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Kaur P, Tomechko S, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting. MAbs 2015; 6:1486-99. [PMID: 25484052 DOI: 10.4161/19420862.2014.975096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Amino acid-specific covalent labeling is well suited to probe protein structure and macromolecular interactions, especially for macromolecules and their complexes that are difficult to examine by alternative means, due to size, complexity, or instability. Here we present a detailed account of carbodiimide-based covalent labeling (with GEE tagging) applied to a glycosylated monoclonal antibody therapeutic, which represents an important class of biologic drugs. Characterization of such proteins and their antigen complexes is essential to development of new biologic-based medicines. In this study, the experiments were optimized to preserve the structural integrity of the protein, and experimental conditions were varied and replicated to establish the reproducibility and precision of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include D, E, and the C-terminus, against the experimental surface accessibility data in order to understand the accuracy of the approach in providing an unbiased assessment of structure. Data from the protein were also compared to reactivity measures of several model peptides to explain sequence or structure-based variations in reactivity. The results highlight several advantages of this approach. These include: the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling (indicating that the label does not significantly perturb the structure of the protein), the high reproducibility of replicate experiments (<2 % variation in modification extent), the similar reactivity of the 3 target probe residues (as suggested by analysis of model peptides), and the overall positive and significant correlation of reactivity and solvent accessible surface area (the latter values predicted by the homology modeling). Attenuation of reactivity, in otherwise solvent accessible probes, is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. The results are also compared with data from hydroxyl radical-mediated oxidative footprinting on the same protein, showing that complementary information is gained from the 2 approaches, although the number of target residues in carbodiimide/GEE labeling is fewer. Overall, this approach is an accurate and precise method for assessing protein structure of biologic drugs.
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Key Words
- ACN, acetonitrile
- CD, circular dichroism
- CL, covalent labeling
- DR, dose response
- EDC, 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
- EIC, extracts the ion chromatogram
- FPOP, fast photochemical oxidation of proteins
- GEE
- GEE, glycine ethyl ester
- HC, heavy chain
- HDX, hydrogen-deuterium exchange
- HRF, hydroxyl radical footprinting
- IT, ion trap
- IgG, immunoglobulin gamma
- LC, light chain
- LysC, Lysyl endopeptidase
- MS, mass spectrometry
- NMR, nuclear magnetic resonance
- RC, rate constant
- SASA, solvent accessible surface area
- SEC, size-exclusion chromatography
- VEGF, vascular endothelial growth factor
- covalent labeling
- footprinting
- mAb, monoclonal antibody
- protein structure
- structural proteomics
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Affiliation(s)
- Parminder Kaur
- a Center for Proteomics and Bioinformatics ; Case Western Reserve University ; Cleveland , OH USA
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Gautier V, Boumeester AJ, Lössl P, Heck AJR. Lysine conjugation properties in human IgGs studied by integrating high-resolution native mass spectrometry and bottom-up proteomics. Proteomics 2015; 15:2756-65. [PMID: 25641908 DOI: 10.1002/pmic.201400462] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/02/2014] [Accepted: 01/13/2015] [Indexed: 11/05/2022]
Abstract
Antibody-drug conjugates (ADCs) are a novel class of biopharmaceuticals several of which are now being investigated in clinical studies. In ADCs, potent cytotoxic drugs are coupled via a linker to reactive residues in IgG monoclonal antibodies. Linkage to lysine residues in the IgGs, using N-hydroxysuccinimide ester based chemistry, is one of the possible options. To control drug load and specificity, proper knowledge is required about which lysine residues are most accessible and reactive. Here, we combine native MS and bottom-up proteomics to monitor the overall drug load and site-specific lysine reactivity, using N-hydroxysuccinimide-based tandem mass tags. High-resolution Orbitrap native MS enables us to monitor and quantify, due to the achieved baseline resolution, the sequential incorporation of up to 69 tandem mass tag molecules into human IgGs. Complementary, bottom-up proteomics facilitates the identification of some very reactive "hot-spot" conjugation sites. However, we also identify lysine residues that are highly resistant to chemical labeling. Our integrated approach gives insight into the conjugation properties of IgGs at both the intact protein and residue levels, providing fundamental information for controlling drug load and specificity in lysine-linked ADCs.
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Affiliation(s)
- Violette Gautier
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands
| | - Anja J Boumeester
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,AbLab, University of Utrecht, Utrecht, The Netherlands
| | - Philip Lössl
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands.,Netherlands Proteomics Center, University of Utrecht, Utrecht, The Netherlands
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53
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Michels DA, Ip AY, Dillon TM, Brorson K, Lute S, Chavez B, Prentice KM, Brady LJ, Miller KJ. Separation Methods and Orthogonal Techniques. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- David A. Michels
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Anna Y. Ip
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Thomas M. Dillon
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Kurt Brorson
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Scott Lute
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Brittany Chavez
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Ken M. Prentice
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Lowell J. Brady
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Karen J. Miller
- Department of Protein Analytical Chemistry, Genentech, South San Francisco, California 94080, United States
- Department of Process and Product Development, Amgen Inc., Thousand Oaks, California 91361, United States
- Division of Monoclonal Antibodies, Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, Maryland 20903, United States
- Department of Process and Product Development, Amgen Inc., Seattle, Washington 98119, United States
- Global Analytical Sciences, Amgen Inc., Thousand Oaks, California 91320, United States
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Gupta S, Celestre R, Petzold CJ, Chance MR, Ralston C. Development of a microsecond X-ray protein footprinting facility at the Advanced Light Source. JOURNAL OF SYNCHROTRON RADIATION 2014; 21:690-9. [PMID: 24971962 PMCID: PMC4073957 DOI: 10.1107/s1600577514007000] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/29/2014] [Indexed: 05/05/2023]
Abstract
X-ray footprinting (XF) is an important structural biology tool used to determine macromolecular conformations and dynamics of both nucleic acids and proteins in solution on a wide range of timescales. With the impending shut-down of the National Synchrotron Light Source, it is ever more important that this tool continues to be developed at other synchrotron facilities to accommodate XF users. Toward this end, a collaborative XF program has been initiated at the Advanced Light Source using the white-light bending-magnet beamlines 5.3.1 and 3.2.1. Accessibility of the microsecond time regime for protein footprinting is demonstrated at beamline 5.3.1 using the high flux density provided by a focusing mirror in combination with a micro-capillary flow cell. It is further reported that, by saturating samples with nitrous oxide, the radiolytic labeling efficiency is increased and the imprints of bound versus bulk water can be distinguished. These results both demonstrate the suitability of the Advanced Light Source as a second home for the XF experiment, and pave the way for obtaining high-quality structural data on complex protein samples and dynamics information on the microsecond timescale.
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Affiliation(s)
- Sayan Gupta
- Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Richard Celestre
- Experimental Systems, Advanced Light Source Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Corie Ralston
- Berkeley Center for Structural Biology, Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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