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Mummadisetti MP, Drake JL, Falkowski PG. The spatial network of skeletal proteins in a stony coral. J R Soc Interface 2021; 18:20200859. [PMID: 33622149 PMCID: PMC8086859 DOI: 10.1098/rsif.2020.0859] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coral skeletons are materials composed of inorganic aragonitic fibres and organic molecules including proteins, sugars and lipids that are highly organized to form a solid biomaterial upon which the animals live. The skeleton contains tens of proteins, all of which are encoded in the animal genome and secreted during the biomineralization process. While recent advances are revealing the functions and evolutionary history of some of these proteins, how they are spatially arranged in the skeleton is unknown. Using a combination of chemical cross-linking and high-resolution tandem mass spectrometry, we identify, for the first time, the spatial interactions of the proteins embedded within the skeleton of the stony coral Stylophora pistillata. Our subsequent network analysis revealed that several coral acid-rich proteins are invariably associated with carbonic anhydrase(s), alpha-collagen, cadherins and other calcium-binding proteins. These spatial arrangements clearly show that protein-protein interactions in coral skeletons are highly coordinated and are key to understanding the formation and persistence of coral skeletons through time.
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Affiliation(s)
- Manjula P Mummadisetti
- Environmental Biophysics and Molecular Biology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Rd, New Brunswick, NJ 08901, USA
| | - Jeana L Drake
- Department of Earth, Planetary, and Space Sciences, University of California, Los Angeles, 595 Charles E. Young Drive East, Los Angeles, CA 90095, USA.,Department of Marine Biology, University of Haifa, 199 Aba Khoushy Avenue, Mount Carmel, Haifa 2498838, Israel
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Biology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, 71 Dudley Rd, New Brunswick, NJ 08901, USA.,Department of Earth and Planetary Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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Khan AK, Jagielnicki M, McIntire WE, Purdy MD, Dharmarajan V, Griffin PR, Yeager M. A Steric “Ball-and-Chain” Mechanism for pH-Mediated Regulation of Gap Junction Channels. Cell Rep 2020; 31:107482. [PMID: 32320665 DOI: 10.1016/j.celrep.2020.03.046] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/10/2019] [Accepted: 03/13/2020] [Indexed: 12/21/2022] Open
Abstract
Gap junction channels (GJCs) mediate intercellular communication and are gated by numerous conditions such as pH. The electron cryomicroscopy (cryo-EM) structure of Cx26 GJC at physiological pH recapitulates previous GJC structures in lipid bilayers. At pH 6.4, we identify two conformational states, one resembling the open physiological-pH structure and a closed conformation that displays six threads of density, that join to form a pore-occluding density. Crosslinking and hydrogen-deuterium exchange mass spectrometry reveal closer association between the N-terminal (NT) domains and the cytoplasmic loops (CL) at acidic pH. Previous electrophysiologic studies suggest an association between NT residue N14 and H100 near M2, which may trigger the observed movement of M2 toward M1 in our cryo-EM maps, thereby accounting for additional NT-CL crosslinks at acidic pH. We propose that these pH-induced interactions and conformational changes result in extension, ordering, and association of the acetylated NT domains to form a hexameric "ball-and-chain" gating particle.
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Remmele RL, Bee JS, Phillips JJ, Mo WD, Higazi DR, Zhang J, Lindo V, Kippen AD. Characterization of Monoclonal Antibody Aggregates and Emerging Technologies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1202.ch005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Richard L. Remmele
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jared S. Bee
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jonathan J. Phillips
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Wenjun David Mo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Daniel R. Higazi
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Jifeng Zhang
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Vivian Lindo
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Alistair D. Kippen
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune One MedImmune Way, Gaithersburg, Maryland 20878, United States
- Analytical Biotechnology, Biopharmaceutical Development, MedImmune Granta Park, Cambridge CB21 6GH, United Kingdom
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Zhang H, Cui W, Gross ML. Mass spectrometry for the biophysical characterization of therapeutic monoclonal antibodies. FEBS Lett 2013; 588:308-17. [PMID: 24291257 DOI: 10.1016/j.febslet.2013.11.027] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 11/16/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
Monoclonal antibodies (mAbs) are powerful therapeutics, and their characterization has drawn considerable attention and urgency. Unlike small-molecule drugs (150-600 Da) that have rigid structures, mAbs (∼150 kDa) are engineered proteins that undergo complicated folding and can exist in a number of low-energy structures, posing a challenge for traditional methods in structural biology. Mass spectrometry (MS)-based biophysical characterization approaches can provide structural information, bringing high sensitivity, fast turnaround, and small sample consumption. This review outlines various MS-based strategies for protein biophysical characterization and then reviews how these strategies provide structural information of mAbs at the protein level (intact or top-down approaches), peptide, and residue level (bottom-up approaches), affording information on higher order structure, aggregation, and the nature of antibody complexes.
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Affiliation(s)
- Hao Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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Kannan R, Santhoshkumar P, Mooney BP, Sharma KK. Identification of subunit-subunit interaction sites in αA-WT crystallin and mutant αA-G98R crystallin using isotope-labeled cross-linker and mass spectrometry. PLoS One 2013; 8:e65610. [PMID: 23755258 PMCID: PMC3673982 DOI: 10.1371/journal.pone.0065610] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 04/30/2013] [Indexed: 12/03/2022] Open
Abstract
Cataract is characterized by progressive protein aggregation and loss of vision. α-Crystallins are the major proteins in the lens responsible for maintaining transparency. They exist in the lens as highly polydisperse oligomers with variable numbers of subunits, and mutations in α-crystallin are associated with some forms of cataract in humans. Because the stability of proteins is dependent on optimal subunit interactions, the structural transformations and aggregation of mutant proteins that underlie cataract formation can be understood best by identifying the residue-specific inter- and intra-subunit interactions. Chemical crosslinking combined with mass spectrometry is increasingly used to provide structural insights into intra- and inter-protein interactions. We used isotope-labeled cross-linker in combination with LC-MS/MS to determine the subunit–subunit interaction sites in cataract-causing mutant αA-G98R crystallin. Peptides cross-linked by isotope-labeled (heavy and light forms) cross-linkers appear as doublets in mass spectra, thus facilitating the identification of cross-linker–containing peptides. In this study, we cross-linked wild-type (αA-WT) and mutant (αA-G98R) crystallins using the homobifunctional amine-reactive, isotope-labeled (d0 and d4) cross-linker–BS2G (bis[sulfosuccinimidyl]glutarate). Tryptic in-solution digest of cross-linked complexes generates a wide array of peptide mixtures. Cross-linked peptides were enriched using strong cation exchange (SCX) chromatography followed by both MS and MS/MS to identify the cross-linked sites. We identified a distinct intermolecular interaction site between K88 — K99 in the β5 strand of the mutant αA-G98R crystallin that is not found in wild-type αA-crystallin. This interaction could explain the conformational instability and aggregation nature of the mutant protein that results from incorrect folding and assembly.
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Affiliation(s)
- Rama Kannan
- Department of Biochemistry, University of Missouri, Columbia, Missouri, United States of America
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Beck A, Wagner-Rousset E, Ayoub D, Van Dorsselaer A, Sanglier-Cianférani S. Characterization of Therapeutic Antibodies and Related Products. Anal Chem 2012; 85:715-36. [DOI: 10.1021/ac3032355] [Citation(s) in RCA: 445] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Alain Beck
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Elsa Wagner-Rousset
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Daniel Ayoub
- Centre d’Immunologie Pierre Fabre (CIPF), 5 Av. Napoléon III, BP 60497, 74164 Saint-Julien-en-Genevois,
France
| | - Alain Van Dorsselaer
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
| | - Sarah Sanglier-Cianférani
- Laboratoire de Spectrométrie
de Masse BioOrganique (LSMBO), Université de Strasbourg, IPHC, 25 rue Becquerel 67087, Strasbourg, France and CNRS, UMR7178, 67037 Strasbourg, France
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