1
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Garcia-Montojo M, Fathi S, Rastegar C, Simula ER, Doucet-O'Hare T, Cheng YHH, Abrams RPM, Pasternack N, Malik N, Bachani M, Disanza B, Maric D, Lee MH, Wang H, Santamaria U, Li W, Sampson K, Lorenzo JR, Sanchez IE, Mezghrani A, Li Y, Sechi LA, Pineda S, Heiman M, Kellis M, Steiner J, Nath A. TDP-43 proteinopathy in ALS is triggered by loss of ASRGL1 and associated with HML-2 expression. Nat Commun 2024; 15:4163. [PMID: 38755145 PMCID: PMC11099023 DOI: 10.1038/s41467-024-48488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
TAR DNA-binding protein 43 (TDP-43) proteinopathy in brain cells is the hallmark of amyotrophic lateral sclerosis (ALS) but its cause remains elusive. Asparaginase-like-1 protein (ASRGL1) cleaves isoaspartates, which alter protein folding and susceptibility to proteolysis. ASRGL1 gene harbors a copy of the human endogenous retrovirus HML-2, whose overexpression contributes to ALS pathogenesis. Here we show that ASRGL1 expression was diminished in ALS brain samples by RNA sequencing, immunohistochemistry, and western blotting. TDP-43 and ASRGL1 colocalized in neurons but, in the absence of ASRGL1, TDP-43 aggregated in the cytoplasm. TDP-43 was found to be prone to isoaspartate formation and a substrate for ASRGL1. ASRGL1 silencing triggered accumulation of misfolded, fragmented, phosphorylated and mislocalized TDP-43 in cultured neurons and motor cortex of female mice. Overexpression of ASRGL1 restored neuronal viability. Overexpression of HML-2 led to ASRGL1 silencing. Loss of ASRGL1 leading to TDP-43 aggregation may be a critical mechanism in ALS pathophysiology.
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Affiliation(s)
- Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Saeed Fathi
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Cyrus Rastegar
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Elena Rita Simula
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | - Tara Doucet-O'Hare
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Y H Hank Cheng
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rachel P M Abrams
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nasir Malik
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Muzna Bachani
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Brianna Disanza
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Dragan Maric
- Flow and Imaging Cytometry Core Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Myoung-Hwa Lee
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Herui Wang
- Neuro-Oncology Branch, National Cancer Institute (NIH), Bethesda, MD, USA
| | - Ulisses Santamaria
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kevon Sampson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Juan Ramiro Lorenzo
- Centro de Investigación Veterinaria de Tandil (CIVETAN), CONICET-CICPBA-UNCPBA, Facultad de Ciencias Veterinarias, Universidad Nacional del Centro (FCV-UNCPBA), Tandil, Argentina
| | - Ignacio E Sanchez
- Protein Physiology Laboratory, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales and IQUIBICEN-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alexandre Mezghrani
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
- Centre de Biologie Structurale, Centre national de la recherche scientifique (CNRS), Montpellier, France
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Leonardo Antonio Sechi
- Struttura Complessa Microbiologia e Virologia, Azienda Ospedaliera Universitaria Sassari, Sassari, Italy
| | | | - Myriam Heiman
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Manolis Kellis
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joseph Steiner
- Translational Neuroscience Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, USA.
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2
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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] [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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3
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Wu HT, Van Orman BL, Julian RR. Localizing Isomerized Residue Sites in Peptides with Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:705-713. [PMID: 38440975 PMCID: PMC10995990 DOI: 10.1021/jasms.3c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/06/2024]
Abstract
Isomerized amino acid residues have been identified in many peptides extracted from tissues or excretions of humans and animals. These isomerized residues can play key roles by affecting biological activity or by exerting an influence on the process of aging. Isomerization occurs spontaneously and does not result in a mass shift. Thus, identifying and localizing isomerized residues in biological samples is challenging. Herein, we introduce a fast and efficient method using tandem mass spectrometry (MS) to locate isomerized residues in peptides. Although MS2 spectra are useful for identifying peptides that contain an isomerized residue, they cannot reliably localize isomerization sites. We show that this limitation can be overcome by utilizing MS3 experiments to further evaluate each fragment ion from the MS2 stage. Comparison at the MS3 level, utilizing statistical analyses, reveals which MS2 fragments differ between samples and, therefore, must contain the isomerized sites. The approach is similar to previous work relying on ion mobility to discriminate MS2 product ions by collision cross-section. The MS3 approach can be implemented using either ion-trap or beam-type collisional activation and is compatible with the quantification of isomer mixtures when coupled to a calibration curve. The method can also be implemented in combination with liquid chromatography in a targeted approach. Enabling the identification and localization of isomerized residues in peptides with an MS-only methodology will expand accessibility to this important information.
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Affiliation(s)
- Hoi-Ting Wu
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Brielle L. Van Orman
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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4
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Miyagi M, Kiesel E, Neumbo K, Nakazawa T. Deuterium Labeling of Isoaspartic and Isoglutamic Acids for Mass Spectrometry Analysis. Anal Chem 2024; 96:3077-3086. [PMID: 38344941 PMCID: PMC10984558 DOI: 10.1021/acs.analchem.3c05194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 04/02/2024]
Abstract
Isoaspartic acid (isoAsp) is a common protein modification that spontaneously arises from asparagine or aspartic acid and has been linked to various diseases and health conditions. However, current methods for identifying isoAsp sites in proteins often suffer from ambiguity and have not gained widespread adoption. We developed a novel method that exclusively labels isoAsp with deuterium. This method capitalizes on the unique structural characteristics of isoAsp residues, which possess a free α-carboxyl group and can form an oxazolone ring. Once the oxazolone ring forms, it facilitates racemization at the Cα-position, incorporating a deuteron from a D2O solvent. The sites of deuterium-incorporated isoAsp in proteins can be unequivocally determined by comparing the precursor and product ion masses of the peptides from proteins reacted in H2O and D2O. The effectiveness of this method has been demonstrated through its application to model proteins lysozyme and rituximab. Furthermore, we have confirmed that the isoAsp deuterium-labeling reaction efficiently labels both l- and d-isoAsp without distinction, as well as isoglutamic acid (isoGlu), for which no effective detection methods currently exist.
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Affiliation(s)
- Masaru Miyagi
- Department
of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, United States
| | - Evan Kiesel
- Department
of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, United States
| | - Kelao Neumbo
- Department
of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, United States
| | - Takashi Nakazawa
- Department
of Chemistry, Nara Women’s University, Nara 630-8506, Japan
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5
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Liu Y, VanAernum Z, Zhang Y, Gao X, Vlad M, Feng B, Cross R, Kilgore B, Newman A, Wang D, Schuessler HA, Richardson DD, Chadwick JS. LC-MS Approach to Decipher a Light Chain Chromatographic Peak Splitting of a Monoclonal Antibody. Pharm Res 2023; 40:3087-3098. [PMID: 37936013 DOI: 10.1007/s11095-023-03631-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
PURPOSE Monoclonal antibodies (mAbs), like other protein therapeutics, are prone to various forms of degradation, some of which are difficult to distinguish from the native form yet may alter potency. A generalizable LC-MS approach was developed to enable quantitative analysis of isoAsp. In-depth understanding of product quality attributes (PQAs) enables optimization of the manufacturing process, better formulation selection, and decreases risk associated with product handling in the clinic or during shipment. METHODS Reversed-phase chromatographic peak splitting was observed when a mAb was exposed to elevated temperatures. Multiple LC-MS based methods were applied to identify the reason for peak splitting. The approach involved the use of complementary HPLC columns, multiple enzymatic digestions and different MS/MS ion dissociation methods. In addition, mAb potency was measured by enzyme-linked immunosorbent assay (ELISA). RESULTS The split peaks had identical masses, and the root cause of the peak splitting was identified as isomerization of an aspartic acid located in the complementarity-determining region (CDR) of the light chain. And the early eluting and late eluting peaks were collected and performed enzymatic digestion to confirm the isoAsp enrichment in the early eluting peak. In addition, decreased potency was observed in the same heat-stressed sample, and the increased isoAsp levels in the CDR correlate well with a decrease of potency. CONCLUSION Liquid chromatography-mass spectrometry (LC-MS) has been utilized extensively to assess PQAs of biological therapeutics. In this study, a generalizable LC-MS-based approach was developed to enable identification and quantitation of the isoAsp-containing peptides.
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Affiliation(s)
- Yanjun Liu
- ProtaGene US, Inc. was Formerly BioAnalytix Inc., 4 Burlington Woods Dr., Burlington, MA, 01803, USA.
| | - Zac VanAernum
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA.
| | - Yue Zhang
- ProtaGene US, Inc. was Formerly BioAnalytix Inc., 4 Burlington Woods Dr., Burlington, MA, 01803, USA
- Biogen, 225 Binney Street, Cambridge, MA, 02142, USA
| | - Xinliu Gao
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Mariana Vlad
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Bo Feng
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Robert Cross
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Bruce Kilgore
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Alice Newman
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Dongdong Wang
- ProtaGene US, Inc. was Formerly BioAnalytix Inc., 4 Burlington Woods Dr., Burlington, MA, 01803, USA
- Takeda Pharmaceutical Company, 35 Landsdowne St, Cambridge, MA, 02139, USA
| | - Hillary A Schuessler
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Douglas D Richardson
- Analytical Research & Development, Merck & Co., Inc., 126 E. Lincoln Ave, Rahway, NJ, 07065, USA
| | - Jennifer S Chadwick
- ProtaGene US, Inc. was Formerly BioAnalytix Inc., 4 Burlington Woods Dr., Burlington, MA, 01803, USA
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6
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Crawford SA, Groegler J, Dang M, Michel C, Powell RL, Hohenstein AC, Reyes K, Haskins K, Wiles TA, Delong T. Hybrid insulin peptide isomers spontaneously form in pancreatic beta-cells from an aspartic anhydride intermediate. J Biol Chem 2023; 299:105264. [PMID: 37734557 PMCID: PMC10590738 DOI: 10.1016/j.jbc.2023.105264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Hybrid insulin peptides (HIPs) form in beta-cells when insulin fragments link to other peptides through a peptide bond. HIPs contain nongenomic amino acid sequences and have been identified as targets for autoreactive T cells in type 1 diabetes. A subgroup of HIPs, in which N-terminal amine groups of various peptides are linked to aspartic acid residues of insulin C-peptide, was detected through mass spectrometry in pancreatic islets. Here, we investigate a novel mechanism that leads to the formation of these HIPs in human and murine islets. Our research herein shows that these HIPs form spontaneously in beta-cells through a mechanism involving an aspartic anhydride intermediate. This mechanism leads to the formation of a regular HIP containing a standard peptide bond as well as a HIP-isomer containing an isopeptide bond by linkage to the carboxylic acid side chain of the aspartic acid residue. We used mass spectrometric analyses to confirm the presence of both HIP isomers in islets, thereby validating the occurrence of this novel reaction mechanism in beta-cells. The spontaneous formation of new peptide bonds within cells may lead to the development of neoepitopes that contribute to the pathogenesis of type 1 diabetes as well as other autoimmune diseases.
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Affiliation(s)
- Samantha A Crawford
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Jason Groegler
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mylinh Dang
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cole Michel
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Roger L Powell
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Anita C Hohenstein
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA; Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kaitlin Reyes
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kathryn Haskins
- Department of Immunology and Microbiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Timothy A Wiles
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Thomas Delong
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
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7
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Bashyal A, Hui JO, Flick T, Dykstra AB, Zhang Q, Campuzano IDG, Brodbelt JS. Differentiation of Aspartic and Isoaspartic Acid Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2023; 95:11510-11517. [PMID: 37458293 PMCID: PMC10588209 DOI: 10.1021/acs.analchem.3c02025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Spontaneous conversion of aspartic acid (Asp) to isoaspartic acid (isoAsp) is a ubiquitous modification that influences the structure and function of proteins. This modification of Asp impacts the stability of biotherapeutics and has been linked to the development of neurodegenerative diseases. We explored the use of 193 nm ultraviolet photodissociation (UVPD) to distinguish Asp and isoAsp in the protonated and deprotonated peptides. The differences in the relative abundances of several fragment ions uniquely generated by UVPD were used to differentiate isomeric peptide standards containing Asp or isoAsp. These fragment ions result from the cleavage of bonds N-terminal to Asp/isoAsp residues in addition to the side-chain losses from Asp/isoAsp or the losses of COOH, CO2, CO, or H2O from y-ions. Fragmentation of Asp-containing tryptic peptides using UVPD resulted in more enhanced w/w + 1/y - 1/x ions, while isoAsp-containing peptides yielded more enhanced y - 18/y - 45/y - 46 ions. UVPD was also used to identify an isomerized peptide from a tryptic digest of a monoclonal antibody. Moreover, UVPD of a protonated nontryptic peptide resulted in more enhanced y ions N- and C-terminal to isoAsp and differences in b/y ion ratios that were used to identify the isoAsp peptide.
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Affiliation(s)
- Aarti Bashyal
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - John O Hui
- Amgen Research, Molecular Analytics, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Tawnya Flick
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Andrew B Dykstra
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Qingchun Zhang
- Process Development, Attribute Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Amgen Research, Molecular Analytics, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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8
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Zhou Y, Wang Y. Direct deamidation analysis of intact adeno-associated virus serotype 9 capsid proteins using reversed-phase liquid chromatography. Anal Biochem 2023; 668:115099. [PMID: 36871622 DOI: 10.1016/j.ab.2023.115099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 03/07/2023]
Abstract
Recombinant adeno-associated viral (AAV) vectors have taken center stage as gene delivery vehicles for gene therapy. Asparagine deamidation of AAV capsid proteins has been reported to reduce vector stability and potency of AAV gene therapy products. Deamidation of asparagine residue is a common post-translational modification of proteins that is detected and quantified by liquid chromatography-tandem mass spectrometry (LC-MS)-based peptide mapping. However, artificial deamidation can be spontaneously induced during sample preparation for peptide mapping prior to LC-MS analysis. We have developed an optimized sample preparation method to reduce and minimize deamidation artifacts induced during sample preparation for peptide mapping, which typically takes several hours to complete. To shorten turnaround time of deamidation results and to avoid artificial deamidation, we developed orthogonal RPLC-MS and RPLC-fluorescence detection methods for direct deamidation analysis at the intact AAV9 capsid protein level to routinely support downstream purification, formulation development, and stability testing. Similar trends of increasing deamidation of AAV9 capsid proteins in stability samples were observed at the intact protein level and peptide level, indicating that the developed direct deamidation analysis of intact AAV9 capsid proteins is comparable to the peptide mapping-based deamidation analysis and both methods are suitable for deamidation monitoring of AAV9 capsid proteins.
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Affiliation(s)
- Yu Zhou
- Analytical Development & Operation, Novartis Pharmaceuticals, 10210 Campus Point Drive, SanDiego, CA92121, USA.
| | - Yueju Wang
- Analytical Development & Operation, Novartis Pharmaceuticals, 10210 Campus Point Drive, SanDiego, CA92121, USA
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9
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Spanov B, Olaleye O, Mesurado T, Govorukhina N, Jungbauer A, van de Merbel NC, Lingg N, Bischoff R. Pertuzumab Charge Variant Analysis and Complementarity-Determining Region Stability Assessment to Deamidation. Anal Chem 2023; 95:3951-3958. [PMID: 36795375 PMCID: PMC9979147 DOI: 10.1021/acs.analchem.2c03275] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Pertuzumab is a monoclonal antibody used for the treatment of HER2-positive breast cancer in combination with trastuzumab. Charge variants of trastuzumab have been extensively described in the literature; however, little is known about the charge heterogeneity of pertuzumab. Here, changes in the ion-exchange profile of pertuzumab were evaluated by pH gradient cation-exchange chromatography after stressing it for up to 3 weeks at physiological and elevated pH and 37 °C. Isolated charge variants arising under stress conditions were characterized by peptide mapping. The results of peptide mapping showed that deamidation in the Fc domain and N-terminal pyroglutamate formation in the heavy chain are the main contributors to charge heterogeneity. The heavy chain CDR2, which is the only CDR containing asparagine residues, was quite resistant to deamidation under stress conditions according to peptide mapping results. Using surface plasmon resonance, it was shown that the affinity of pertuzumab for the HER2 target receptor does not change under stress conditions. Peptide mapping analysis of clinical samples showed an average of 2-3% deamidation in the heavy chain CDR2, 20-25% deamidation in the Fc domain, and 10-15% N-terminal pyroglutamate formation in the heavy chain. These findings suggest that in vitro stress studies are able to predict in vivo modifications.
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Affiliation(s)
- Baubek Spanov
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Oladapo Olaleye
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Tomés Mesurado
- Department
of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Natalia Govorukhina
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alois Jungbauer
- Department
of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Nico C. van de Merbel
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands,Bioanalytical
Laboratory, ICON, Amerikaweg 18, 9407 TK Assen, The Netherlands
| | - Nico Lingg
- Department
of Biotechnology, Institute of Bioprocess Science and Engineering, University of Natural Resources and Life Sciences,
Vienna, Muthgasse 18, Vienna 1190, Austria
| | - Rainer Bischoff
- Department
of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, A Deusinglaan 1, 9713 AV Groningen, The Netherlands,
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10
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Aki K, Okamura E. Real-Time 1H NMR reveals position and sequence dependences of amino acid isomerization in amyloid beta fragments in situ. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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11
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Liu B, Huang L, Xu R, Fan H, Wang Y. An Improved Isotope Labelling Method for Quantifying Deamidated Cobratide Using High-Resolution Quadrupole-Orbitrap Mass Spectrometry. Molecules 2022; 27:molecules27196154. [PMID: 36234709 PMCID: PMC9572859 DOI: 10.3390/molecules27196154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Protein deamidation can severely alter the physicochemical characteristics and biological functions of protein therapeutics. Cobratide is a non-addictive analgesic with wide clinical acceptance. However, the Asn residue at position 48 from the N-terminus of the cobratide amino acid sequence (N48) tends to degrade during purification, storage, and transport. This characteristic could severely affect the drug safety and clinical efficacy of cobratide. Traditional methods for quantitating deamidation reported in previous research are characterised by low efficiency and accuracy; the quality control of cobratide via this method is limited. Herein, we developed an improved 18O-labelling method based on the detection of a unique peptide (i.e., the protein fragment of cobratide containing the N48 deamidation hotspot after enzymolysis) using an Orbitrap high-resolution mass spectrometer to quantify deamidated cobratide. The limits of detection and quantification of this method reached 0.02 and 0.025 μM, respectively, and inter- and intra-day precision values of the method were <3%. The accuracy of the 18O-labelling strategy was validated by using samples containing synthesised peptides with a known ratio of deamidation impurities and also by comparing the final total deamidation results with our previously developed capillary electrophoresis method. The recoveries for deamidation (Asp), deamidation isomerisation (iso-Asp), and total deamidation were 101.52 ± 1.17, 102.42 ± 1.82, and 103.55 ± 1.07, respectively. The robustness of the method was confirmed by verifying the chromatographic parameters. Our results demonstrate the applicability of the 18O-labelling strategy for detecting protein deamidation and lay a robust foundation for protein therapeutics studies and drug quality consistency evaluations.
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Affiliation(s)
- Bo Liu
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
| | - Lu Huang
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
| | - Rongrong Xu
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
| | - Huihong Fan
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
- Correspondence:
| | - Yue Wang
- National Institutes for Food and Drug Control, 31st Huatuo Rd., Daxing Dist., Beijing 102629, China
- NMPA Key Laboratory for Quality Research and Evaluation of Chemical Drugs, Beijing 102629, China
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12
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Zhou Y, Wang Y. Sample Preparation Matters for Peptide Mapping to Evaluate Deamidation of Adeno-Associated Virus (AAV) Capsid Proteins using LC-MS/MS. Hum Gene Ther 2022; 33:821-828. [PMID: 35570652 DOI: 10.1089/hum.2021.207] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adeno-associated viral capsid proteins (AAV VP) are the major components that determine the tissue specificity and immunogenicity, and in vivo transduction performance of the vector. It was reported that asparagine deamidation of AAV capsid proteins leads to charge variants/heterogeneity and altered vector function, reduction of stability and potency of AAV gene therapy products. Deamidation of asparagine residue is a common post-translational modification of proteins and is mostly detected and quantified by liquid chromatography-tandem mass spectrometry (LC-MS/MS) based peptide mapping. However, deamidation can be spontaneously introduced during sample preparation prior to LC-MS/MS analysis. So far, no optimal sample preparations, instead, traditional sample preparation has been used for AAV VP peptide mapping, resulting in exaggerating the original deamidation levels. It is important to accurately monitor and provide true value of asparagine deamidation for development of AAV gene therapy products. In this study, we evaluated denaturation temperatures, digestion durations, and digestion temperatures using three different sample preparation formats for LC-MS/MS based assessment of deamidation of AAV9 capsid proteins. The results demonstrated that the optimal sample preparation method for AAV9 VP peptide mapping minimized asparagine deamidation artifacts. Although AAV9 was used for method optimization, this study may also provide a guidance on how to control deamidation artifacts for other AAV serotypes.
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Affiliation(s)
- Yu Zhou
- Novartis Gene Therapies, Analytical Development, 10210 Campus Point Drive, 250 Suite, San Diego, California, United States, 92121;
| | - Yueju Wang
- Novartis Gene Therapies, Analytical Development, San Diego, California, United States;
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13
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Butler KE, Dodds JN, Flick T, Campuzano IDG, Baker ES. High-Resolution Demultiplexing (HRdm) Ion Mobility Spectrometry-Mass Spectrometry for Aspartic and Isoaspartic Acid Determination and Screening. Anal Chem 2022; 94:6191-6199. [PMID: 35421308 DOI: 10.1021/acs.analchem.1c05533] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Isomeric peptide analyses are an analytical challenge of great importance to therapeutic monoclonal antibody and other biotherapeutic product development workflows. Aspartic acid (Asp, D) to isoaspartic acid (isoAsp, isoD) isomerization is a critical quality attribute (CQA) that requires careful control, monitoring, and quantitation during the drug discovery and production processes. While the formation of isoAsp has been implicated in a variety of disease states such as autoimmune diseases and several types of cancer, it is also understood that the formation of isoAsp results in a structural change impacting efficacy, potency, and immunogenic properties, all of which are undesirable. Currently, lengthy ultrahigh-performance liquid chromatography (UPLC) separations are coupled with MS for CQA analyses; however, these measurements often take over an hour and drastically limit analysis throughput. In this manuscript, drift tube ion mobility spectrometry-mass spectrometry (DTIMS-MS) and both a standard and high-resolution demultiplexing approach were utilized to study eight isomeric Asp and isoAsp peptide pairs. While the limited resolving power associated with the standard DTIMS analysis only separated three of the eight pairs, the application of HRdm distinguished seven of the eight and was only unable to separate DL and isoDL. The rapid high-throughput HRdm DTIMS-MS method was also interfaced with both flow injection and an automated solid phase extraction system to present the first application of HRdm for isoAsp and Asp assessment and demonstrate screening capabilities for isomeric peptides in complex samples, resulting in a workflow highly suitable for biopharmaceutical research needs.
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Affiliation(s)
- Karen E Butler
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Tawnya Flick
- Pivotal Attribute Sciences, Amgen Process Development, Thousand Oaks, California 91320, United States
| | - Iain D G Campuzano
- Discovery Attribute Sciences, Amgen Research, Thousand Oaks, California 91320, United States
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695, United States.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina 27695, United States
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14
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Silzel JW, Lambeth TR, Julian RR. PIMT-Mediated Labeling of l-Isoaspartic Acid with Tris Facilitates Identification of Isomerization Sites in Long-Lived Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:548-556. [PMID: 35113558 PMCID: PMC9930442 DOI: 10.1021/jasms.1c00355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Isomerization of individual residues in long-lived proteins (LLPs) is a subject of growing interest in connection with many age-related human diseases. When isomerization occurs in LLPs, it can lead to deleterious changes in protein structure, function, and proteolytic degradation. Herein, we present a novel labeling technique for rapid identification of l-isoAsp using the enzyme protein l-isoaspartyl methyltransferase (PIMT) and Tris. The succinimide intermediate formed during reaction of l-isoAsp-containing peptides with PIMT and S-adenosyl methionine (SAM) is reactive with Tris base and results in a Tris-modified aspartic acid residue with a mass shift of +103 Da. Tris-modified aspartic acid exhibits prominent and repeated neutral loss of water when subjected to collisional activation. In addition, another dissociation pathway regenerates the original peptide following loss of a characteristic mass shift. Furthermore, it is demonstrated that Tris modification can be used to identify sites of isomerization in LLPs from biological samples such as the lens of the eye. This approach simplifies identification by labeling isomerization sites with a tag that causes a mass shift and provides characteristic loss during collisional activation.
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Affiliation(s)
| | | | - Ryan R. Julian
- Corresponding Author correspondence should be sent to: , Department of Chemistry, University of California, Riverside, 501 Big Springs Road, Riverside, CA 92521, USA, (951) 827-3959
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15
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Specht H, Slavov N. Beyond Protein Sequence: Protein Isomerization in Alzheimer's Disease. J Proteome Res 2022; 21:299-300. [PMID: 35114789 DOI: 10.1021/acs.jproteome.2c00016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harrison Specht
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States.,Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nikolai Slavov
- Department of Bioengineering, Northeastern University, Boston, Massachusetts 02115, United States.,Barnett Institute, Northeastern University, Boston, Massachusetts 02115, United States
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16
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Tomczyk N, Giles K, Richardson K, Ujma J, Palmer M, Nielsen PK, Haselmann KF. Mapping Isomeric Peptides Derived from Biopharmaceuticals Using High-Resolution Ion Mobility Mass Spectrometry. Anal Chem 2021; 93:16379-16384. [PMID: 34842410 DOI: 10.1021/acs.analchem.1c02834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The identification and localization of isomeric peptide modifications is a critical requirement of the biopharmaceutical industry. Despite the ability of liquid chromatography-mass spectrometry to identify many of the common post translational modifications, the identification of isobaric or racemized peptides is confounded by modern mass spectrometry-based techniques. Here, we present a novel approach combining liquid chromatography with a high-resolution ion mobility mass spectrometry system to differentiate peptide and peptide fragments based upon their mobility and mass.
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Affiliation(s)
- Nick Tomczyk
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Kevin Giles
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | | | - Jakub Ujma
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Martin Palmer
- Waters Corporation, Stamford Avenue, Wilmslow SK9 4AX, U.K
| | - Peter Kresten Nielsen
- Novo Nordisk A/S, Global Research Technologies, Novo Nordisk Park, Maaloev DK-2760, Denmark
| | - Kim F Haselmann
- Novo Nordisk A/S, Global Research Technologies, Novo Nordisk Park, Maaloev DK-2760, Denmark
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17
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Abdulbagi M, Wang L, Siddig O, Di B, Li B. D-Amino Acids and D-Amino Acid-Containing Peptides: Potential Disease Biomarkers and Therapeutic Targets? Biomolecules 2021; 11:1716. [PMID: 34827714 PMCID: PMC8615943 DOI: 10.3390/biom11111716] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 12/17/2022] Open
Abstract
In nature, amino acids are found in two forms, L and D enantiomers, except for glycine which does not have a chiral center. The change of one form to the other will lead to a change in the primary structure of proteins and hence may affect the function and biological activity of proteins. Indeed, several D-amino acid-containing peptides (DAACPs) were isolated from patients with cataracts, Alzheimer's and other diseases. Additionally, significant levels of free D-amino acids were found in several diseases, reflecting the disease conditions. Studying the molecular mechanisms of the DAACPs formation and the alteration in D-amino acids metabolism will certainly assist in understanding these diseases and finding new biomarkers and drug targets. In this review, the presence of DAACPs and free D-amino acids and their links with disease development and progress are summarized. Similarly, we highlight some recent advances in analytical techniques that led to improvement in the discovery and analysis of DAACPs and D-amino acids.
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Affiliation(s)
- Mohamed Abdulbagi
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Liya Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Orwa Siddig
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
| | - Bin Di
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
| | - Bo Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 210009, China; (M.A.); (L.W.); (O.S.)
- Center Key Laboratory on Protein Chemistry and Structural Biology, China Pharmaceutical University, Nanjing 210009, China
- MOE Key Laboratory of Drug Quality Control and Pharmacovigilance, China Pharmaceutical University, Nanjing 210009, China
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18
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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: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [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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19
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Sang-Aroon W, Phatchana R, Tontapha S, Ruangpornvisuti V. A DFT calculation on nonenzymatic degradation of isoaspartic residue. J Mol Model 2021; 27:300. [PMID: 34570254 DOI: 10.1007/s00894-021-04920-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 11/30/2022]
Abstract
βAsp is an isomer of Asp that can be formed by either deamidation of Asn or isomerization of Asp and known as biological clock. The presence of βAsp affects the proteolytic stability of the protein. Formation of the isomerized Asp plays a diverse and crucial role in aging, cancer, autoimmune, neurodegenerative, and other diseases. A number of methods have been developed to detect βAsp, and they are usually used in conjunction. Because of identical mass, differentiation of βAsp and Asp residues is challenged. Degradation of βAsp is still unclear and needed to be explored. The energetics and mechanism of five possible pathways for cleavages at βAsp in peptide model have been investigated by DFT/B3LYP/6-311 + + G(d,p) level of the theory. The calculations show that peptide bond cleavage at α-chain (amino side) due to αOC → αCN ring closure is the most favorable reaction. The result is in agreement with experiment utilizing PSD/CRF method. The second most favorable pathway is due to αOC → βC ring closure results in β-chain cleavage. The cleavage products βAsp and Asp fragments can be used to signify an abundance of βAsp residue in nonenzymatic condition. Other three cyclizations initiated by either α- or β-amino nitrogen result in various cleavages, isomerization to Asp, and reconversion to original βAsp. These three cyclization pathways are obstructed because they require mostly high activation barriers and their intermediates are quite less thermodynamically stable. Thus, computational results also confirm that βAsp → Asp is prohibited in case of nonenzymatic condition which means that protein L-isoaspartyl O-methyl transferase (PIMT) is needed for this modification.
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Affiliation(s)
- Wichien Sang-Aroon
- Department of Chemistry, Faculty of Engineering, Rajamangala University of Technology Isan, KhonKaen Campus, Khon Kaen, 40000, Thailand.
| | - Ratchanee Phatchana
- Department of Chemistry, Faculty of Engineering, Rajamangala University of Technology Isan, KhonKaen Campus, Khon Kaen, 40000, Thailand
| | - Sarawut Tontapha
- Post Doctoral Research Fellow, Integrated Nanotechnology Research Center, Department of Physics, Faculty of Science, KhonKaen University, Khon Kaen, 40001, Thailand
| | - Vithaya Ruangpornvisuti
- Supramolecular Chemistry Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, 10320, Thailand
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20
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Lian Z, Wang N, Tian Y, Huang L. Characterization of Synthetic Peptide Therapeutics Using Liquid Chromatography-Mass Spectrometry: Challenges, Solutions, Pitfalls, and Future Perspectives. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1852-1860. [PMID: 34110145 DOI: 10.1021/jasms.0c00479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Synthetic peptides represent an important and expanding class of therapeutics. Despite having a relatively small size as compared to monoclonal antibodies and other proteins, synthetic peptides are subject to many complex structural modifications originating from the starting materials, manufacturing process, and storage conditions. Although mass spectrometry has been increasingly used to characterize impurities of synthetic peptides, systematic review of this field is scarce. In this paper, an overview of the impurities in synthetic peptide therapeutics is provided in the context of how the knowledge from detailed characterization of the impurities using liquid chromatography-mass spectrometry (LC-MS) can be used to develop the manufacturing process and control strategy for synthetic peptide therapeutics following the critical quality attribute (CQA)-driven and risk-based approach. The thresholds for identifying and controlling the impurities are discussed based on currently available regulatory guidance. Specific LC-MS techniques for identification of various types of impurities based on their structural characteristics are discussed with the focus on structural isomers and stereoisomers (i.e., peptide epimers). Absolute and relative quantitation methods for the peptide impurities are critiqued. Potential pitfalls in characterization of synthetic peptide therapeutics using LC-MS are discussed. Finally, a systematic LC-MS workflow for characterizing the impurities in synthetic peptide therapeutics is proposed, and future perspectives on applying emerging LC-MS techniques to address the remaining challenges in the development of synthetic peptide therapeutics are presented.
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Affiliation(s)
- Zhirui Lian
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Ning Wang
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Yuwei Tian
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Lihua Huang
- Bioproducts Research and Development, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
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21
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Kuang J, Tao Y, Song Y, Chemmalil L, Mussa N, Ding J, Li ZJ. Understanding the pathway and kinetics of aspartic acid isomerization in peptide mapping methods for monoclonal antibodies. Anal Bioanal Chem 2021; 413:2113-2123. [PMID: 33543314 DOI: 10.1007/s00216-021-03176-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 12/28/2020] [Accepted: 01/13/2021] [Indexed: 11/26/2022]
Abstract
Isomerization of aspartic acid (Asp) in therapeutic proteins could lead to safety and efficacy concerns. Thus, accurate quantitation of various Asp isomerization along with kinetic understanding of the variant formations is needed to ensure optimal process development and sufficient product quality control. In this study, we first observed Asp-succinimide conversion in complementarity-determining regions (CDRs) Asp-Gly motif of a recombinant mAb through ion exchange chromatography, intact protein analysis by mass spectrometry, and LC-MS/MS. Then, we developed a specific peptide mapping method, with optimized sample digestion conditions, to accurately quantitate Asp-succinimide-isoAsp variants at peptide level without method-induced isomerization. Various kinetics of Asp-succinimide-isoAsp isomerization pathways were elucidated using 18O labeling followed by LC-MS analysis. Molecular modeling and molecular dynamic simulation provide additional insight on the kinetics of Asp-succinimide formation and stability of succinimide intermediate. Findings of this work shed light on the molecular construct and the kinetics of the formation of isoAsp and succinimide in peptides and proteins, which facilitates analytical method development, protein engineering, and late phase development for commercialization of therapeutic proteins.
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Affiliation(s)
- June Kuang
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
| | - Yuanqi Tao
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
- Analytical Science Biologics, Takeda Pharmaceutical Company, Lexington, MA, 02421, USA
| | - Yuanli Song
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
- Process Development & Manufacture Operations, GSK, MA, 02451, Waltham, USA
| | - Letha Chemmalil
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
| | - Nesredin Mussa
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
- Ultragenyx, CA, 94005, Brisbane, USA
| | - Julia Ding
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA.
| | - Zheng Jian Li
- Biologics Development Organization, Bristol-Myers Squibb Company, Devens, MA, 01434, USA
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22
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Villacrés C, Spicer V, Krokhin OV. Confident Identification of Citrullination and Carbamylation Assisted by Peptide Retention Time Prediction. J Proteome Res 2021; 20:1571-1581. [PMID: 33523662 DOI: 10.1021/acs.jproteome.0c00775] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chromatographic behavior of peptides carrying citrulline and homocitrulline residues in proteomic two-dimensional (2D) liquid chromatography-mass spectrometry (LC-MS) experiments has been investigated. The primary goal of this study was to determine the chromatographic conditions that allow differentiating between arginine citrullination and deamidation of asparagine based on retention data, improving the confidence of MS-based identifications. Carbamylation was used as a reference point due to a high degree of similarity between modification products and anticipated changes in chromatographic behavior. We applied 2D LC-MS/MS (a high-pH-low-pH reversed phase (RP), hydrophilic interaction liquid chromatography (HILIC)-low-pH RP, and strong cation exchange (SCX)-low-pH RP) to acquire retention data for modified-nonmodified peptide pairs in the four separation modes. Modifications of a standard protein mixture were induced enzymatically (PAD-2) or chemically (urea) for citrullination and carbamylation, respectively. Deamidation occurs spontaneously. Similar retention shifts were observed for all three modifications in a high-pH RP (decrease) and a low-pH RP (increase), thus limiting the applicability of this 2D LC combination. HILIC on bare silica and strong cation exchange separations have been probed to amplify the effect of charge loss upon citrullination, with SCX demonstrating the most differentiating power: the elimination of basic residues upon citrullination/carbamylation results in an ∼58 mM KCl retention decrease, while retention of deamidated products decreases slightly.
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Affiliation(s)
- Carina Villacrés
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Victor Spicer
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
| | - Oleg V Krokhin
- Manitoba Centre for Proteomics and Systems Biology, Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada.,Internal Medicine, University of Manitoba, Winnipeg, MB R3E 3P4, Canada
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23
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Hinterholzer A, Stanojlovic V, Regl C, Huber CG, Cabrele C, Schubert M. Detecting aspartate isomerization and backbone cleavage after aspartate in intact proteins by NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2021; 75:71-82. [PMID: 33475951 PMCID: PMC7897204 DOI: 10.1007/s10858-020-00356-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
The monitoring of non-enzymatic post-translational modifications (PTMs) in therapeutic proteins is important to ensure drug safety and efficacy. Together with methionine and asparagine, aspartic acid (Asp) is very sensitive to spontaneous alterations. In particular, Asp residues can undergo isomerization and peptide-bond hydrolysis, especially when embedded in sequence motifs that are prone to succinimide formation or when followed by proline (Pro). As Asp and isoAsp have the same mass, and the Asp-Pro peptide-bond cleavage may lead to an unspecific mass difference of + 18 Da under native conditions or in the case of disulfide-bridged cleavage products, it is challenging to directly detect and characterize such modifications by mass spectrometry (MS). Here we propose a 2D NMR-based approach for the unambiguous identification of isoAsp and the products of Asp-Pro peptide-bond cleavage, namely N-terminal Pro and C-terminal Asp, and demonstrate its applicability to proteins including a therapeutic monoclonal antibody (mAb). To choose the ideal pH conditions under which the NMR signals of isoAsp and C-terminal Asp are distinct from other random coil signals, we determined the pKa values of isoAsp and C-terminal Asp in short peptides. The characteristic 1H-13C chemical shift correlations of isoAsp, N-terminal Pro and C-terminal Asp under standardized conditions were used to identify these PTMs in lysozyme and in the therapeutic mAb rituximab (MabThera) upon prolonged storage under acidic conditions (pH 4-5) and 40 °C. The results show that the application of our 2D NMR-based protocol is straightforward and allows detecting chemical changes of proteins that may be otherwise unnoticed with other analytical methods.
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Affiliation(s)
- Arthur Hinterholzer
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Vesna Stanojlovic
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Christof Regl
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Christian G Huber
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, Division of Chemistry and Bioanalytics, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
| | - Chiara Cabrele
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Mario Schubert
- Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization, University of Salzburg, Hellbrunnerstrasse 34, 5020, Salzburg, Austria.
- Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
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24
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Zhu HJ, Liu D, Tran VP, Wu Z, Jiang K, Zhu H, Zhang J, Gibbons C, Xue B, Shi H, Wang PG. N-Linked Glycosylation Prevents Deamidation of Glycopeptide and Glycoprotein. ACS Chem Biol 2020; 15:3197-3205. [PMID: 33270417 DOI: 10.1021/acschembio.0c00734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deamidation has been recognized as a common spontaneous pathway of protein degradation and a prevalent concern in the pharmaceutical industry; deamidation caused the reduction of protein/peptide drug efficacy and shelf life in several cases. More importantly, deamidation of physiological proteins is related to several human diseases and considered a "timer" for the diseases. N-linked glycosylation has a variety of significant biological functions, and it interestingly occurs right on the deamidation site-asparagine. It has been perceived that N-glycosylation could prevent deamidation, but experimental support is still lacking for clearly understanding the role of N-glycosylation on deamidation. Our results presented that deamidation is prevented by naturally occurring N-linked glycosylation. Glycopeptides and corresponding nonglycosylated peptides were used to compare their deamidation rates. All the nonglycosylated peptides have different half-lives ranging from one to 20 days, for the corresponding glycosylated peptides; all the results showed that the deamidation reaction was significantly reduced by the introduction of N-linked glycosylation. A glycoprotein, RNase B, also showed a significantly elongated deamidation half-life compared to nonglycosylated protein RNase A. At last, N-linked glycosylation on INGAP-P, a therapeutic peptide, increased the deamidation half-life of INGAP-P as well as its therapeutic potency.
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Affiliation(s)
- Hailiang Joshua Zhu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Ding Liu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Vy P. Tran
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Zhigang Wu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Kuan Jiang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - He Zhu
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Jiabin Zhang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Christopher Gibbons
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | - Bingzhong Xue
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Hang Shi
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Peng George Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
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25
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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] [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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26
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Mass spectrometric analysis of protein deamidation – A focus on top-down and middle-down mass spectrometry. Methods 2020; 200:58-66. [DOI: 10.1016/j.ymeth.2020.08.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 07/16/2020] [Accepted: 08/06/2020] [Indexed: 11/22/2022] Open
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27
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Ying Y, Li H. Recent progress in the analysis of protein deamidation using mass spectrometry. Methods 2020; 200:42-57. [PMID: 32544593 DOI: 10.1016/j.ymeth.2020.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/15/2020] [Accepted: 06/11/2020] [Indexed: 02/06/2023] Open
Abstract
Deamidation is a nonenzymatic and spontaneous posttranslational modification (PTM) that introduces changes in both structure and charge of proteins, strongly associated with aging proteome instability and degenerative diseases. Deamidation is also a common PTM occurring in biopharmaceutical proteins, representing a major cause of degradation. Therefore, characterization of deamidation alongside its inter-related modifications, isomerization and racemization, is critically important to understand their roles in protein stability and diseases. Mass spectrometry (MS) has become an indispensable tool in site-specific identification of PTMs for proteomics and structural studies. In this review, we focus on the recent advances of MS analysis in protein deamidation. In particular, we provide an update on sample preparation, chromatographic separation, and MS technologies at multi-level scales, for accurate and reliable characterization of protein deamidation in both simple and complex biological samples, yielding important new insight on how deamidation together with isomerization and racemization occurs. These technological progresses will lead to a better understanding of how deamidation contributes to the pathology of aging and other degenerative diseases and the development of biopharmaceutical drugs.
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Affiliation(s)
- Yujia Ying
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; School of Pharmacy, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Huilin Li
- School of Pharmaceutical Sciences, University of Sun Yat-sen University, No.132 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center, Guangzhou 510006, China; Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, China.
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28
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Aspartic Acid Isomerization Characterized by High Definition Mass Spectrometry Significantly Alters the Bioactivity of a Novel Toxin from Poecilotheria. Toxins (Basel) 2020; 12:toxins12040207. [PMID: 32218140 PMCID: PMC7232244 DOI: 10.3390/toxins12040207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/23/2020] [Indexed: 11/25/2022] Open
Abstract
Research in toxinology has created a pharmacological paradox. With an estimated 220,000 venomous animals worldwide, the study of peptidyl toxins provides a vast number of effector molecules. However, due to the complexity of the protein-protein interactions, there are fewer than ten venom-derived molecules on the market. Structural characterization and identification of post-translational modifications are essential to develop biological lead structures into pharmaceuticals. Utilizing advancements in mass spectrometry, we have created a high definition approach that fuses conventional high-resolution MS-MS with ion mobility spectrometry (HDMSE) to elucidate these primary structure characteristics. We investigated venom from ten species of “tiger” spider (Genus: Poecilotheria) and discovered they contain isobaric conformers originating from non-enzymatic Asp isomerization. One conformer pair conserved in five of ten species examined, denominated PcaTX-1a and PcaTX-1b, was found to be a 36-residue peptide with a cysteine knot, an amidated C-terminus, and isoAsp33Asp substitution. Although the isomerization of Asp has been implicated in many pathologies, this is the first characterization of Asp isomerization in a toxin and demonstrates the isomerized product’s diminished physiological effects. This study establishes the value of a HDMSE approach to toxin screening and characterization.
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29
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Chiu ML, Goulet DR, Teplyakov A, Gilliland GL. Antibody Structure and Function: The Basis for Engineering Therapeutics. Antibodies (Basel) 2019; 8:antib8040055. [PMID: 31816964 PMCID: PMC6963682 DOI: 10.3390/antib8040055] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/25/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Antibodies and antibody-derived macromolecules have established themselves as the mainstay in protein-based therapeutic molecules (biologics). Our knowledge of the structure–function relationships of antibodies provides a platform for protein engineering that has been exploited to generate a wide range of biologics for a host of therapeutic indications. In this review, our basic understanding of the antibody structure is described along with how that knowledge has leveraged the engineering of antibody and antibody-related therapeutics having the appropriate antigen affinity, effector function, and biophysical properties. The platforms examined include the development of antibodies, antibody fragments, bispecific antibody, and antibody fusion products, whose efficacy and manufacturability can be improved via humanization, affinity modulation, and stability enhancement. We also review the design and selection of binding arms, and avidity modulation. Different strategies of preparing bispecific and multispecific molecules for an array of therapeutic applications are included.
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Affiliation(s)
- Mark L. Chiu
- Drug Product Development Science, Janssen Research & Development, LLC, Malvern, PA 19355, USA
- Correspondence:
| | - Dennis R. Goulet
- Department of Medicinal Chemistry, University of Washington, P.O. Box 357610, Seattle, WA 98195-7610, USA;
| | - Alexey Teplyakov
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
| | - Gary L. Gilliland
- Biologics Research, Janssen Research & Development, LLC, Spring House, PA 19477, USA; (A.T.); (G.L.G.)
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30
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Mishra PKK, Mahawar M. PIMT-Mediated Protein Repair: Mechanism and Implications. BIOCHEMISTRY (MOSCOW) 2019; 84:453-463. [PMID: 31234761 DOI: 10.1134/s0006297919050018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Amino acids undergo many covalent modifications, but only few amino acid repair enzymes have been identified. Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PIMT), also known as L-isoaspartyl/D-aspartyl protein carboxyl methyltransferase (PCMT), methylates covalently modified isoaspartate (isoAsp) residues accumulated in proteins via Asn deamidation and Asp hydrolysis. This cytoplasmic reaction occurs through the formation of succinimide cyclical intermediate and generates either isoAsp or Asp from succinimide. Succinimide conversion into Asp is spontaneous, while isoAsp is restored by PIMT using S-adenosylmethionine as a methyl donor. PIMT transforms isoAsp into succinimide, thereby creating an opportunity for the later to be converted into Asp. Apart from normal cell physiology, formation of isoAsp in proteins is promoted by various stress conditions. The resulting isoAsp can form a kink or bend in the protein backbone thus making the protein conformationally and functionally distorted. Many PIMT-interacting proteins (proteins with isoAsp residues) have been reported in eukaryotes, but only few of them have been found in prokaryotes. Extensive studies in mice have shown the importance of PIMT in neurodegeneration. Detail elucidation of PIMT function can create a platform for addressing various disorders such as Alzheimer's disease and cancer.
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Affiliation(s)
- P K K Mishra
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - M Mahawar
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
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31
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Warmack RA, Shawa H, Liu K, Lopez K, Loo JA, Horwitz J, Clarke SG. The l-isoaspartate modification within protein fragments in the aging lens can promote protein aggregation. J Biol Chem 2019; 294:12203-12219. [PMID: 31239355 DOI: 10.1074/jbc.ra119.009052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Indexed: 01/15/2023] Open
Abstract
Transparency in the lens is accomplished by the dense packing and short-range order interactions of the crystallin proteins in fiber cells lacking organelles. These features are accompanied by a lack of protein turnover, leaving lens proteins susceptible to a number of damaging modifications and aggregation. The loss of lens transparency is attributed in part to such aggregation during aging. Among the damaging post-translational modifications that accumulate in long-lived proteins, isomerization at aspartate residues has been shown to be extensive throughout the crystallins. In this study of the human lens, we localize the accumulation of l-isoaspartate within water-soluble protein extracts primarily to crystallin peptides in high-molecular weight aggregates and show with MS that these peptides are from a variety of crystallins. To investigate the consequences of aspartate isomerization, we investigated two αA crystallin peptides 52LFRTVLDSGISEVR65 and 89VQDDFVEIH98, identified within this study, with the l-isoaspartate modification introduced at Asp58 and Asp91, respectively. Importantly, whereas both peptides modestly increase protein precipitation, the native 52LFRTVLDSGISEVR65 peptide shows higher aggregation propensity. In contrast, the introduction of l-isoaspartate within a previously identified anti-chaperone peptide from water-insoluble aggregates, αA crystallin 66SDRDKFVIFL(isoAsp)VKHF80, results in enhanced amyloid formation in vitro The modification of this peptide also increases aggregation of the lens chaperone αB crystallin. These findings may represent multiple pathways within the lens wherein the isomerization of aspartate residues in crystallin peptides differentially results in peptides associating with water-soluble or water-insoluble aggregates. Here the eye lens serves as a model for the cleavage and modification of long-lived proteins within other aging tissues.
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Affiliation(s)
- Rebeccah A Warmack
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Harrison Shawa
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Kate Liu
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Katia Lopez
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Joseph A Loo
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095
| | - Joseph Horwitz
- Molecular Biology Institute, UCLA, Los Angeles, California 90095; Jules Stein Eye Institute, UCLA, Los Angeles, California 90095
| | - Steven G Clarke
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095; Molecular Biology Institute, UCLA, Los Angeles, California 90095.
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32
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Lyon YA, Collier MP, Riggs DL, Degiacomi MT, Benesch JLP, Julian RR. Structural and functional consequences of age-related isomerization in α-crystallins. J Biol Chem 2019; 294:7546-7555. [PMID: 30804217 PMCID: PMC6514633 DOI: 10.1074/jbc.ra118.007052] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/15/2019] [Indexed: 12/31/2022] Open
Abstract
Long-lived proteins are subject to spontaneous degradation and may accumulate a range of modifications over time, including subtle alterations such as side-chain isomerization. Recently, tandem MS has enabled identification and characterization of such peptide isomers, including those differing only in chirality. However, the structural and functional consequences of these perturbations remain largely unexplored. Here, we examined the impact of isomerization of aspartic acid or epimerization of serine at four sites mapping to crucial oligomeric interfaces in human αA- and αB-crystallin, the most abundant chaperone proteins in the eye lens. To characterize the effect of isomerization on quaternary assembly, we utilized synthetic peptide mimics, enzyme assays, molecular dynamics calculations, and native MS experiments. The oligomerization of recombinant forms of αA- and αB-crystallin that mimic isomerized residues deviated from native behavior in all cases. Isomerization also perturbs recognition of peptide substrates, either enhancing or inhibiting kinase activity. Specifically, epimerization of serine (αASer-162) dramatically weakened inter-subunit binding. Furthermore, phosphorylation of αBSer-59, known to play an important regulatory role in oligomerization, was severely inhibited by serine epimerization and altered by isomerization of nearby αBAsp-62. Similarly, isomerization of αBAsp-109 disrupted a vital salt bridge with αBArg-120, a contact that when broken has previously been shown to yield aberrant oligomerization and aggregation in several disease-associated variants. Our results illustrate how isomerization of amino acid residues, which may seem to be only a minor structural perturbation, can disrupt native structural interactions with profound consequences for protein assembly and activity.
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Affiliation(s)
- Yana A Lyon
- From the Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Miranda P Collier
- the Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom, and
| | - Dylan L Riggs
- From the Department of Chemistry, University of California, Riverside, Riverside, California 92521
| | - Matteo T Degiacomi
- the Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Justin L P Benesch
- the Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom, and
| | - Ryan R Julian
- From the Department of Chemistry, University of California, Riverside, Riverside, California 92521,
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33
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Ayrton ST, Chen X, Bain RM, Pulliam CJ, Achmatowicz M, Flick TG, Ren D, Cooks RG. Gas Phase Ion Chemistry to Determine Isoaspartate in a Peptide Backbone. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1339-1344. [PMID: 29546595 DOI: 10.1007/s13361-018-1923-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Proof of concept evidence is presented for a new method for the determination of isoaspartate, an important post-translational modification. Chemical derivatization is performed using common reagents for the modification of carboxylic acids and shown to yield suitable diagnostic information with regard to isomerization at the aspartate residue. The diagnostic gas phase chemistry is probed by collision-induced dissociation mass spectrometry, on the timescale of the MS experiment and semi-quantitative calibration of the percentage of isoaspartate in a peptide sample is demonstrated. Graphical Abstract ᅟ.
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Affiliation(s)
- S T Ayrton
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - X Chen
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - R M Bain
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - C J Pulliam
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA
| | - M Achmatowicz
- Department of Analytical Research & Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - T G Flick
- Department of Analytical Research & Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - D Ren
- Department of Analytical Research & Development, Amgen Inc., 1 Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - R G Cooks
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907, USA.
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34
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Coupling of on-column trypsin digestion–peptide mapping and principal component analysis for stability and biosimilarity assessment of recombinant human growth hormone. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1072:105-115. [DOI: 10.1016/j.jchromb.2017.11.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/01/2023]
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35
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Hao P, Adav SS, Gallart-Palau X, Sze SK. Recent advances in mass spectrometric analysis of protein deamidation. MASS SPECTROMETRY REVIEWS 2017; 36:677-692. [PMID: 26763661 DOI: 10.1002/mas.21491] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 12/28/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
Protein deamidation has been proposed to represent a "molecular clock" that progressively disrupts protein structure and function in human degenerative diseases and natural aging. Importantly, this spontaneous process can also modify therapeutic proteins by altering their purity, stability, bioactivity, and antigenicity during drug synthesis and storage. Deamidation occurs non-enzymatically in vivo, but can also take place spontaneously in vitro, hence artificial deamidation during proteomic sample preparation can hamper efforts to identify and quantify endogenous deamidation of complex proteomes. To overcome this, mass spectrometry (MS) can be used to conduct rigorous site-specific characterization of protein deamidation due to the high sensitivity, speed, and specificity offered by this technique. This article reviews recent progress in MS analysis of protein deamidation and discusses the strengths and limitations of common "top-down" and "bottom-up" approaches. Recent advances in sample preparation methods, chromatographic separation, MS technology, and data processing have for the first time enabled the accurate and reliable characterization of protein modifications in complex biological samples, yielding important new data on how deamidation occurs across the entire proteome of human cells and tissues. These technological advances will lead to a better understanding of how deamidation contributes to the pathology of biological aging and major degenerative diseases. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:677-692, 2017.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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36
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Jansson ET. Strategies for analysis of isomeric peptides. J Sep Sci 2017; 41:385-397. [PMID: 28922569 DOI: 10.1002/jssc.201700852] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023]
Abstract
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion-mobility spectrometry.
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Affiliation(s)
- Erik T Jansson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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37
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Zheng X, Deng L, Baker ES, Ibrahim YM, Petyuk VA, Smith RD. Distinguishing d- and l-aspartic and isoaspartic acids in amyloid β peptides with ultrahigh resolution ion mobility spectrometry. Chem Commun (Camb) 2017; 53:7913-7916. [PMID: 28654112 PMCID: PMC5555368 DOI: 10.1039/c7cc03321d] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While α-linked amino acids in the l-form are exclusively utilized in mammalian protein building, β-linked and d-form amino acids also have important biological roles. Unfortunately, the structural elucidation and separation of these different amino acid types in peptides has been analytically challenging to date due to the numerous isomers present, limiting our knowledge about their existence and biological roles. Here, we utilized an ultrahigh resolution ion mobility spectrometry platform coupled with mass spectrometry (IMS-MS) to separate amyloid β (Aβ) peptides containing l-aspartic acid, d-aspartic acid, l-isoaspartic acid, and d-isoaspartic acid residues which span α- and β-linked amino acids in both d- and l-forms. The results illustrate how IMS-MS could be used to better understand age-related diseases or protein folding disorders resulting from amino acid modifications.
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Affiliation(s)
- Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Liulin Deng
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Erin S. Baker
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Yehia M. Ibrahim
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Vladislav A. Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, Richland, WA 99352 USA
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38
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Wang H, Shu Q, Frieden C, Gross ML. Deamidation Slows Curli Amyloid-Protein Aggregation. Biochemistry 2017; 56:2865-2872. [PMID: 28497950 DOI: 10.1021/acs.biochem.7b00241] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nonenzymatic deamidation of asparagine and glutamine in peptides and proteins is a frequent modification both in vivo and in vitro. The biological effect is not completely understood, but it is often associated with protein degradation and loss of biological function. Here we describe the deamidation of CsgA, the major protein subunit of curli, which are important proteinaceous components of biofilms. CsgA has a high content of Asn and Gln, a feature seen in a few proteins that self-aggregate. We have implemented an approach to monitor deamidation rapidly by following the globally centroid mass shift, providing guidance for studies at the residue level. From the global mass measurement, we identified, using LC-MS/MS, extensive deamidation of several Asn residues and discovered three "Asn-Gly" sites to be the hottest spots for deamidation. The fibrillization of deamidated CsgA was measured using thioflavin T (ThT) fluorescence, circular dichroism (CD), and a previously reported hydrogen-deuterium exchange (HDX) platform. Deamidated proteins exhibit a longer lag phase and lower final ThT fluorescence, strongly suggesting slower and less amyloid fibril formation. CD spectra show that extensively deamidated CsgA remains unstructured and loses its ability to form amyloids. Mass-spectrometry-based HDX also shows that deamidated CsgA aggregates more slowly than wild-type CsgA. Taken together, the results show that deamidation of CsgA slows its fibrillization and disrupts its function, suggesting an opportunity to modulate CsgA fibrillization and affect curli and biofilm formation.
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Affiliation(s)
- Hanliu Wang
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
| | - Qin Shu
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Carl Frieden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine , St. Louis, Missouri 63110, United States
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis , St. Louis, Missouri 63130, United States
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39
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Faserl K, Sarg B, Maurer V, Lindner HH. Exploiting charge differences for the analysis of challenging post-translational modifications by capillary electrophoresis-mass spectrometry. J Chromatogr A 2017; 1498:215-223. [DOI: 10.1016/j.chroma.2017.01.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 12/27/2022]
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40
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Young C, Podtelejnikov AV, Nielsen ML. Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature. J Proteome Res 2017; 16:2307-2317. [DOI: 10.1021/acs.jproteome.6b01055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Clifford Young
- The
Novo Nordisk Foundation Center for Protein Research, Proteomics Program,
Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | | | - Michael L. Nielsen
- The
Novo Nordisk Foundation Center for Protein Research, Proteomics Program,
Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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41
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Patel CN, Bauer SP, Davies J, Durbin JD, Shiyanova TL, Zhang K, Tang JX. N+1 Engineering of an Aspartate Isomerization Hotspot in the Complementarity-Determining Region of a Monoclonal Antibody. J Pharm Sci 2016; 105:512-518. [PMID: 26869414 DOI: 10.1016/s0022-3549(15)00185-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 01/22/2023]
Abstract
Aspartate (Asp) isomerization is a common degradation pathway and a potential critical quality attribute that needs to be well characterized during the optimization and development of therapeutic antibodies. A putative Asp-serine (Ser) isomerization motif was identified in the complementarity-determining region of a humanized monoclonal antibody and shown to be a developability risk using accelerated stability analyses. To address this issue, we explored different antibody engineering strategies. Direct engineering of the Asp residue resulted in a greater than 5× loss of antigen-binding affinity and bioactivity, indicating a critical role for this residue. In contrast, rational engineering of the Ser residue at the n+1 position had a negligible impact on antigen binding affinity and bioactivity compared with the parent molecule. Furthermore, the n+1 engineering strategy effectively eliminated Asp isomerization as determined by accelerated stability analysis. This outcome affirms that the rate of Asp isomerization is strongly dependent on the identity of the n+1 residue. This report highlights a systematic antibody engineering strategy for mitigating an Asp isomerization developability risk during lead optimization.
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Affiliation(s)
- Chetan N Patel
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285.
| | - Scott P Bauer
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Julian Davies
- Lilly Biotechnology Center, Biotechnology Discovery Research, Eli Lilly and Company, San Diego, California 92121
| | - Jim D Durbin
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Tatiyana L Shiyanova
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
| | - Kai Zhang
- Lilly Biotechnology Center, Biotechnology Discovery Research, Eli Lilly and Company, San Diego, California 92121
| | - Jason X Tang
- Lilly Research Laboratories, Biotechnology Discovery Research, Eli Lilly and Company, Indianapolis, Indiana 46285
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42
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DeGraan-Weber N, Zhang J, Reilly JP. Distinguishing Aspartic and Isoaspartic Acids in Peptides by Several Mass Spectrometric Fragmentation Methods. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:2041-2053. [PMID: 27613306 PMCID: PMC5748252 DOI: 10.1007/s13361-016-1487-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/17/2016] [Accepted: 08/19/2016] [Indexed: 05/21/2023]
Abstract
Six ion fragmentation techniques that can distinguish aspartic acid from its isomer, isoaspartic acid, were compared. MALDI post-source decay (PSD), MALDI 157 nm photodissociation, tris(2,4,6-trimethoxyphenyl)phosphonium bromide (TMPP) charge tagging in PSD and photodissociation, ESI collision-induced dissociation (CID), electron transfer dissociation (ETD), and free-radical initiated peptide sequencing (FRIPS) with CID were applied to peptides containing either aspartic or isoaspartic acid. Diagnostic ions, such as the y-46 and b+H2O, are present in PSD, photodissociation, and charge tagging. c•+57 and z-57 ions are observed in ETD and FRIPS experiments. For some molecules, aspartic and isoaspartic acid yield ion fragments with significantly different intensities. ETD and charge tagging appear to be most effective at distinguishing these residues. Graphical Abstract ᅟ.
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Affiliation(s)
- Nick DeGraan-Weber
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA
| | - Jun Zhang
- Pre-Pivotal Drug Product Technologies, Amgen Inc., Thousand Oaks, CA, 91320, USA
| | - James P Reilly
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, IN, 47405, USA.
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43
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Kabadi PG, Sankaran PK, Palanivelu DV, Adhikary L, Khedkar A, Chatterjee A. Mass Spectrometry Based Mechanistic Insights into Formation of Tris Conjugates: Implications on Protein Biopharmaceutics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1677-1685. [PMID: 27488315 DOI: 10.1007/s13361-016-1447-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/23/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
We present here extensive mass spectrometric studies on the formation of a Tris conjugate with a therapeutic monoclonal antibody. The results not only demonstrate the reactive nature of the Tris molecule but also the sequence and reaction conditions that trigger this reactivity. The results corroborate the fact that proteins are, in general, prone to conjugation and/or adduct formation reactions and any modification due to this essentially leads to formation of impurities in a protein sample. Further, the results demonstrate that the conjugation reaction happens via a succinimide intermediate and has sequence specificity. Additionally, the data presented in this study also shows that the Tris formation is produced in-solution and is not an in-source phenomenon. We believe that the facts given here will open further avenues on exploration of Tris as a conjugating agent as well as ensure that the use of Tris or any ionic buffer in the process of producing a biopharmaceutical drug is monitored closely for the presence of such conjugate formation. Graphical Abstract ᅟ.
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Affiliation(s)
- Pradeep G Kabadi
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore, 560099, India
| | - Praveen Kallamvalliillam Sankaran
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore, 560099, India
| | - Dinesh V Palanivelu
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore, 560099, India
| | - Laxmi Adhikary
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore, 560099, India
| | - Anand Khedkar
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore, 560099, India
| | - Amarnath Chatterjee
- Molecular Characterization Laboratory, Biocon Research Limited, Biocon Limited, Biocon Park, Bommasandra - Jigani Link Road, Bommasandra Industrial Area Phase IV, Bangalore, 560099, India.
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44
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Kumar S, Prakash S, Gupta K, Dongre A, Balaram P, Balaram H. Unexpected functional implication of a stable succinimide in the structural stability of Methanocaldococcus jannaschii glutaminase. Nat Commun 2016; 7:12798. [PMID: 27677693 PMCID: PMC5052720 DOI: 10.1038/ncomms12798] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
Protein ageing is often mediated by the formation of succinimide intermediates. These short-lived intermediates derive from asparaginyl deamidation and aspartyl dehydration and are rapidly converted into β-aspartyl or D-aspartyl residues. Here we report the presence of a highly stable succinimide intermediate in the glutaminase subunit of GMP synthetase from the hyperthermophile Methanocaldoccocus jannaschii. By comparing the biophysical properties of the wild-type protein and of several mutants, we show that the presence of succinimide increases the structural stability of the glutaminase subunit. The protein bearing this modification in fact remains folded at 100 °C and in 8 M guanidinium chloride. Mutation of the residue following the reactive asparagine provides insight into the factors that contribute to the hydrolytic stability of the succinimide. Our findings suggest that sequences that stabilize succinimides from hydrolysis may be evolutionarily selected to confer extreme thermal stability. Succinimide is a post-translational modification susceptible to rapid hydrolysis and generally associated with protein destabilisation. Here, the authors use mass spectroscopy to identify a stable succinimide intermediate that is responsible for the high thermostability of a thermophilic enzyme.
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Affiliation(s)
- Sanjeev Kumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Sunita Prakash
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Kallol Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Dongre
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Hemalatha Balaram
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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45
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Comparison of Protein N-Homocysteinylation in Rat Plasma under Elevated Homocysteine Using a Specific Chemical Labeling Method. Molecules 2016; 21:molecules21091195. [PMID: 27617989 PMCID: PMC5292613 DOI: 10.3390/molecules21091195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 11/30/2022] Open
Abstract
Elevated blood concentrations of homocysteine have been well established as a risk factor for cardiovascular diseases and neuropsychiatric diseases, yet the etiologic relationship of homocysteine to these disorders remains poorly understood. Protein N-homocysteinylation has been hypothesized as a contributing factor; however, it has not been examined globally owing to the lack of suitable detection methods. We recently developed a selective chemical method to label N-homocysteinylated proteins with a biotin-aldehyde tag followed by Western blotting analysis, which was further optimized in this study. We then investigated the variation of protein N-homocysteinylation in plasma from rats on a vitamin B12 deficient diet. Elevated “total homocysteine” concentrations were determined in rats with a vitamin B12 deficient diet. Correspondingly, overall levels of plasma protein N-homocysteinylation displayed an increased trend, and furthermore, more pronounced and statistically significant changes (e.g., 1.8-fold, p-value: 0.03) were observed for some individual protein bands. Our results suggest that, as expected, a general metabolic correlation exists between “total homocysteine” and N-homocysteinylation, although other factors are involved in homocysteine/homocysteine thiolactone metabolism, such as the transsulfuration of homocysteine by cystathionine β-synthase or the hydrolysis of homocysteine thiolactone by paraoxonase 1 (PON1), may play more significant or direct roles in determining the level of N-homocysteinylation.
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46
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Mildly acidic conditions eliminate deamidation artifact during proteolysis: digestion with endoprotease Glu-C at pH 4.5. Amino Acids 2016; 48:1059-1067. [PMID: 26748652 DOI: 10.1007/s00726-015-2166-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/25/2015] [Indexed: 10/22/2022]
Abstract
Common yet often overlooked, deamidation of peptidyl asparagine (Asn or N) generates aspartic acid (Asp or D) or isoaspartic acid (isoAsp or isoD). Being a spontaneous, non-enzymatic protein post-translational modification, deamidation artifact can be easily introduced during sample preparation, especially proteolysis where higher-order structures are removed. This artifact not only complicates the analysis of bona fide deamidation but also affects a wide range of chemical and enzymatic processes; for instance, the newly generated Asp and isoAsp residues may block or introduce new proteolytic sites, and also convert one Asn peptide into multiple species that affect quantification. While the neutral to mildly basic conditions for common proteolysis favor deamidation, mildly acidic conditions markedly slow down the process. Unlike other commonly used endoproteases, Glu-C remains active under mildly acid conditions. As such, as demonstrated herein, deamidation artifact during proteolysis was effectively eliminated by simply performing Glu-C digestion at pH 4.5 in ammonium acetate, a volatile buffer that is compatible with mass spectrometry. Moreover, nearly identical sequence specificity was observed at both pH's (8.0 for ammonium bicarbonate), rendering Glu-C as effective at pH 4.5. In summary, this method is generally applicable for protein analysis as it requires minimal sample preparation and uses the readily available Glu-C protease.
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47
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Yu X, Sargaeva NP, Thompson CJ, Costello CE, Lin C. In-Source Decay Characterization of Isoaspartate and β-Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:101-109. [PMID: 26644780 PMCID: PMC4669973 DOI: 10.1016/j.ijms.2015.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Deamidation and the subsequent formation of isoaspartic acid (isoAsp) are common modifications of asparagine (Asn) residues in proteins. Differentiation of isoAsp and Asp residues is a challenging task owing to their similar chemical properties and identical molecular mass. Recent studies showed that they can be differentiated using electron capture dissociation (ECD) which generates diagnostic fragments c'+57 and z•-57 specific to the isoAsp residue. However, the ECD approach is only applicable towards multiply charged precursor ions and generally does not work for β-amino acids other than isoAsp. In this study, the potential of in-source decay (ISD) in characterization of isoAsp and other β-amino acids was explored. For isoAsp-containing peptides, ISD with a conventional hydrogen-donating matrix produced ECD-like, c'+57 and z•-57 diagnostic ions, even for singly charged precursor ions. For other β-amino acids, a hydrogen-accepting matrix was used to induce formation of site-specific a-14 ions from a synthetic β-analogue of substance P. These results indicated that ISD can be broadly applied for β-peptide characterization.
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Affiliation(s)
- Xiang Yu
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | | | - Catherine E. Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
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48
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Bults P, van de Merbel NC, Bischoff R. Quantification of biopharmaceuticals and biomarkers in complex biological matrices: a comparison of liquid chromatography coupled to tandem mass spectrometry and ligand binding assays. Expert Rev Proteomics 2015; 12:355-74. [DOI: 10.1586/14789450.2015.1050384] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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49
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Tsiatsiani L, Heck AJR. Proteomics beyond trypsin. FEBS J 2015; 282:2612-26. [PMID: 25823410 DOI: 10.1111/febs.13287] [Citation(s) in RCA: 215] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 03/19/2015] [Accepted: 03/26/2015] [Indexed: 12/13/2022]
Abstract
Peptide-centered shotgun analysis of proteins has been the core technology in mass spectrometry based proteomics and has enabled numerous biological discoveries, such as the large-scale charting of protein-protein interaction networks, the quantitative analysis of protein post-translational modifications and even the first drafts of the human proteome. The conversion of proteins into peptides in these so-called bottom-up approaches is nearly uniquely done by using trypsin as a proteolytic reagent. Here, we argue that our view of the proteome still remains incomplete and this is partially due to the nearly exclusive use of trypsin. Newly emerging alternative proteases and/or multi-protease protein digestion aim to increase proteome sequence coverage and improve the identification of post-translational modifications, through the analysis of complementary and often longer peptides, introducing an approach termed middle-down proteomics. Of pivotal importance for this purpose is the identification of proteases beneficial for use in proteomics. Here, we describe some of the shortcomings of the nearly exclusive use of trypsin in proteomics and review the properties of other proteomics-appropriate proteases. We describe favorable protease traits with an emphasis on middle-down proteomics and suggest potential sources for the discovery of new proteases. We also highlight a few examples wherein the use of other proteases than trypsin enabled the generation of more comprehensive data sets leading to previously unexplored knowledge of the proteome.
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Affiliation(s)
- Liana Tsiatsiani
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Netherlands Proteomics Center, The Netherlands
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50
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Wang D, Wynne C, Gu F, Becker C, Zhao J, Mueller HM, Li H, Shameem M, Liu YH. Characterization of Drug-Product-Related Impurities and Variants of a Therapeutic Monoclonal Antibody by Higher Energy C-Trap Dissociation Mass Spectrometry. Anal Chem 2015; 87:914-21. [DOI: 10.1021/ac503158g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Deyun Wang
- Eurofins-Lancaster Laboratories Inc., 2425
New Holland Pike, Lancaster, Pennsylvania 17601, United States
| | - Colin Wynne
- Eurofins-Lancaster Laboratories Inc., 2425
New Holland Pike, Lancaster, Pennsylvania 17601, United States
| | - Flora Gu
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Chris Becker
- Protein Metrics Inc., 1622 San
Carlos Avenue, Suite C, San Carlos, California 94070, United States
| | - Jia Zhao
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hans-Martin Mueller
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Huijuan Li
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mohammed Shameem
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yan-Hui Liu
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| |
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