Yang L, Huang LF, Wang WL, Hu Y, Jiang JJ, Zhou ZS. Temperature- and Relative Humidity-Dependent Life History Traits of Phenacoccus solenopsis (Hemiptera: Pseudococcidae) on Hibiscus rosa-sinensis (Malvales: Malvaceae). Environ Entomol 2015; 44:1230-1239. [PMID: 26314069 DOI: 10.1093/ee/nvv085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 05/15/2015] [Indexed: 06/04/2023]
Abstract
Phenacoccus solenopsis Tinsley (Hemiptera: Pseudococcidae), a worldwide distributive invasive pest, originated from the United States, and it was first reported in Guangdong province, China, in 2008. The effects of temperature and relative humidity (RH) on the life history traits of P. solenopsis on Hibiscus rosa-sinensis L. (Malvales: Malvaceae) were studied at seven constant temperatures (15, 20, 25, 27.5, 30, 32.5, and 35°C) and three RHs (45, 60, and 75%). The results showed that temperature, RH, and their interactions significantly influenced the life history traits of P. solenopsis. First instar was the most sensitive stage to extreme temperatures with very low survival rates at 15 and 35°C. At 25-32.5°C and the three RHs, the developmental periods of entire immature stage were shorter with values between 12.5-18.6 d. The minimum threshold temperature and the effective accumulative temperature for the pest to complete one generation were 13.2°C and 393.7 degree-days, respectively. The percentage and longevity of female adults significantly differed among different treatments. It failed to complete development at 15 or 35°C and the three RHs. Female fecundity reached the maximum value at 27.5°C and 45% RH. The intrinsic rate for increase (r), the net reproductive rate (R0), and the finite rate of increase (λ) reached the maximum values at 27.5°C and 45% RH (0.22 d(-1), 244.6 hatched eggs, and 1.25 d(-1), respectively). Therefore, we conclude that 27.5°C and 45% RH are the optimum conditions for the population development of the pest.
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Affiliation(s)
- H S Chen
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning 530007, China. The authors contributed equally to this work
| | - L Yang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning 530007, China. The authors contributed equally to this work
| | - L F Huang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - W L Wang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Y Hu
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning 530007, China. College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - J J Jiang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Z S Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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19
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Chumsae C, Hossler P, Raharimampionona H, Zhou Y, McDermott S, Racicot C, Radziejewski C, Zhou ZS. When Good Intentions Go Awry: Modification of a Recombinant Monoclonal Antibody in Chemically Defined Cell Culture by Xylosone, an Oxidative Product of Ascorbic Acid. Anal Chem 2015; 87:7529-34. [DOI: 10.1021/acs.analchem.5b00801] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Chris Chumsae
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Patrick Hossler
- Cell
Culture, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Haly Raharimampionona
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Yu Zhou
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Sean McDermott
- Cell
Culture, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Chris Racicot
- Cell
Culture, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Czeslaw Radziejewski
- Protein
Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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20
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Abstract
Selenium is an essential micronutrient in humans due to the important roles of the selenocysteine-containing selenoproteins. Organoselenium metabolites are generally found to be substrates for the biochemical pathways of their sulfur analogs, and the redox chemistry of selenomethionine and some other metabolites have been previously reported. We now report the first synthesis and characterization of Se-adenosylselenohomocysteine selenoxide (SeAHO) prepared via hydrogen peroxide oxidation of Se-adenosylselenohomocysteine (SeAH). The selenoxide SeAHO, in contrast to its corresponding sulfoxide S-adenosylhomocysteine (SAHO), can form hydrate, has an electrostatic interaction between the α-amino acid moiety and the highly polar selenoxide functional group, and readily oxidizes glutathione (GSH) and cysteine thiols.
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Affiliation(s)
- Richard I Duclos
- Department of Pharmaceutical Sciences, 140 The Fenway Bldg., Room 206, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 3163
| | - Dillon C Cleary
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
| | - Kalli C Catcott
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Hurtig Hall, Room 102, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115-5000, Tel: +1 617 373 2800
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21
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Chumsae C, Zhou LL, Shen Y, Wohlgemuth J, Fung E, Burton R, Radziejewski C, Zhou ZS. Discovery of a chemical modification by citric acid in a recombinant monoclonal antibody. Anal Chem 2014; 86:8932-6. [PMID: 25136741 PMCID: PMC4165448 DOI: 10.1021/ac502179m] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 08/19/2014] [Indexed: 01/07/2023]
Abstract
Recombinant therapeutic monoclonal antibodies exhibit a high degree of heterogeneity that can arise from various post-translational modifications. The formulation for a protein product is to maintain a specific pH and to minimize further modifications. Generally Recognized as Safe (GRAS), citric acid is commonly used for formulation to maintain a pH at a range between 3 and 6 and is generally considered chemically inert. However, as we reported herein, citric acid covalently modified a recombinant monoclonal antibody (IgG1) in a phosphate/citrate-buffered formulation at pH 5.2 and led to the formation of so-called "acidic species" that showed mass increases of 174 and 156 Da, respectively. Peptide mapping revealed that the modification occurred at the N-terminus of the light chain. Three additional antibodies also showed the same modification but displayed different susceptibilities of the N-termini of the light chain, heavy chain, or both. Thus, ostensibly unreactive excipients under certain conditions may increase heterogeneity and acidic species in formulated recombinant monoclonal antibodies. By analogy, other molecules (e.g., succinic acid) with two or more carboxylic acid groups and capable of forming an anhydride may exhibit similar reactivities. Altogether, our findings again reminded us that it is prudent to consider formulations as a potential source for chemical modifications and product heterogeneity.
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Affiliation(s)
- Chris Chumsae
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000, United States
| | - Liqiang Lisa Zhou
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Yang Shen
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Jessica Wohlgemuth
- NBE
Analytical Research and Development, AbbVie, Ludwigshafen 67061, Germany
| | - Emma Fung
- Biologics, AbbVie
Bioresearch Center, Worcester, Massachusetts 01605, United States
| | - Randall Burton
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Czeslaw Radziejewski
- Protein
Analytics, Process Sciences, AbbVie Bioresearch
Center, Worcester, Massachusetts 01605, United States
| | - Zhaohui Sunny Zhou
- Barnett
Institute of Chemical and Biological Analysis, Department of Chemistry
and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000, United States
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22
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Klaene JJ, Ni W, Alfaro JF, Zhou ZS. Detection and quantitation of succinimide in intact protein via hydrazine trapping and chemical derivatization. J Pharm Sci 2014; 103:3033-42. [PMID: 25043726 DOI: 10.1002/jps.24074] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Revised: 06/01/2014] [Accepted: 06/04/2014] [Indexed: 12/19/2022]
Abstract
The formation of aspartyl succinimide is a common post-translational modification of protein pharmaceuticals under acidic conditions. We present a method to detect and quantitate succinimide in intact protein via hydrazine trapping and chemical derivatization. Succinimide, which is labile under typical analytical conditions, is first trapped with hydrazine to form stable hydrazide and can be directly analyzed by mass spectrometry. The resulting aspartyl hydrazide can be selectively derivatized by various tags, such as fluorescent rhodamine sulfonyl chloride that absorbs strongly in the visible region (570 nm). Our tagging strategy allows the labeled protein to be analyzed by orthogonal methods, including HPLC-UV-Vis, liquid chromatography mass spectrometry (LC-MS), and SDS-PAGE coupled with fluorescence imaging. A unique advantage of our method is that variants containing succinimide, after derivatization, can be readily resolved via either affinity enrichment or chromatographic separation. This allows further investigation of individual factors in a complex protein mixture that affect succinimide formation. Some additional advantages are imparted by fluorescence labeling including the facile detection of the intact protein without proteolytic digestion to peptides; and high sensitivity, for example, without optimization, 0.41% succinimide was readily detected. As such, our method should be useful for rapid screening, optimization of formulation conditions, and related processes relevant to protein pharmaceuticals.
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Affiliation(s)
- Joshua J Klaene
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
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23
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Liu M, Zhang Z, Cheetham J, Ren D, Zhou ZS. Discovery and characterization of a photo-oxidative histidine-histidine cross-link in IgG1 antibody utilizing ¹⁸O-labeling and mass spectrometry. Anal Chem 2014; 86:4940-8. [PMID: 24738698 PMCID: PMC4030806 DOI: 10.1021/ac500334k] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A novel photo-oxidative cross-linking
between two histidines (His-His)
has been discovered and characterized in an IgG1 antibody via the
workflow of XChem-Finder, 18O labeling and mass spectrometry
(2013, 85, 5900−590823634697). Its structure was elucidated by peptide
mapping with multiple proteases with various specificities (e.g.,
trypsin, Asp-N, and GluC combined with trypsin or Asp-N) and mass
spectrometry with complementary fragmentation modes (e.g., collision-induced
dissociation (CID) and electron-transfer dissociation (ETD)). Our
data indicated that cross-linking occurred across two identical conserved
histidine residues on two separate heavy chains in the hinge region,
which is highly flexible and solvent accessible. On the basis of model
studies with short peptides, it has been proposed that singlet oxygen
reacts with the histidyl imidazole ring to form an endoperoxide and
then converted to the 2-oxo-histidine (2-oxo-His) and His+32 intermediates, the latter is
subject to a
nucleophilic attack by the unmodified histidine; and finally, elimination
of a water molecule leads to the final adduct with a net mass increase
of 14 Da. Our findings are consistent with this mechanism. Successful
discovery of cross-linked His-His again demonstrates the broad applicability
and utility of our XChem-Finder approach in the discovery and elucidation
of protein cross-linking, particularly without a priori knowledge of the chemical nature and site of cross-linking.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen , One Amgen Center Drive, Thousand Oaks, California 91320, United States
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24
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Hodgson NW, Waly MI, Al-Farsi YM, Al-Sharbati MM, Al-Farsi O, Ali A, Ouhtit A, Zang T, Zhou ZS, Deth RC. Decreased glutathione and elevated hair mercury levels are associated with nutritional deficiency-based autism in Oman. Exp Biol Med (Maywood) 2014; 239:697-706. [DOI: 10.1177/1535370214527900] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetic, nutrition, and environmental factors have each been implicated as sources of risk for autism. Oxidative stress, including low plasma levels of the antioxidant glutathione, has been reported by numerous autism studies, which can disrupt methylation-dependent epigenetic regulation of gene expression with neurodevelopmental consequences. We investigated the status of redox and methylation metabolites, as well as the level of protein homocysteinylation and hair mercury levels, in autistic and neurotypical control Omani children, who were previously shown to exhibit significant nutritional deficiencies in serum folate and vitamin B12. The serum level of glutathione in autistic subjects was significantly below control levels, while levels of homocysteine and S-adenosylhomocysteine were elevated, indicative of oxidative stress and decreased methionine synthase activity. Autistic males had lower glutathione and higher homocysteine levels than females, while homocysteinylation of serum proteins was increased in autistic males but not females. Mercury levels were markedly elevated in the hair of autistic subjects vs. control subjects, consistent with the importance of glutathione for its elimination. Thus, autism in Oman is associated with decreased antioxidant resources and decreased methylation capacity, in conjunction with elevated hair levels of mercury.
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Affiliation(s)
- Nathaniel W Hodgson
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, MA 02115, USA
| | - Mostafa I Waly
- Department of Food Science and Nutrition, Sultan Qaboos University, P.O.Box 34, P.C. 123, Al-Khoud, Muscat, Sultanate of Oman
- Nutrition Department, High Institute of Public Health, Alexandria University, P.C. 165, El-Hadra, Alexandria, Egypt
| | - Yahya M Al-Farsi
- Department of Family Medicine and Public Health, College of Medicine and Health Sciences, Sultan Qaboos University, P.O.Box 35, P.C. 123, Al-Khoud, Muscat, Sultanate of Oman
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA 02118, USA
| | - Marwan M Al-Sharbati
- Department of Behavioral Medicine, College of Medicine and Health Sciences, Sultan Qaboos University, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Omar Al-Farsi
- Department of Family Medicine and Public Health, College of Medicine and Health Sciences, Sultan Qaboos University, P.O.Box 35, P.C. 123, Al-Khoud, Muscat, Sultanate of Oman
| | - Amanat Ali
- Department of Food Science and Nutrition, Sultan Qaboos University, P.O.Box 34, P.C. 123, Al-Khoud, Muscat, Sultanate of Oman
| | - Allal Ouhtit
- Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Al-Khoud 123, Muscat, Sultanate of Oman
| | - Tianzhu Zang
- Barnett Institute of Chemical and Biological Analysis, College of Science, Northeastern University, Boston, MA 02115, USA
| | - Zhaohui Sunny Zhou
- Barnett Institute of Chemical and Biological Analysis, College of Science, Northeastern University, Boston, MA 02115, USA
| | - Richard C Deth
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, Boston, MA 02115, USA
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25
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Chumsae C, Gifford K, Lian W, Liu H, Radziejewski CH, Zhou ZS. Arginine modifications by methylglyoxal: discovery in a recombinant monoclonal antibody and contribution to acidic species. Anal Chem 2013; 85:11401-9. [PMID: 24168114 PMCID: PMC3869466 DOI: 10.1021/ac402384y] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heterogeneity is common among protein therapeutics. For example, the so-called acidic species (charge variants) are typically observed when recombinant monoclonal antibodies (mAbs) are analyzed by weak-cation exchange chromatography (WCX). Several protein post-translational modifications have been established as contributors but still cannot completely account for all heterogeneity. As reported herein, an unexpected modification by methylglyoxal (MGO) was identified, for the first time, in a recombinant monoclonal antibody expressed in Chinese hamster ovary (CHO) cells. Modifications of arginine residues by methylglyoxal lead to two adducts (dihydroxyimidazolidine and hydroimidazolone) with increases of molecular weights of 72 and 54 Da, respectively. In addition, the modification by methylglyoxal causes the antibody to elute earlier in the weak cation exchange chromatogram. Consequently, the extent to which an antibody was modified at multiple sites corresponds to the degree of shift in elution time. Furthermore, cell culture parameters also affected the extent of modifications by methylglyoxal, a highly reactive metabolite that can be generated from glucose or lipids or other metabolic pathways. Our findings again highlight the impact that cell culture conditions can have on the product quality of recombinant protein pharmaceuticals.
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Affiliation(s)
- Chris Chumsae
- Protein Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, USA
| | - Kathreen Gifford
- Protein Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, USA
| | - Wei Lian
- Cell Culture, Manufacturing Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, USA
| | - Hongcheng Liu
- Protein Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, USA
| | - Czeslaw H. Radziejewski
- Protein Analytics, Process Sciences Department, AbbVie Bioresearch Center, Worcester, Massachusetts 01605, USA
| | - Zhaohui Sunny Zhou
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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26
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Liu M, Zhang Z, Zang T, Spahr C, Cheetham J, Ren D, Sunny Zhou Z. Discovery of undefined protein cross-linking chemistry: a comprehensive methodology utilizing 18O-labeling and mass spectrometry. Anal Chem 2013; 85:5900-8. [PMID: 23634697 PMCID: PMC3691076 DOI: 10.1021/ac400666p] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Characterization of protein cross-linking, particularly without prior knowledge of the chemical nature and site of cross-linking, poses a significant challenge, because of their intrinsic structural complexity and the lack of a comprehensive analytical approach. Toward this end, we have developed a generally applicable workflow-XChem-Finder-that involves four stages: (1) detection of cross-linked peptides via (18)O-labeling at C-termini; (2) determination of the putative partial sequences of each cross-linked peptide pair using a fragment ion mass database search against known protein sequences coupled with a de novo sequence tag search; (3) extension to full sequences based on protease specificity, the unique combination of mass, and other constraints; and (4) deduction of cross-linking chemistry and site. The mass difference between the sum of two putative full-length peptides and the cross-linked peptide provides the formulas (elemental composition analysis) for the functional groups involved in each cross-linking. Combined with sequence restraint from MS/MS data, plausible cross-linking chemistry and site were inferred, and ultimately confirmed, by matching with all data. Applying our approach to a stressed IgG2 antibody, 10 cross-linked peptides were discovered and found to be connected via thioethers originating from disulfides at locations that had not been previously recognized. Furthermore, once the cross-link chemistry was revealed, a targeted cross-link search yielded 4 additional cross-linked peptides that all contain the C-terminus of the light chain.
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Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Zhongqi Zhang
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Tianzhu Zang
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
| | - Chris Spahr
- Biologic Optimization, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Janet Cheetham
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Da Ren
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, CA 91320, USA
| | - Zhaohui Sunny Zhou
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA
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27
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Xu CN, Zhou ZS, Wu YX, Chi FM, Ji ZR, Zhang HJ. First Report of Stem and Leaf Anthracnose on Blueberry Caused by Colletotrichum gloeosporioides in China. Plant Dis 2013; 97:845. [PMID: 30722632 DOI: 10.1094/pdis-11-12-1056-pdn] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Blueberry (Vaccinium spp.) is becoming increasingly popular in China as a nutritional berry crop. With the expansion of blueberry production, many diseases have become widespread in different regions of China. In August of 2012, stem and leaf spots symptomatic of anthracnose were sporadically observed on highbush blueberries in a field located in Liaoning, China, where approximately 15% of plants were diseased. Symptoms first appeared as yellow to reddish, irregularly-shaped lesions on leaves and stems. The lesions then expanded, becoming dark brown in the center and surrounded by a reddish halo. Leaf and stem tissues (5 × 5 mm) were cut from the lesion margins and surface-disinfected in 70% ethanol for 30 s, followed by three rinses with sterile water before placing on potato dextrose agar (PDA). Plates were incubated at 28°C. Colonies were initially white, becoming grayish-white to gray with yellow spore masses. Conidia were one-celled, hyaline, and cylindrical with rounded ends, measuring 15.0 to 25.0 × 4.0 to 7.5 μm. No teleomorph was observed. The fungus was tentatively identified as Colletotrichum gloeosporioides (PenZ.) PenZ & Sacc. (teleomorph Glomerella cingulata (Stoneman) Spauld. & H. Schrenk) based on morphological characteristics of the colony and conidia (1). Genomic DNA was extracted from isolate XCG1 and the internal transcribed spacer (ITS) region of the ribosomal DNA (ITS1-5.8S-ITS2) was amplified with primer pairs ITS1 and ITS4. BLAST searches showed 99% identity with C. gloeosporioides isolates in GenBank (Accession No. AF272779). The sequence of isolate XCG1 (C. gloeosporioides) was deposited into GenBank (JX878503). Pathogenicity tests were conducted on 2-year-old potted blueberries, cv. Berkeley. Stems and leaves of 10 potted blueberry plants were wounded with a sterilized needle and sprayed with a suspension of 105 conidia per ml of sterilized water. Five healthy potted plants were inoculated with sterilized water as control. Dark brown lesions surrounded by reddish halos developed on all inoculated leaves and stems after 7 days, and the pathogen was reisolated from lesions of 50% of inoculated plants as described above. The colony and conidial morphology were identical to the original isolate XCG1. No symptoms developed on the control plants. The causal agent of anthracnose on blueberry was identified as C. gloeosporioides on the basis of morphological and molecular characteristics, and its pathogenicity was confirmed with Koch's postulates. Worldwide, it has been reported that blueberry anthracnose might be caused by C. acutatum and C. gloeosporioides (2). However, we did not isolate C. acutatum during this study. To our knowledge, this is the first report of stem and leaf anthracnose of blueberry caused by C. gloeosporioides in China. References: (1) J. M. E. Mourde. No 315. CMI Descriptions of Pathogenic Fungi and Bacteria. Kew, Surrey, UK, 1971. (2) N. Verma, et al. Plant Pathol. 55:442, 2006.
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Affiliation(s)
- C N Xu
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125199, China
| | - Z S Zhou
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125199, China
| | - Y X Wu
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125199, China
| | - F M Chi
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125199, China
| | - Z R Ji
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125199, China
| | - H J Zhang
- Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, 125199, China
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Abstract
Modification of small molecules and proteins by methyltransferases impacts a wide range of biological processes. Here we report two methods for measuring methyltransferase activity. First we describe an enzyme-coupled continuous spectrophotometric assay used to quantitatively characterize S-adenosyl-L-methionine (AdoMet or SAM)-dependent methyltransferase activity. In this assay, S-adenosyl-L-homocysteine (AdoHcy or SAH), the transmethylation product of AdoMet-dependent methyltransferase, is hydrolyzed to S-ribohomocysteine and adenine by recombinant AdoHcy nucleosidase. Subsequently, the adenine generated from AdoHcy is further hydrolyzed to homoxanthine and ammonia by recombinant adenine deaminase. This deamination is associated with a decrease in absorbance at 265 nm that can be monitored continuously. Secondly, we describe a discontinuous assay that follows radiolabel incorporation into the methyl receptor. An advantage of both assays is the destruction of AdoHcy by AdoHcy nucleosidase, which alleviates AdoHcy product feedback inhibition of S-adenosylmethionine-dependent methyltransferases. Importantly both methods are inexpensive, robust, and amenable to high throughput.
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Affiliation(s)
- Whitney L Wooderchak
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
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29
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Dai S, Ni W, Patananan AN, Clarke SG, Karger BL, Zhou ZS. Integrated proteomic analysis of major isoaspartyl-containing proteins in the urine of wild type and protein L-isoaspartate O-methyltransferase-deficient mice. Anal Chem 2013; 85:2423-30. [PMID: 23327623 DOI: 10.1021/ac303428h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The formation of isoaspartyl residues (isoAsp or isoD) via either aspartyl isomerization or asparaginyl deamidation alters protein structure and potentially biological function. This is a spontaneous and nonenzymatic process, ubiquitous both in vivo and in nonbiological systems, such as in protein pharmaceuticals. In almost all organisms, protein L-isoaspartate O-methyltransferase (PIMT, EC2.1.1.77) recognizes and initiates the conversion of isoAsp back to aspartic acid. Additionally, alternative proteolytic and excretion pathways to metabolize isoaspartyl-containing proteins have been proposed but not fully explored, largely due to the analytical challenges for detecting isoAsp. We report here the relative quantitation and site profiling of isoAsp in urinary proteins from wild type and PIMT-deficient mice, representing products from excretion pathways. First, using a biochemical approach, we found that the total isoaspartyl level of proteins in urine of PIMT-deficient male mice was elevated. Subsequently, the major isoaspartyl protein species in urine from these mice were identified as major urinary proteins (MUPs) by shotgun proteomics. To enhance the sensitivity of isoAsp detection, a targeted proteomic approach using electron transfer dissociation-selected reaction monitoring (ETD-SRM) was developed to investigate isoAsp sites in MUPs. A total of 38 putative isoAsp modification sites in MUPs were investigated, with five derived from the deamidation of asparagine that were confirmed to contribute to the elevated isoAsp levels. Our findings lend experimental evidence for the hypothesized excretion pathway for isoAsp proteins. Additionally, the developed method opens up the possibility to explore processing mechanisms of isoaspartyl proteins at the molecular level, such as the fate of protein pharmaceuticals in circulation.
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Affiliation(s)
- Shujia Dai
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston Massachusetts 02115, United States
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30
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Gui S, Wooderchak-Donahue WL, Zang T, Chen D, Daly MP, Zhou ZS, Hevel JM. Substrate-Induced Control of Product Formation by Protein Arginine Methyltransferase 1. Biochemistry 2012; 52:199-209. [DOI: 10.1021/bi301283t] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shanying Gui
- Chemistry
and Biochemistry Department, Utah State University, 0300 Old Main Hill, Logan, Utah
84322, United States
| | | | - Tianzhu Zang
- The
Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston,
Massachusetts 02115-5000, United States
| | - Dong Chen
- Synthetic Bio-manufacturing Institute, Utah State University, 620 East 1600 North, Suite 226,
Logan, Utah 84341, United States
| | - Michael P. Daly
- Waters Corporation, 100 Cummings Center,
Suite 407N, Beverly, Massachusetts 01915,
United States
| | - Zhaohui Sunny Zhou
- The
Barnett Institute of Chemical
and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston,
Massachusetts 02115-5000, United States
| | - Joan M. Hevel
- Chemistry
and Biochemistry Department, Utah State University, 0300 Old Main Hill, Logan, Utah
84322, United States
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31
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Tian S, Yu Q, Xin L, Zhou ZS, Upur H. Chemical Fingerprinting by RP-RRLC-DAD and Principal Component Analysis of Ziziphora clinopodioides from Different Locations. Nat Prod Commun 2012. [DOI: 10.1177/1934578x1200700919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
An efficient and accurate fingerprinting method using reversed-phase rapid-resolution liquid-chromatography coupled with photodiode array detection has been developed and optimized to examine the variance in active compounds among Ziziphora clinopodioides Lam from different locations. Three active components, diosmin, linarin and pulegone, were identified by matching their retention times and UV spectra with the corresponding reference compounds. Our results indicated that chromatographic fingerprints, in combination with principal component analysis (PCA) and hierarchical clustering analysis (HCA), could efficiently identify and distinguish Z. clinopodioides from different sources. Our fingerprinting methods and data will be useful for quality control, and thus, more effective dosing in clinical application of Z. clinopodioides.
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Affiliation(s)
- Shuge Tian
- Xinjiang Key Laboratory of Famous Prescription and Science of Formulas, Urumqi-830011, Xinjiang, China
- College of TCM, Xinjiang Medical University, Urumqi-830011, Xinjiang, China
| | - Qian Yu
- Xinjiang Key Laboratory of Famous Prescription and Science of Formulas, Urumqi-830011, Xinjiang, China
- College of TCM, Xinjiang Medical University, Urumqi-830011, Xinjiang, China
| | - Lude Xin
- Xinjiang Key Laboratory of Famous Prescription and Science of Formulas, Urumqi-830011, Xinjiang, China
- College of TCM, Xinjiang Medical University, Urumqi-830011, Xinjiang, China
| | - Zhaohui Sunny Zhou
- The Barnett Institute of Chemical and Biological Analysis and the Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115 USA
| | - Halmuart· Upur
- Xinjiang Key Laboratory of Famous Prescription and Science of Formulas, Urumqi-830011, Xinjiang, China
- College of TCM, Xinjiang Medical University, Urumqi-830011, Xinjiang, China
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32
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Tiana S, Yu Q, Xin L, Zhou ZS, Upur H. Chemical fingerprinting by RP-RRLC-DAD and principal component analysis of Ziziphora clinopodioides from different locations. Nat Prod Commun 2012; 7:1181-1184. [PMID: 23074902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
An efficient and accurate fingerprinting method using reversed-phase rapid-resolution liquid-chromatography coupled with photodiode array detection has been developed and optimized to examine the variance in active compounds among Ziziphora clinopodioides Lam from different locations. Three active components, diosmin, linarin and pulegone, were identified by matching their retention times and UV spectra with the corresponding reference compounds. Our results indicated that chromatographic fingerprints, in combination with principal component analysis (PCA) and hierarchical clustering analysis (HCA), could efficiently identify and distinguish Z. clinopodioides from different sources. Our fingerprinting methods and data will be useful for quality control, and thus, more effective dosing in clinical application of Z. clinopodioides.
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Affiliation(s)
- Shuge Tiana
- Xinjiang Key Laboratory of Famous Prescription and Science of Formulas, Urumqi-830011, Xinjiang, China.
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33
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Cheng J, Jiang SW, Zhang LZ, Zhou ZS, Li JB, Li X, Sun QL. Acute hepatitis C infection with unclear route of transmission. W INDIAN MED J 2012; 61:202-203. [PMID: 23155971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A 43-year old man acquired acute hepatitis C virus (HCV) infection with unclear route of transmission. There were no known sexual or other risk factors for HCV acquisition. Phylogenetic analysis confirmed that the case was infected with identical genotype 1b strain. After symptomatic treatment for three weeks, the HCV was spontaneously cleared and liver function recovered.
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Affiliation(s)
- J Cheng
- Department of Infectious Diseases, the First Affiliated Hospital of Anhui Medical University, 230022, Hefei, Anhui Province, China
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34
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Liu M, Cheetham J, Cauchon N, Ostovic J, Ni W, Ren D, Zhou ZS. Protein Isoaspartate Methyltransferase-Mediated 18O-Labeling of Isoaspartic Acid for Mass Spectrometry Analysis. Anal Chem 2011; 84:1056-62. [DOI: 10.1021/ac202652z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Min Liu
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, California
91320, United States
- Department
of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115, United States
- Barnett Institute of Chemical
and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Janet Cheetham
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, California
91320, United States
| | - Nina Cauchon
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, California
91320, United States
| | - Judy Ostovic
- Analytical Research and Development, Amgen, One Amgen Center Drive, Thousand Oaks, California
91320, United States
| | - Wenqin Ni
- Department
of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115, United States
- Barnett Institute of Chemical
and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Da Ren
- Process and Product Development, Amgen, One Amgen Center Drive, Thousand Oaks, California
91320, United States
| | - Zhaohui Sunny Zhou
- Department
of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115, United States
- Barnett Institute of Chemical
and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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35
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Ni W, Dai S, Karger BL, Zhou ZS. Analysis of isoaspartic Acid by selective proteolysis with Asp-N and electron transfer dissociation mass spectrometry. Anal Chem 2011; 82:7485-91. [PMID: 20712325 DOI: 10.1021/ac101806e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A ubiquitous yet underappreciated protein post-translational modification, isoaspartic acid (isoAsp, isoD, or beta-Asp), generated via the deamidation of asparagine or isomerization of aspartic acid in proteins, plays a diverse and crucial role in aging, as well as autoimmune, cancer, neurodegeneration, and other diseases. In addition, formation of isoAsp is a major concern in protein pharmaceuticals, as it may lead to aggregation or activity loss. The scope and significance of isoAsp have, up to now, not been fully explored, as an unbiased screening of isoAsp at low abundance remains challenging. This difficulty is due to the subtle difference in the physicochemical properties between isoAsp and Asp, e.g., identical mass. In contrast, endoprotease Asp-N (EC 3.4.24.33) selectively cleaves aspartyl peptides but not the isoaspartyl counterparts. As a consequence, isoaspartyl peptides can be differentiated from those containing Asp and also enriched by Asp-N digestion. Subsequently, the existence and site of isoaspartate can be confirmed by electron transfer dissociation (ETD) mass spectrometry. As little as 0.5% of isoAsp was detected in synthetic beta-amyloid and cytochrome c peptides, even though both were initially assumed to be free of isoAsp. Taken together, our approach should expedite the unbiased discovery of isoAsp.
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Affiliation(s)
- Wenqin Ni
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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36
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Chen T, Nayak N, Majee SM, Lowenson J, Schäfermeyer KR, Eliopoulos AC, Lloyd TD, Dinkins R, Perry SE, Forsthoefel NR, Clarke SG, Vernon DM, Zhou ZS, Rejtar T, Downie AB. Substrates of the Arabidopsis thaliana protein isoaspartyl methyltransferase 1 identified using phage display and biopanning. J Biol Chem 2010; 285:37281-92. [PMID: 20870712 DOI: 10.1074/jbc.m110.157008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The role of protein isoaspartyl methyltransferase (PIMT) in repairing a wide assortment of damaged proteins in a host of organisms has been inferred from the affinity of the enzyme for isoaspartyl residues in a plethora of amino acid contexts. The identification of PIMT target proteins in plant seeds, where the enzyme is highly active and proteome long-lived, has been hindered by large amounts of isoaspartate-containing storage proteins. Mature seed phage display libraries circumvented this problem. Inclusion of the PIMT co-substrate, S-adenosylmethionine (AdoMet), during panning permitted PIMT to retain aged phage in greater numbers than controls lacking co-substrate or when PIMT protein binding was poisoned with S-adenosyl homocysteine. After four rounds, phage titer plateaued in AdoMet-containing pans, whereas titer declined in both controls. This strategy identified 17 in-frame PIMT target proteins, including a cupin-family protein similar to those identified previously using on-blot methylation. All recovered phage had at least one susceptible Asp or Asn residue. Five targets were recovered independently. Two in-frame targets were produced in Escherichia coli as recombinant proteins and shown by on-blot methylation to acquire isoAsp, becoming a PIMT target. Both gained isoAsp rapidly in solution upon thermal insult. Mutant analysis of plants deficient in any of three in-frame PIMT targets resulted in demonstrable phenotypes. An over-representation of clones encoding proteins involved in protein production suggests that the translational apparatus comprises a subgroup for which PIMT-mediated repair is vital for orthodox seed longevity. Impaired PIMT activity would hinder protein function in these targets, possibly resulting in poor seed performance.
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Affiliation(s)
- Tingsu Chen
- Department of Horticulture, University of Kentucky, Lexington, Kentucky 40546-0312, USA
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37
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Lee BWK, Sun HG, Zang T, Kim BJ, Alfaro JF, Zhou ZS. Enzyme-catalyzed transfer of a ketone group from an S-adenosylmethionine analogue: a tool for the functional analysis of methyltransferases. J Am Chem Soc 2010; 132:3642-3. [PMID: 20196537 DOI: 10.1021/ja908995p] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
S-adenosylmethionine (AdoMet or SAM)-dependent methyltransferases belong to a large and diverse family of group-transfer enzymes that perform vital biological functions on a host of substrates. Despite the progress in genomics, structural proteomics, and computational biology, functional annotation of methyltransferases remains a challenge. Herein, we report the synthesis and activity of a new AdoMet analogue functionalized with a ketone group. Using catechol O-methyltransferase (COMT, EC 2.1.1.6) and thiopurine S-methyltransferase (TPMT, EC 2.1.1.67) as model enzymes, this robust and readily accessible analogue displays kinetic parameters that are comparable to AdoMet and exhibits multiple turnovers with enzyme. More importantly, this AdoMet surrogate displays the same substrate specificity as the natural methyl donor. Incorporation of the ketone group allows for subsequent modification via bio-orthogonal labeling strategies and sensitive detection of the tagged ketone products. Hence, this AdoMet analogue expands the toolbox available to interrogate the biochemical functions of methyltransferases.
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Affiliation(s)
- Bobby W K Lee
- The Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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38
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Liu M, Ronk M, Ren D, Ostovic J, Cauchon N, Zhou ZS, Cheetham J. Structure elucidation of highly polar basic degradants by on-line hydrogen/deuterium exchange hydrophilic interaction chromatography coupled to tandem mass spectrometry. J Chromatogr A 2010; 1217:3598-611. [DOI: 10.1016/j.chroma.2010.03.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 03/16/2010] [Accepted: 03/23/2010] [Indexed: 10/19/2022]
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39
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Wang Z, Rejtar T, Zhou ZS, Karger BL. Desulfurization of cysteine-containing peptides resulting from sample preparation for protein characterization by mass spectrometry. Rapid Commun Mass Spectrom 2010; 24:267-75. [PMID: 20049891 PMCID: PMC2908508 DOI: 10.1002/rcm.4383] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In this study, we have examined two cysteine modifications resulting from sample preparation for protein characterization by mass spectrometry (MS): (1) a previously observed conversion of cysteine into dehydroalanine, now found in the case of disulfide mapping and (2) a novel modification corresponding to conversion of cysteine into alanine. Using model peptides, the conversion of cysteine into dehydroalanine via beta-elimination of a disulfide bond was seen to result from the conditions of typical tryptic digestion (37 degrees C, pH 7.0-9.0) without disulfide reduction and alkylation. Furthermore, the surprising conversion of cysteine into alanine was shown to occur by heating cysteine-containing peptides in the presence of a phosphine (tris(2-carboxyethyl)phosphine hydrochloride (TCEP)). The formation of alanine from cysteine, investigated by performing experiments in H(2)O or D(2)O, suggested a radical-based desulfurization mechanism unrelated to beta-elimination. Importantly, an understanding of the mechanism and conditions favorable for cysteine desulfurization provides insight for the establishment of improved sample preparation procedures of protein analysis.
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Kong P, Lee BWK, Zhou ZS, Hong C. Zoosporic plant pathogens produce bacterial autoinducer-2 that affects Vibrio harveyi quorum sensing. FEMS Microbiol Lett 2009; 303:55-60. [PMID: 20002192 DOI: 10.1111/j.1574-6968.2009.01861.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The frequent coisolation of bacteria with Phytophthora and Pythium species suggests possible interspecies communication. Zoospore-free fluids (ZFF) from bacteria-free and nutrient-depleted zoospore suspensions were examined to investigate the production of autoinducer-2 (AI-2), a bacterial interspecies signal molecule, by zoosporic oomycetes. ZFF from Phytophthora nicotianae, Phytophthora sojae, and Pythium aphanidermatum triggered luminescence of the Vibrio harve7yi AI-2 reporter, indicating the presence of AI-2 in zoospore extracellular products and the potential of cross-kingdom communication between oomycetes and bacteria. The production of AI-2 by zoospores was confirmed by chemical assays. These results provide a new insight into the physiology and ecology of oomycetes.
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Affiliation(s)
- Ping Kong
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Virginia Beach, VA 23455-3363, USA
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41
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Zang T, Dai S, Chen D, Lee BWK, Liu S, Karger BL, Zhou ZS. Chemical methods for the detection of protein N-homocysteinylation via selective reactions with aldehydes. Anal Chem 2009; 81:9065-71. [PMID: 19874060 PMCID: PMC2771319 DOI: 10.1021/ac9017132] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Elevated blood levels of homocysteine (Hcy), hyperhomocysteinemia or homocystinuria, have been associated with various diseases and conditions. Homocysteine thiolactone (Hcy TL) is a metabolite of Hcy and reacts with amine groups in proteins to form stable amides, homocystamides, or N-homocysteinylated proteins. It has been proposed that protein N-homocysteinylation contributes to the cytotoxicity of elevated Hcy. Due to its heterogeneity and relatively low abundance, detection of this posttranslational modification remains challenging. On the other hand, the gamma-aminothiol group in homocystamides imparts different chemical reactivities than the native proteins. Under mildly acidic conditions, gamma-aminothiols irreversibly and stoichiometrically react with aldehydes to form stable 1,3-thiazines, whereas the reversible Schiff base formation between aldehydes and amino groups in native proteins is markedly disfavored due to protonation of amines. As such, we have developed highly selective chemical methods to derivatize N-homocysteinylated proteins with various aldehyde tags, thereby facilitating the subsequent analyses. For instance, fluorescent or biotin tagging coupled with gel electrophoresis permits quantification and global profiling of complex biological samples, such as hemoglobin and plasma from rat, mouse and human; affinity enrichment with aldehyde resins drastically reduces sample complexity. In addition, different reactivities of lysine residues in hemoglobin toward Hcy TL were observed.
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Affiliation(s)
- Tianzhu Zang
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Shujia Dai
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Dajun Chen
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Bobby W. K. Lee
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Suli Liu
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Barry L. Karger
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
| | - Zhaohui Sunny Zhou
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115
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42
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Zang T, Lee BWK, Cannon LM, Ritter KA, Dai S, Ren D, Wood TK, Zhou ZS. A naturally occurring brominated furanone covalently modifies and inactivates LuxS. Bioorg Med Chem Lett 2009; 19:6200-4. [PMID: 19775890 DOI: 10.1016/j.bmcl.2009.08.095] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 08/26/2009] [Accepted: 08/31/2009] [Indexed: 11/20/2022]
Abstract
Halogenated furanones, a group of natural products initially isolated from marine red algae, are known to inhibit bacterial biofilm formation, swarming, and quorum sensing. However, their molecular targets and the precise mode of action remain elusive. Herein, we show that a naturally occurring brominated furanone covalently modifies and inactivates LuxS (S-ribosylhomocysteine lyase, EC 4.4.1.21), the enzyme which produces autoinducer-2 (AI-2).
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Affiliation(s)
- Tianzhu Zang
- The Barnett Institute and the Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
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43
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Wooderchak WL, Zang T, Zhou ZS, Acuña M, Tahara SM, Hevel JM. Substrate Profiling of PRMT1 Reveals Amino Acid Sequences That Extend Beyond the “RGG” Paradigm. Biochemistry 2008; 47:9456-66. [DOI: 10.1021/bi800984s] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Whitney L. Wooderchak
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Tianzhu Zang
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Zhaohui Sunny Zhou
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Marcela Acuña
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Stanley M. Tahara
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
| | - Joan M. Hevel
- Chemistry and Biochemistry Department, Utah State University,
0300 Old Main Hill, Logan, Utah 84322, The Barnett Institute of Chemical
and Biological Analysis and Department of Chemistry and Chemical Biology,
Northeastern University, 360 Huntington Avenue, Boston, Massachusetts
02115-5000, Molecular Microbiology and Neurology, University of Southern
California School of Medicine, 2011 Zonal Avenue, Los Angeles, California
90033, and Affiliate of the Center for Integrated Biosystems, Utah
State University
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44
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Alfaro JF, Gillies LA, Sun HG, Dai S, Zang T, Klaene JJ, Kim BJ, Lowenson JD, Clarke SG, Karger BL, Zhou ZS. Chemo-enzymatic detection of protein isoaspartate using protein isoaspartate methyltransferase and hydrazine trapping. Anal Chem 2008; 80:3882-9. [PMID: 18419136 DOI: 10.1021/ac800251q] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isoaspartate formation is a ubiquitous post-translation modification arising from spontaneous asparagine deamidation or aspartate isomerization. The formation of isoaspartate inserts a methylene group into the protein backbone, generating a "kink", and may drastically alter protein structure and function, thereby playing critical roles in a myriad of biological processes, human diseases, and protein pharmaceutical development. Herein, we report a chemo-enzymatic detection method for the isoaspartate protein, which in particular allows the affinity enrichment of isoaspartate-containing proteins. In the initial step, protein isoaspartate methyltransferase selectively converts isoaspartates into the corresponding methyl esters. Subsequently, the labile methyl ester is trapped by strong nucleophiles in aqueous solutions, such as hydrazines to form hydrazides. The stable hydrazide products can be analyzed by standard proteomic techniques, such as matrix-assisted laser desorption ionization and electrospray ionization mass spectrometry. Furthermore, the chemical trapping step allows us to introduce several tagging strategies for product identification and quantification, such as UV-vis and fluorescence detection through a dansyl derivative. Most significantly, the hydrazide product can be enriched by affinity chromatography using aldehyde resins, thus drastically reducing sample complexity. Our method hence represents the first technique for the affinity enrichment of isoaspartyl proteins and should be amendable to the systematic and comprehensive characterization of isoaspartate, particularly in complex systems.
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Affiliation(s)
- Joshua F Alfaro
- Department of Chemistry, Washington State University, Pullman, Washington 99164, USA
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45
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Biastoff S, Teuber M, Zhou ZS, Dräger B. Colorimetric activity measurement of a recombinant putrescine N-methyltransferase from Datura stramonium. Planta Med 2006; 72:1136-41. [PMID: 16924584 DOI: 10.1055/s-2006-947191] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Putrescine N-methyltransferase (PMT, EC 2.1.1.53) catalyses the S-adenosyl- L-methionine (SAM or AdoMet)-dependent methylation of putrescine to N-methylputrescine within the biosynthetic pathways of calystegines, nicotine, and tropane alkaloids in medicinal plants and produces S-adenosyl- L-homocysteine (SAH or AdoHcy). Determination of PMT activity was time-consuming and hardly reproducible in the past because it required tedious separation steps after chemical derivatisation or radioactive labelling of N-methylputrescine. A convenient and accurate enzyme-coupled colorimetric assay is based on the conversion of SAH to homocysteine by 5'-methylthioadenosine/ S-adenosylhomocysteine nucleosidase (MTAN/SAHN, EC 3.2.2.9) and S-ribosylhomocysteine lyase (LuxS, EC 4.4.1.21). Homocysteine is quantified by 5,5'-dithiobis-2-nitrobenzoic acid. Putrescine was shown not to interfere with MTAN or LuxS. The colorimetric assay was validated by HPLC analysis. K(m) values determined by the assay, 108 microM for putrescine and 42 microM for SAM, are lower than the previously reported values, due to alleviation of PMT inhibition by SAH. DTNB:5,5'-dithiobis-2-nitrobenzoic acid LuxS: S-ribosylhomocysteine lyase MTAN:5'-methylthioadenosine nucleosidase PMT:putrescine N-methyltransferase SAH: S-adenosyl- L-homocysteine SAM: S-adenosyl- L-methionine TNB:2-nitro-5-thiobenzoic acid.
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Affiliation(s)
- Stefan Biastoff
- Institute of Pharmaceutical Biology and Pharmacology, Martin-Luther-University Halle-Wittenberg, Halle/Saale, Germany
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46
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Mosley SL, Bakke BA, Sadler JM, Sunkara NK, Kathleen MD, Zhou ZS, Seley-Radtke KL. Carbocyclic pyrimidine nucleosides as inhibitors of S-adenosylhomocysteine hydrolase. Bioorg Med Chem 2006; 14:7967-71. [PMID: 16904326 PMCID: PMC1702506 DOI: 10.1016/j.bmc.2006.07.052] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 07/14/2006] [Accepted: 07/26/2006] [Indexed: 11/23/2022]
Abstract
The design, synthesis, and unexpected inhibitory activity against S-adenosyl-homocysteine (SAH) hydrolase (SAHase, EC 3.3.1.1) for a series of truncated carbocyclic pyrimidine nucleoside analogues is presented. Of the four nucleosides obtained, 10 was found to be active with a Ki value of 5.0 microM against SAHase.
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Affiliation(s)
- Sylvester L. Mosley
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Brian A. Bakke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Joshua M. Sadler
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - Naresh K. Sunkara
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
| | - M. Dorgan Kathleen
- Department of Chemistry, Washington State University, Pullman, WA 99164 USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry, Washington State University, Pullman, WA 99164 USA
| | - Katherine L. Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250 USA
- *Corresponding author: Tel. +1-410-455-8684; fax: +1-410-455-2608;
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47
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Wooderchak WL, Dorgan KM, Karschner EL, Wynn DP, Alfaro JF, Cui Y, Zhou ZS, Hevel JM. Continuous assay measures methyltransferase activity: Defining the substrate specificity of rat Protein Arginine Methyltransferase 1 (PRMT1). FASEB J 2006. [DOI: 10.1096/fasebj.20.5.lb50-c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Whitney Lyn Wooderchak
- Chemistry and Biochemistry DepartmentUtah State University0300 Old Main HillLoganUtah84322
| | - Kathy M. Dorgan
- Department of ChemistryWashington State University470 Fulmer HallPullmanWashington99164
| | - Erin L. Karschner
- Departments of Chemistry and BiologyLycoming College700 College PlaceWilliamsportPA17701
| | - DonRaphael P. Wynn
- Department of ChemistryWashington State University470 Fulmer HallPullmanWashington99164
| | - Joshua F. Alfaro
- Department of ChemistryWashington State University470 Fulmer HallPullmanWashington99164
| | - Yinqiu Cui
- Department of ChemistryWashington State University470 Fulmer HallPullmanWashington99164
| | - Zhaohui Sunny Zhou
- Department of ChemistryWashington State University470 Fulmer HallPullmanWashington99164
| | - Joan M. Hevel
- Chemistry and Biochemistry DepartmentUtah State University0300 Old Main HillLoganUtah84322
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48
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Dorgan KM, Wooderchak WL, Wynn DP, Karschner EL, Alfaro JF, Cui Y, Zhou ZS, Hevel JM. An enzyme-coupled continuous spectrophotometric assay for S-adenosylmethionine-dependent methyltransferases. Anal Biochem 2006; 350:249-55. [PMID: 16460659 DOI: 10.1016/j.ab.2006.01.004] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2005] [Revised: 12/30/2005] [Accepted: 01/04/2006] [Indexed: 10/25/2022]
Abstract
Modification of small molecules and proteins by methyltransferases affects a wide range of biological processes. Here, we report an enzyme-coupled continuous spectrophotometric assay to quantitatively characterize S-adenosyl-L-methionine (AdoMet/SAM)-dependent methyltransferase activity. In this assay, S-adenosyl-L-homocysteine (AdoHcy/SAH), the transmethylation product of AdoMet-dependent methyltransferases, is hydrolyzed to S-ribosylhomocysteine and adenine by recombinant S-adenosylhomocysteine/5'-methylthioadenosine nucleosidase (SAHN/MTAN, EC 3.2.2.9). Subsequently, adenine generated from AdoHcy is further hydrolyzed to hypoxanthine and ammonia by recombinant adenine deaminase (EC 3.5.4.2). This deamination is associated with a decrease in absorbance at 265 nm that can be monitored continuously. Coupling enzymes are recombinant and easily purified. The utility of this assay was shown using recombinant rat protein arginine N-methyltransferase 1 (PRMT1, EC 2.1.1.125), which catalyzes the mono- and dimethylation of guanidino nitrogens of arginine residues in select proteins. Using this assay, the kinetic parameters of PRMT1 with three synthetic peptides were determined. An advantage of this assay is the destruction of AdoHcy by AdoHcy nucleosidase, which alleviates AdoHcy product feedback inhibition of S-adenosylmethionine-dependent methyltransferases. Finally, this method may be used to assay other enzymes that produce AdoHcy, 5'-methylthioadenosine, or compounds that can be cleaved by AdoHcy nucleosidase.
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Affiliation(s)
- Kathleen M Dorgan
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA
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49
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Abstract
[reaction: see text] Quorum sensing is a process by which bacteria sense cell density. This cell-cell communication process is mediated by autoinducers. A cross-species messenger, autoinducer-2 (AI-2) is produced from S-ribosyl-L-homocysteine by the LuxS enzyme. A proposed mechanism for LuxS is an aldose-ketose isomerization of S-ribosylhomocysteine followed by a beta-elimination. We report here the synthesis of two substrate analogues, S-anhydroribosyl-L-homocysteine and S-homoribosyl-L-cysteine, which prevent the initial and final step of the mechanism, respectively.
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Affiliation(s)
- Joshua F Alfaro
- Department of Chemistry, School of Molecular Biosciences, Center for Integrated Biotechnology, Graduate Program in Pharmacology and Toxicology, Washington State University, Pullman, Washington 99164-4630, USA
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50
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Hendricks CL, Ross JR, Pichersky E, Noel JP, Zhou ZS. An enzyme-coupled colorimetric assay for S-adenosylmethionine-dependent methyltransferases. Anal Biochem 2004; 326:100-5. [PMID: 14769341 DOI: 10.1016/j.ab.2003.11.014] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2003] [Indexed: 10/26/2022]
Abstract
We report here an enzyme-coupled colorimetric assay for salicylic acid carboxyl methyltransferase (SAMT), which utilizes S-adenosyl-l-methionine (AdoMet or SAM) as the methyl donor. In this assay, S-adenosyl-l-homocysteine (AdoHcy or SAH), a common product of AdoMet-dependent transmethylation reactions, is first hydrolyzed by recombinant AdoHcy nucleosidase (EC 3.2.2.9) into adenine and S-ribosylhomocysteine. Recombinant LuxS (S-ribosylhomocysteinase, EC 3.2.1.148) cleaves the latter compound to form homocysteine. Finally, homocysteine is quantified using Ellman's reagent and the accompanying absorption change at 412nm through recording using a microplate format. Notably, SAMT and most AdoMet-dependent methyltransferases undergo marked AdoHcy-mediated product inhibition. As such, an additional advantage of this assay which includes AdoHcy nucleosidase is the destruction of AdoHcy, thus alleviating product inhibition. Under our assay conditions, complete substrate conversion is observed and precise kinetic parameters can be determined in a facile and quantitative manner. This assay should be generally applicable to other AdoMet-dependent methyltransferases. Moreover, the procedure is easily amendable to batch assay and high-throughput screening approaches.
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Affiliation(s)
- Cheryl L Hendricks
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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