1
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Grauslund LR, Ständer S, Veggi D, Andreano E, Rand KD, Norais N. Epitope Mapping of Human Polyclonal Antibodies to the fHbp Antigen of a Neisseria Meningitidis Vaccine by Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS). Mol Cell Proteomics 2024; 23:100734. [PMID: 38342408 PMCID: PMC10959699 DOI: 10.1016/j.mcpro.2024.100734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/22/2023] [Accepted: 02/08/2024] [Indexed: 02/13/2024] Open
Abstract
Antigen-antibody interactions play a key role in the immune response post vaccination and the mechanism of action of antibody-based biopharmaceuticals. 4CMenB is a multicomponent vaccine against Neisseria meningitidis serogroup B in which factor H binding protein (fHbp) is one of the key antigens. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to identify epitopes in fHbp recognized by polyclonal antibodies (pAb) from two human donors (HDs) vaccinated with 4CMenB. Our HDX-MS data reveal several epitopes recognized by the complex mixture of human pAb. Furthermore, we show that the pAb from the two HDs recognize the same epitope regions. Epitope mapping of total pAb and purified fHbp-specific pAb from the same HD reveals that the two antibody samples recognize the same main epitopes, showing that HDX-MS based epitope mapping can, in this case at least, be performed directly using total IgG pAb samples that have not undergone Ab-selective purification. Two monoclonal antibodies (mAb) were previously produced from B-cell repertoire sequences from one of the HDs and used for epitope mapping of fHbp with HDX-MS. The epitopes identified for the pAb from the same HD in this study, overlap with the epitopes recognized by the two individual mAbs. Overall, HDX-MS epitope mapping appears highly suitable for simultaneous identification of epitopes recognized by pAb from human donors and to thus both guide vaccine development and study basic human immunity to pathogens, including viruses.
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Affiliation(s)
- Laura R Grauslund
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; GSK Vaccines, GSK, Siena, Italy
| | - Susanne Ständer
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark; GSK Vaccines, GSK, Siena, Italy
| | | | - Emanuele Andreano
- Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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2
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Code C, Qiu D, Solov’yov IA, Lee JG, Shin HC, Roland C, Sagui C, Houde D, Rand KD, Jørgensen TJD. Conformationally Restricted Glycopeptide Backbone Inhibits Gas-Phase H/D Scrambling between Glycan and Peptide Moieties. J Am Chem Soc 2023; 145:23925-23938. [PMID: 37883679 PMCID: PMC10636759 DOI: 10.1021/jacs.3c04068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Protein glycosylation is a common post-translational modification on extracellular proteins. The conformational dynamics of several glycoproteins have been characterized by hydrogen/deuterium exchange mass spectrometry (HDX-MS). However, it is, in most cases, not possible to extract information about glycan conformation and dynamics due to the general difficulty of separating the deuterium content of the glycan from that of the peptide (in particular, for O-linked glycans). Here, we investigate whether the fragmentation of protonated glycopeptides by collision-induced dissociation (CID) can be used to determine the solution-specific deuterium content of the glycan. Central to this concept is that glycopeptides can undergo a facile loss of glycans upon CID, thereby allowing for the determination of their masses. However, an essential prerequisite is that hydrogen and deuterium (H/D) scrambling can be kept in check. Therefore, we have measured the degree of scrambling upon glycosidic bond cleavage in glycopeptides that differ in the conformational flexibility of their backbone and glycosylation pattern. Our results show that complete scrambling precedes the glycosidic bond cleavage in normal glycopeptides derived from a glycoprotein; i.e., all labile hydrogens have undergone positional randomization prior to loss of the glycan. In contrast, the glycosidic bond cleavage occurs without any scrambling in the glycopeptide antibiotic vancomycin, reflecting that the glycan cannot interact with the peptide moiety due to a conformationally restricted backbone as revealed by molecular dynamics simulations. Scrambling is also inhibited, albeit to a lesser degree, in the conformationally restricted glycopeptides ristocetin and its pseudoaglycone, demonstrating that scrambling depends on an intricate interplay between the flexibility and proximity of the glycan and the peptide backbone.
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Affiliation(s)
- Christian Code
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Danwen Qiu
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ilia A. Solov’yov
- Department
of Physics, Chemistry and Pharmacy, University
of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
- Department
of Physics, Carl von Ossietzky University
Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Research
Centre for Neurosensory Science, Carl von
Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, 26129 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg Institut für Physik, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Jung-Goo Lee
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Hyeon-Cheol Shin
- Center for
Molecular Intelligence, The State University
of New York (SUNY), Korea,
119 Songdo Munwha-ro, Yeonsu-gu, 21985 Incheon, Korea
| | - Christopher Roland
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Celeste Sagui
- Department
of Physics, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Damian Houde
- Department
of Protein Pharmaceutical Development, Biogen, Cambridge, Massachusetts 02142, United States
| | - Kasper D. Rand
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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3
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Lambert T, Gramlich M, Stutzke L, Smith L, Deng D, Kaiser PD, Rothbauer U, Benesch JLP, Wagner C, Koenig M, Pompach P, Novak P, Zeck A, Rand KD. Development of a PNGase Rc Column for Online Deglycosylation of Complex Glycoproteins during HDX-MS. J Am Soc Mass Spectrom 2023; 34:2556-2566. [PMID: 37756257 PMCID: PMC10623573 DOI: 10.1021/jasms.3c00268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023]
Abstract
Protein glycosylation is one of the most common PTMs and many cell surface receptors, extracellular proteins, and biopharmaceuticals are glycosylated. However, HDX-MS analysis of such important glycoproteins has so far been limited by difficulties in determining the HDX of the protein segments that contain glycans. We have developed a column containing immobilized PNGase Rc (from Rudaea cellulosilytica) that can readily be implemented into a conventional HDX-MS setup to allow improved analysis of glycoproteins. We show that HDX-MS with the PNGase Rc column enables efficient online removal of N-linked glycans and the determination of the HDX of glycosylated regions in several complex glycoproteins. Additionally, we use the PNGase Rc column to perform a comprehensive HDX-MS mapping of the binding epitope of a mAb to c-Met, a complex glycoprotein drug target. Importantly, the column retains high activity in the presence of common quench-buffer additives like TCEP and urea and performed consistent across 114 days of extensive use. Overall, our work shows that HDX-MS with the integrated PNGase Rc column can enable fast and efficient online deglycosylation at harsh quench conditions to provide comprehensive analysis of complex glycoproteins.
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Affiliation(s)
- Thomas Lambert
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Marius Gramlich
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Luisa Stutzke
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Luke Smith
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, England
| | - Dingyu Deng
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Philipp D. Kaiser
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Ulrich Rothbauer
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
- Pharmaceutical
Biotechnology, Eberhard Karls University, 72074 Tübingen, Germany
| | - Justin L. P. Benesch
- Physical
and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, OX1 3QZ Oxford, England
| | - Cornelia Wagner
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Maximiliane Koenig
- Roche
Pharma Research and Early Development, Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany
| | - Petr Pompach
- BioCev,
Institute of Biotechnology of the CAS, 252 50 Prumyslova, Czech Republic
| | - Petr Novak
- BioCeV,
Institute of Microbiology of the CAS, 142 20 Prumyslova, Czech Republic
| | - Anne Zeck
- NMI
Natural and Medical Sciences Institute at the University of Tübingen, 72770 Reutlingen, Germany
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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Guo R, Zhang T, Lambert TOT, Wang T, Voglmeir J, Rand KD, Liu L. PNGase H + variant from Rudaea cellulosilytica with improved deglycosylation efficiency for rapid analysis of eukaryotic N-glycans and hydrogen deuterium exchange mass spectrometry analysis of glycoproteins. Rapid Commun Mass Spectrom 2022; 36:e9376. [PMID: 35945033 PMCID: PMC9541014 DOI: 10.1002/rcm.9376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/14/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
The analysis of glycoproteins and the comparison of protein N-glycosylation from different eukaryotic origins require unbiased and robust analytical workflows. The structural and functional analysis of vertebrate protein N-glycosylation currently depends extensively on bacterial peptide-N4-(N-acetyl-β-glucosaminyl) asparagine amidases (PNGases), which are indispensable enzymatic tools in releasing asparagine-linked oligosaccharides (N-glycans) from glycoproteins. So far, only limited PNGase candidates are available for N-glycans analysis, and particularly the analysis of plant and invertebrate N-glycans is hampered by the lack of suitable PNGases. Furthermore, liquid chromatography-mass spectrometry (LC-MS) workflows, such as hydrogen deuterium exchange mass spectrometry (HDX-MS), require a highly efficient enzymatic release of N-glycans at low pH values to facilitate the comprehensive structural analysis of glycoproteins. Herein, we describe a previously unstudied superacidic bacterial N-glycanase (PNGase H+ ) originating from the soil bacterium Rudaea cellulosilytica (Rc), which has significantly improved enzymatic properties compared to previously described PNGase H+ variants. Active and soluble recombinant PNGase Rc was expressed at a higher protein level (3.8-fold) and with higher specific activity (~56% increase) compared to the currently used PNGase H+ variant from Dyella japonicum (Dj). Recombinant PNGase Rc was able to deglycosylate the glycoproteins horseradish peroxidase and bovine lactoferrin significantly faster than PNGase Dj (10 min vs. 6 h). The versatility of PNGase Rc was demonstrated by releasing N-glycans from a diverse array of samples such as peach fruit, king trumpet mushroom, mouse serum, and the soil nematode Caenorhabditis elegans. The presence of only two disulfide bonds shown in the AlphaFold protein model (so far all other superacidic PNGases possess more disulfide bonds) could be corroborated by intact mass- and peptide mapping analysis and provides a possible explanation for the improved recombinant expression yield of PNGase Rc.
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Affiliation(s)
- Rui‐Rui Guo
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Tian‐Chan Zhang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | | | - Ting Wang
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
| | - Kasper D. Rand
- Protein Analysis Group, Department of PharmacyUniversity of CopenhagenCopenhagenDenmark
| | - Li Liu
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and TechnologyNanjing Agricultural UniversityNanjingChina
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5
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Comamala G, Krogh CC, Nielsen VS, Kutter JP, Voglmeir J, Rand KD. Hydrogen/Deuterium Exchange Mass Spectrometry with Integrated Electrochemical Reduction and Microchip-Enabled Deglycosylation for Epitope Mapping of Heavily Glycosylated and Disulfide-Bonded Proteins. Anal Chem 2021; 93:16330-16340. [PMID: 34843209 DOI: 10.1021/acs.analchem.1c01728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a recognized method to study protein conformational dynamics and interactions. Proteins encompassing post-translational modifications (PTMs), such as disulfide bonds and glycosylations, present challenges to HDX-MS, as disulfide bond reduction and deglycosylation is often required to extract HDX information from regions containing these PTMs. In-solution deglycosylation with peptide-N4-(N-acetyl-β-d-glucosaminyl)-asparagine amidase A (PNGase A) or PNGase H+ combined with chemical reduction using tris-(2-carboxyethyl)phosphine (TCEP) has previously been used for HDX-MS analysis of disulfide-linked glycoproteins. However, this workflow requires extensive manual sample preparation and consumes large amounts of enzyme. Furthermore, large amounts of TCEP and glycosidases often result in suboptimal liquid chromatography-mass spectrometry (LC-MS) performance. Here, we compare the in-solution activity of PNGase A, PNGase H+, and the newly discovered PNGase Dj under quench conditions and immobilize them onto thiol-ene microfluidic chips to create HDX-MS-compatible immobilized microfluidic enzyme reactors (IMERs). The IMERS retain deglycosylation activity, also following repeated use and long-term storage. Furthermore, we combine a PNGase Dj IMER, a pepsin IMER, and an electrochemical cell to develop an HDX-MS setup capable of efficient online disulfide-bond reduction, deglycosylation, and proteolysis. We demonstrate the applicability of this setup by mapping the epitope of a monoclonal antibody (mAb) on the heavily disulfide-bonded and glycosylated sema-domain of the tyrosine-protein kinase Met (SD c-Met). We achieve near-complete sequence coverage and extract HDX data to identify regions of SD c-Met involved in mAb binding. The described methodology thus presents an integrated and online workflow for improved HDX-MS analysis of challenging PTM-rich proteins.
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Affiliation(s)
- Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Camilla C Krogh
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Vibe S Nielsen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jörg P Kutter
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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6
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Calvaresi V, Truelsen LT, Larsen SB, Petersen NHT, Kirkegaard T, Rand KD. Conformational dynamics of free and membrane-bound human Hsp70 in model cytosolic and endo-lysosomal environments. Commun Biol 2021; 4:1369. [PMID: 34876699 PMCID: PMC8651726 DOI: 10.1038/s42003-021-02892-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 11/10/2021] [Indexed: 11/21/2022] Open
Abstract
The binding of the major stress-inducible human 70-kDa heat shock protein (Hsp70) to the anionic phospholipid bis-(monoacylglycero)-phosphate (BMP) in the lysosomal membrane is crucial for its impact on cellular pathology in lysosomal storage disorders. However, the conformational features of this protein-lipid complex remain unclear. Here, we apply hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the dynamics of the full-length Hsp70 in the cytosol and its conformational changes upon translocation into lysosomes. Using wild-type and W90F mutant proteins, we also map and discriminate the interaction of Hsp70 with BMP and other lipid components of the lysosomal membrane. We identify the N-terminal of the nucleotide binding domain (residues 87-118) as the primary orchestrator of BMP interaction. We show that the conformation of this domain is significantly reorganized in the W90F mutant, explaining its inability to stabilize lysosomal membranes. Overall, our results reveal important new molecular details of the protective effect of Hsp70 in lysosomal storage diseases, which, in turn, could guide future drug development.
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Affiliation(s)
- Valeria Calvaresi
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Line T. Truelsen
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Sidsel B. Larsen
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | | | | | - Kasper D. Rand
- grid.5254.60000 0001 0674 042XProtein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
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7
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Calugareanu D, Möller IR, Schmidt SG, Loland CJ, Rand KD. Probing the Impact of Temperature and Substrates on the Conformational Dynamics of the Neurotransmitter:Sodium symporter LeuT. J Mol Biol 2021; 434:167356. [PMID: 34780780 DOI: 10.1016/j.jmb.2021.167356] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 12/21/2022]
Abstract
The crucial function of neurotransmitter:sodium symporters (NSS) in facilitating the reuptake of neurotransmitters into neuronal cells makes them attractive drug targets for treating multiple mental diseases. Due to the challenges in working with eukaryotic NSS proteins, LeuT, a prokaryotic amino acid transporter, has served as a model protein for studying structure-function relationships of NSS family proteins. With hydrogen-deuterium exchange mass spectrometry (HDX-MS), slow unfolding/refolding kinetics were identified in multiple regions of LeuT, suggesting that substrate translocation involves cooperative fluctuations of helical stretches. Earlier work has solely been performed at non-native temperatures (25 °C) for LeuT, which is evolutionarily adapted to function at high temperatures (85 - 95 °C). To address the effect of temperature on LeuT dynamics, we have performed HDX-MS experiments at elevated temperatures (45 °C and 60 °C). At these elevated temperatures, multiple regions in LeuT exhibited increased dynamics compared to 25 °C. Interestingly, coordinated slow unfolding/refolding of key regions could still be observed, though considerably faster. We have further investigated the conformational impact of binding the efficiently transported substrate alanine (Ala) relative to the much slower transported substrate leucine (Leu). Comparing the HDX of the Ala-bound versus Leu-bound state of LeuT, we observe distinct differences that could explain the faster transport rate (kcat) of Ala relative to Leu. Importantly, slow unfolding/refolding dynamics could still be observed in regions of Ala-bound LeuT . Overall, our work brings new insights into the conformational dynamics of LeuT and provides a better understanding of the transport mechanism of LeuT and possibly other transporters bearing the LeuT fold.
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Affiliation(s)
- Dionisie Calugareanu
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Solveig G Schmidt
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen Ø, Denmark.
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8
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Calvaresi V, Redsted A, Norais N, Rand KD. Hydrogen-Deuterium Exchange Mass Spectrometry with Integrated Size-Exclusion Chromatography for Analysis of Complex Protein Samples. Anal Chem 2021; 93:11406-11414. [PMID: 34387074 DOI: 10.1021/acs.analchem.1c01171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The growing use of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for studying membrane proteins, large protein assemblies, and highly disulfide-bonded species is often challenged by the presence in the sample of large amounts of lipids, protein ligands, and/or highly ionizable reducing agents. Here, we describe how a short size-exclusion chromatography (SEC) column can be integrated with a conventional temperature-controlled HDX-MS setup to achieve fast and online removal of unwanted species from the HDX sample prior to chromatographic separation and MS analysis. Dual-mode valves permit labeled proteins eluting after SEC to be directed to the proteolytic and chromatographic columns, while unwanted sample components are led to waste. The SEC-coupled HDX-MS method allows analyses to be completed with lower or similar back-exchange compared to conventional experiments. We demonstrate the suitability of the method for the analysis of challenging protein samples, achieving efficient online removal of lipid components from protein-lipid systems, depletion of an antibody from an antigen during epitope mapping, and elimination of MS interfering compounds such as tris(2-carboxyethyl)phosphine (TCEP) during HDX-MS analysis of a disulfide-bonded protein. The implementation of the short SEC column to the conventional HDX-MS setup is straightforward and could be of significant general utility during the HDX-MS analysis of complex protein states.
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Affiliation(s)
- Valeria Calvaresi
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,GSK, Siena 53100, Italy
| | - Andreas Redsted
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark.,GSK, Siena 53100, Italy
| | | | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen 2100, Denmark
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9
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Grauslund LR, Calvaresi V, Pansegrau W, Norais N, Rand KD. Epitope and Paratope Mapping by HDX-MS Combined with SPR Elucidates the Difference in Bactericidal Activity of Two Anti-NadA Monoclonal Antibodies. J Am Soc Mass Spectrom 2021; 32:1575-1582. [PMID: 33683906 DOI: 10.1021/jasms.0c00431] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Characterization of antigen-antibody interactions is crucial for understanding antibody-mediated protection against pathogens, biopharmaceutical development, as well as evaluation of the immune response post vaccination. Bexsero is a multicomponent vaccine against Neisseria meningitidis serogroup B in which one of the key vaccine antigens is Neisserial adhesin A (NadA), a trimeric coiled-coil protein. Two NadA-specific monoclonal antibodies (mAbs) isolated from Bexsero-vaccinated individuals have been shown to have similar binding affinity and appear to recognize a similar antigen region, yet only one of the mAbs is bactericidal. In this study, we use hydrogen/deuterium exchange mass spectrometry (HDX-MS) to perform an in-depth study of the interaction of the two mAbs with NadA antigen using a combined epitope and paratope mapping strategy. In addition, we use surface plasmon resonance (SPR) to investigate the stoichiometry of the binding of the two mAbs to NadA. While epitope mapping only identifies a clear binding impact of one of the mAbs on NadA, the paratope mapping analyses shows that both mAbs are binding to NadA through several complementarity determining regions spanning both heavy and light chains. Our results highlight the advantage of combined epitope and paratope mapping HDX-MS experiments and supporting biochemical experiments to characterize antigen-antibody interactions. Through this combined approach, we provide a rationale for how the binding stoichiometry of the two mAbs to the trimeric NadA antigen can explain the difference in bactericidal activity of the two mAbs.
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Affiliation(s)
- Laura R Grauslund
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
- GSK, Siena 53100, Italy
| | - Valeria Calvaresi
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
- GSK, Siena 53100, Italy
| | | | | | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
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10
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Merkle PS, Trabjerg E, Hongjian S, Ferber M, Cuendet MA, Jørgensen TJD, Luescher I, Irving M, Zoete V, Michielin O, Rand KD. Probing the Conformational Dynamics of Affinity-Enhanced T Cell Receptor Variants upon Binding the Peptide-Bound Major Histocompatibility Complex by Hydrogen/Deuterium Exchange Mass Spectrometry. Biochemistry 2021; 60:859-872. [PMID: 33689297 DOI: 10.1021/acs.biochem.1c00035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Binding of the T cell receptor (TCR) to its cognate, peptide antigen-loaded major histocompatibility complex (pMHC) is a key interaction for triggering T cell activation and ultimately elimination of the target cell. Despite the importance of this interaction for cellular immunity, a comprehensive molecular understanding of TCR specificity and affinity is lacking. We conducted hydrogen/deuterium exchange mass spectrometry (HDX-MS) analyses of individual affinity-enhanced TCR variants and clinically relevant pMHC class I molecules (HLA-A*0201/NY-ESO-1157-165) to investigate the causality between increased binding affinity and conformational dynamics in TCR-pMHC complexes. Differential HDX-MS analyses of TCR variants revealed that mutations for affinity enhancement in TCR CDRs altered the conformational response of TCR to pMHC ligation. Improved pMHC binding affinity was in general observed to correlate with greater differences in HDX upon pMHC binding in modified TCR CDR loops, thereby providing new insights into the TCR-pMHC interaction. Furthermore, a specific point mutation in the β-CDR3 loop of the NY-ESO-1 TCR associated with a substantial increase in binding affinity resulted in a substantial change in pMHC binding kinetics (i.e., very slow kon, revealed by the detection of EX1 HDX kinetics), thus providing experimental evidence for a slow induced-fit binding mode. We also examined the conformational impact of pMHC binding on an unrelated TRAV12-2 gene-encoded TCR directed against the immunodominant MART-126-35 cancer antigen restricted by HLA-A*0201. Our findings provide a molecular basis for the observed TRAV12-2 gene bias in natural CD8+ T cell-based immune responses against the MART-1 antigen, with potential implications for general ligand discrimination and TCR cross-reactivity processes.
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Affiliation(s)
- Patrick S Merkle
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Esben Trabjerg
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Song Hongjian
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland.,Weill Cornell Medical College, 1300 York Avenue, New York, New York 10065, United States
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense, Denmark
| | - Immanuel Luescher
- Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland.,Ludwig Branch for Cancer Research of the University of Lausanne, 8001 Zurich, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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11
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Svejdal RR, Sticker D, Sønderby C, Kutter JP, Rand KD. Thiol-ene microfluidic chip for fast on-chip sample clean-up, separation and ESI mass spectrometry of peptides and proteins. Anal Chim Acta 2020; 1140:168-177. [DOI: 10.1016/j.aca.2020.09.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/13/2023]
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12
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Comamala G, Madsen JB, Voglmeir J, Du YM, Jensen PF, Østerlund EC, Trelle MB, Jørgensen TJD, Rand KD. Deglycosylation by the Acidic Glycosidase PNGase H + Enables Analysis of N-Linked Glycoproteins by Hydrogen/Deuterium Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2020; 31:2305-2312. [PMID: 32955262 DOI: 10.1021/jasms.0c00258] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Hydrogen/deuterium exchange monitored by mass spectrometry (HDX-MS) has become an important method to study the structural dynamics of proteins. However, glycoproteins represent a challenge to the traditional HDX-MS workflow for determining the deuterium uptake of the protein segments that contain the glycan. We have recently demonstrated the utility of the glycosidase PNGase A to enable HDX-MS analysis of N-glycosylated protein regions. Here, we have investigated the use of the acidic glycosidase PNGase H+, which has a pH optimum at 2.6, to efficiently deglycosylate N-linked glycosylated peptides during HDX-MS analysis of glycoproteins. Our results show that PNGase H+ retains high deglycosylation activity at HDX quench conditions. When used in an HDX-MS workflow, PNGase H+ allowed the extraction of HDX data from all five glycosylated regions of the serpin α1-antichymotrypsin. We demonstrate that PNGase A and PNGase H+ are capable of similar deglycosylation performance during HDX-MS analysis of α1-antichymotrypsin and the IgG1 antibody trastuzumab (TZ). However, PNGase H+ provides broader specificity and greater tolerance to the disulfide-bond reducing agent TCEP, while PNGase A offers advantages in terms of commercial availability and purity. Overall, our findings demonstrate the unique features of PNGase H+ for improving conformational analysis of glycoproteins by HDX-MS, in particular, challenging glycoproteins containing both glycosylations and disulfide bonds.
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Affiliation(s)
- Gerard Comamala
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jeppe B Madsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Josef Voglmeir
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ya-Min Du
- Glycomics and Glycan Bioengineering Research Center (GGBRC), College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Pernille F Jensen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Eva C Østerlund
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Morten B Trelle
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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13
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Wu S, Nguyen TTTN, Moroz OV, Turkenburg JP, Nielsen JE, Wilson KS, Rand KD, Teilum K. Conformational heterogeneity of Savinase from NMR, HDX-MS and X-ray diffraction analysis. PeerJ 2020; 8:e9408. [PMID: 32617193 PMCID: PMC7323712 DOI: 10.7717/peerj.9408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/02/2020] [Indexed: 12/11/2022] Open
Abstract
Background Several examples have emerged of enzymes where slow conformational changes are of key importance for function and where low populated conformations in the resting enzyme resemble the conformations of intermediate states in the catalytic process. Previous work on the subtilisin protease, Savinase, from Bacillus lentus by NMR spectroscopy suggested that this enzyme undergoes slow conformational dynamics around the substrate binding site. However, the functional importance of such dynamics is unknown. Methods Here we have probed the conformational heterogeneity in Savinase by following the temperature dependent chemical shift changes. In addition, we have measured changes in the local stability of the enzyme when the inhibitor phenylmethylsulfonyl fluoride is bound using hydrogen-deuterium exchange mass spectrometry (HDX-MS). Finally, we have used X-ray crystallography to compare electron densities collected at cryogenic and ambient temperatures and searched for possible low populated alternative conformations in the crystals. Results The NMR temperature titration shows that Savinase is most flexible around the active site, but no distinct alternative states could be identified. The HDX shows that modification of Savinase with inhibitor has very little impact on the stability of hydrogen bonds and solvent accessibility of the backbone. The most pronounced structural heterogeneities detected in the diffraction data are limited to alternative side-chain rotamers and a short peptide segment that has an alternative main-chain conformation in the crystal at cryo conditions. Collectively, our data show that there is very little structural heterogeneity in the resting state of Savinase and hence that Savinase does not rely on conformational selection to drive the catalytic process.
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Affiliation(s)
- Shanshan Wu
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | - Tam T T N Nguyen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen Ø, Denmark
| | - Olga V Moroz
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Johan P Turkenburg
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | | | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen Ø, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen N, Denmark
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14
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Möller IR, Merkle PS, Calugareanu D, Comamala G, Schmidt SG, Loland CJ, Rand KD. Probing the conformational impact of detergents on the integral membrane protein LeuT by global HDX-MS. J Proteomics 2020; 225:103845. [PMID: 32480080 DOI: 10.1016/j.jprot.2020.103845] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/17/2020] [Accepted: 05/24/2020] [Indexed: 01/11/2023]
Abstract
Neurotransmitter:sodium symporters (NSS) are integral membrane proteins (IMP), responsible for reuptake of neurotransmitters from the synaptic cleft. Due to challenges in production of mammalian NSS in their active form, the prokaryotic hydrophobic amino acid transporter, LeuT, served here as a steadfast model for elucidation of structure-function relationship. As NSS proteins reside within phospholipid bilayer, they require stabilization by artificial membrane systems upon their extraction. Right choice of artificial membrane system is crucial as suboptimal detergent and/or lipids can lead to destabilization or non-native stabilization. Here we study the effect of related detergents, dodecyl maltoside (DDM) and lauryl maltose neopentyl glycol (LMNG), on the conformational dynamics of LeuT by global HDX-MS, in the presence of functionally relevant ligands. We observed that LeuT is more dynamic when solubilized in DDM compared to LMNG. Moreover, LeuT exhibited increased HDX in the presence of K+ compared to Na+, indicating a more dynamic conformation in the presence of K+. Upon addition of leucine, LeuT underwent additional stabilization relative to the Na+-bound state. Finally, peak broadening was observed, suggesting that LeuT undergoes slow unfolding/refolding dynamics in detergent solution. These slow dynamics were verified by local HDX, also proving that detergents modulate the rate of these dynamics. SIGNIFICANCE: Overall, we show the efficacy of global HDX-MS to evaluate the effect of artificial membrane systems on integral membrane proteins and the importance of carefully selecting compatible detergent (and/or lipid) for the solubilization of this class of proteins.
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Affiliation(s)
- Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Patrick S Merkle
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Dionisie Calugareanu
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Solveig Gaarde Schmidt
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark.
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15
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Fogh JR, Jacobsen AM, Nguyen TTTN, Rand KD, Olsen LR. Investigating surrogate cerebrospinal fluid matrix compositions for use in quantitative LC-MS analysis of therapeutic antibodies in the cerebrospinal fluid. Anal Bioanal Chem 2020; 412:1653-1661. [PMID: 32008082 PMCID: PMC7026242 DOI: 10.1007/s00216-020-02403-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 12/17/2019] [Accepted: 01/10/2020] [Indexed: 11/29/2022]
Abstract
As quantitative analysis of biotherapeutics in cerebrospinal fluid (CSF) with LC-MS becomes increasingly widespread, there is a need for method developments towards higher sensitivity. By using artificial CSF (aCSF) in the development phase, the consumption of costly and sparsely available CSF can be limited. The aCSF compositions tested here were made from various dilutions of bovine serum albumin (BSA) or rat plasma to mimic the total protein concentration found in CSF. Focusing on monoclonal antibodies, the aCSF was spiked with human immunoglobulin (hIgG) and prepared with the bottom-up analysis technique using LC-MS. Assuming that the composition of the aCSF would affect the digest, the response from aCSF matrices was compared with CSF from rat, monkey, and dog in terms of estimated sample concentration and matrix effects. The samples were spiked with hIgG in the range of 10 to 1000 ng/mL and volumes of 10 μL were transferred to sample preparation. The results indicate that BSA dilutions from 300 to 2000 μg/mL and rat plasma dilutions of 0.5–2% provide the most accurate concentration estimates when compared with rat CSF. 1000 μg/mL BSA did not produce significantly different concentration estimates for 500 ng/mL samples when compared with CSF from rat, monkey, and dog, and can therefore be used as aCSF for several different species.
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Affiliation(s)
- Jens Rose Fogh
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark.,Translational DMPK, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark
| | | | - Tam T T N Nguyen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2200, Copenhagen, Denmark
| | - Line Rørbæk Olsen
- Translational DMPK, H. Lundbeck A/S, Ottiliavej 9, 2500, Valby, Denmark.
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16
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Castelli R, Scalvini L, Vacondio F, Lodola A, Anselmi M, Vezzosi S, Carmi C, Bassi M, Ferlenghi F, Rivara S, Møller IR, Rand KD, Daglian J, Wei D, Dotsey EY, Ahmed F, Jung KM, Stella N, Singh S, Mor M, Piomelli D. Benzisothiazolinone Derivatives as Potent Allosteric Monoacylglycerol Lipase Inhibitors That Functionally Mimic Sulfenylation of Regulatory Cysteines. J Med Chem 2019; 63:1261-1280. [PMID: 31714779 DOI: 10.1021/acs.jmedchem.9b01679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We describe a set of benzisothiazolinone (BTZ) derivatives that are potent inhibitors of monoacylglycerol lipase (MGL), the primary degrading enzyme for the endocannabinoid 2-arachidonoyl-sn-glycerol (2-AG). Structure-activity relationship studies evaluated various substitutions on the nitrogen atom and the benzene ring of the BTZ nucleus. Optimized derivatives with nanomolar potency allowed us to investigate the mechanism of MGL inhibition. Site-directed mutagenesis and mass spectrometry experiments showed that BTZs interact in a covalent reversible manner with regulatory cysteines, Cys201 and Cys208, causing a reversible sulfenylation known to modulate MGL activity. Metadynamics simulations revealed that BTZ adducts favor a closed conformation of MGL that occludes substrate recruitment. The BTZ derivative 13 protected neuronal cells from oxidative stimuli and increased 2-AG levels in the mouse brain. The results identify Cys201 and Cys208 as key regulators of MGL function and point to the BTZ scaffold as a useful starting point for the discovery of allosteric MGL inhibitors.
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Affiliation(s)
- Riccardo Castelli
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Laura Scalvini
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Federica Vacondio
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy.,Centro Interdipartimentale Biopharmanet-tec , Università degli Studi di Parma, Parco Area delle Scienze , Tecnopolo Padiglione 33 , I-43124 Parma , Italy
| | - Alessio Lodola
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Mattia Anselmi
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Stefano Vezzosi
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Caterina Carmi
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Michele Bassi
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy
| | - Francesca Ferlenghi
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy.,Centro Interdipartimentale Biopharmanet-tec , Università degli Studi di Parma, Parco Area delle Scienze , Tecnopolo Padiglione 33 , I-43124 Parma , Italy
| | - Silvia Rivara
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy.,Centro Interdipartimentale Biopharmanet-tec , Università degli Studi di Parma, Parco Area delle Scienze , Tecnopolo Padiglione 33 , I-43124 Parma , Italy
| | - Ingvar R Møller
- Department of Pharmacy , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Kasper D Rand
- Department of Pharmacy , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | | | | | | | | | | | - Nephi Stella
- Department of Pharmacology, Psychiatry and Behavioral Sciences , University of Washington , Seattle , Washington 98195-7280 , United States
| | - Simar Singh
- Department of Pharmacology, Psychiatry and Behavioral Sciences , University of Washington , Seattle , Washington 98195-7280 , United States
| | - Marco Mor
- Dipartimento di Scienze degli Alimenti e del Farmaco , Università degli Studi di Parma , Parco Area delle Scienze 27/A , I-43124 Parma , Italy.,Centro Interdipartimentale Biopharmanet-tec , Università degli Studi di Parma, Parco Area delle Scienze , Tecnopolo Padiglione 33 , I-43124 Parma , Italy
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17
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Masson GR, Burke JE, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC, Rand KD. Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods 2019; 16:595-602. [PMID: 31249422 PMCID: PMC6614034 DOI: 10.1038/s41592-019-0459-y] [Citation(s) in RCA: 375] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/23/2019] [Indexed: 12/20/2022]
Abstract
Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful biophysical technique being increasingly applied to a wide variety of problems. As the HDX-MS community continues to grow, adoption of best practices in data collection, analysis, presentation and interpretation will greatly enhance the accessibility of this technique to nonspecialists. Here we provide recommendations arising from community discussions emerging out of the first International Conference on Hydrogen-Exchange Mass Spectrometry (IC-HDX; 2017). It is meant to represent both a consensus viewpoint and an opportunity to stimulate further additions and refinements as the field advances.
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Affiliation(s)
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - Natalie G Ahn
- Department of Biochemistry, University of Colorado, Boulder, CO, USA
| | - Ganesh S Anand
- Department of Biological Science, National University of Singapore, Singapore, Singapore
| | - Christoph Borchers
- Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sébastien Brier
- Institut Pasteur, Chemistry and Structural Biology Department, Paris, France
| | | | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - S Walter Englander
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Patrick R Griffin
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Miklos Guttman
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Yoshitomo Hamuro
- Johnson & Johnson Pharmaeutical Research and Development, Jersey City, NJ, USA
| | - Albert J R Heck
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, the Netherlands
| | | | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej, Odense, Denmark
| | - Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Judith P Klinman
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON, Canada
| | - Petr Man
- Institute of Microbiology, Czech Academy of Sciences, Prague, Czech Republic
| | - Leland Mayne
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Bruce D Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
| | - Dana Reichmann
- Department of Biological Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joost Snijder
- Department of Medicinal Chemistry, School of Pharmacy, University of Washington, Seattle, WA, USA
| | - Timothy S Strutzenberg
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - Eric S Underbakke
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA
| | | | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Benjamin T Walters
- Department of Early Stage Pharmaceutical Development, Genentech, Inc., South San Francisco, CA, USA
| | - David D Weis
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Derek J Wilson
- Department of Chemistry, York University, Toronto, ON, Canada
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD, USA
| | | | - Jie Zheng
- Department of Integrative Structural and Computational Biology, Scripps Florida, The Scripps Research Institute, Jupiter, FL, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB, Canada.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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18
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Nielsen AK, Möller IR, Wang Y, Rasmussen SGF, Lindorff-Larsen K, Rand KD, Loland CJ. Substrate-induced conformational dynamics of the dopamine transporter. Nat Commun 2019; 10:2714. [PMID: 31221956 PMCID: PMC6586795 DOI: 10.1038/s41467-019-10449-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 05/09/2019] [Indexed: 02/02/2023] Open
Abstract
The dopamine transporter is a member of the neurotransmitter:sodium symporters (NSSs), which are responsible for termination of neurotransmission through Na+-driven reuptake of neurotransmitter from the extracellular space. Experimental evidence elucidating the coordinated conformational rearrangements related to the transport mechanism has so far been limited. Here we probe the global Na+- and dopamine-induced conformational dynamics of the wild-type Drosophila melanogaster dopamine transporter using hydrogen-deuterium exchange mass spectrometry. We identify Na+- and dopamine-induced changes in specific regions of the transporter, suggesting their involvement in protein conformational transitions. Furthermore, we detect ligand-dependent slow cooperative fluctuations of helical stretches in several domains of the transporter, which could be a molecular mechanism that assists in the transporter function. Our results provide a framework for understanding the molecular mechanism underlying the function of NSSs by revealing detailed insight into the state-dependent conformational changes associated with the alternating access model of the dopamine transporter.
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Affiliation(s)
- Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Ingvar R Möller
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100, Copenhagen Ø, Denmark
| | - Yong Wang
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kresten Lindorff-Larsen
- Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 2200, Copenhagen N, Denmark
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100, Copenhagen Ø, Denmark.
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, 2200, Copenhagen N, Denmark.
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19
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Möller IR, Slivacka M, Hausner J, Nielsen AK, Pospíšilová E, Merkle PS, Lišková R, Polák M, Loland CJ, Kádek A, Man P, Rand KD. Improving the Sequence Coverage of Integral Membrane Proteins during Hydrogen/Deuterium Exchange Mass Spectrometry Experiments. Anal Chem 2019; 91:10970-10978. [DOI: 10.1021/acs.analchem.9b00973] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Ingvar R. Möller
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Marika Slivacka
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Jiří Hausner
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen N DK-2200, Denmark
| | - Eliška Pospíšilová
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Patrick S. Merkle
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Růžena Lišková
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Marek Polák
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Claus J. Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Blegdamsvej 3, Copenhagen N DK-2200, Denmark
| | - Alan Kádek
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Petr Man
- BioCeV - Institute of Microbiology of the CAS, Prumyslova 595, CZ-252 50 Vestec, Czech Republic
- Faculty of Science, Charles University, Hlavova 8, CZ-128 20 Prague, Czech Republic
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen E DK-2100, Denmark
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20
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Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study. Anal Chem 2019; 91:6953-6961. [PMID: 31045356 PMCID: PMC6625963 DOI: 10.1021/acs.analchem.9b00658] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.
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Affiliation(s)
- Claudio Iacobucci
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Christine Piotrowski
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,Faculty of Science , University of Zurich , 8006 Zurich , Switzerland
| | - Bruno C Amaral
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Philip Andrews
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Katja Bernfur
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Christoph Borchers
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada.,Department of Biochemistry and Microbiology , University of Victoria , Petch Building, Room 270d, 3800 Finnerty Road , Victoria , British Columbia V8P 5C2 , Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montréal , Quebec H3T 1E2 , Canada
| | - Nicolas I Brodie
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - James E Bruce
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Yong Cao
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Stéphane Chaignepain
- CBMN, UMR 5248, CNRS , Université de Bordeaux, INP Bordeaux , Pessac 33607 , France
| | - Juan D Chavez
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Stéphane Claverol
- Centre de Génomique Fonctionnelle, Plateforme Protéome , Université de Bordeaux , Bordeaux 33000 , France
| | - Jürgen Cox
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Trisha Davis
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Gianluca Degliesposti
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Meng-Qiu Dong
- National Institute of Biological Sciences , Beijing 7 Science Park Road, ZGC Life Science Park , 102206 Beijing , China
| | - Nufar Edinger
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science , Lund University , 221 00 Lund , Sweden
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Michael Götze
- Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Francisco Gomes-Neto
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Fabio C Gozzo
- Institute of Chemistry , University of Campinas , Campinas São Paulo 13083-970 , Brazil
| | - Craig Gutierrez
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Caroline Haupt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Lan Huang
- Department of Physiology & Biophysics , University of California , Irvine , California 92697 , United States
| | - Michael R Hoopmann
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nir Kalisman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Oleg Klykov
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Zdeněk Kukačka
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Fan Liu
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Michael J MacCoss
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Karl Mechtler
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Ravit Mesika
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Robert L Moritz
- Institute for Systems Biology , 401 Terry Avenue North , Seattle , Washington 98109 , United States
| | - Nagarjuna Nagaraj
- Biochemistry Core Facility , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Victor Nesati
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Ana G C Neves-Ferreira
- Laboratory of Toxinology , Oswaldo Cruz Institute , Fiocruz, Avenida Brasil 4365 (Moorish Castle) , Manguinhos, Rio de Janeiro , Rio de Janeiro 21040-900 , Brazil
| | - Robert Ninnis
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Petr Novák
- Institute of Microbiology , BIOCEV , Prumyslova 595 , 252 50 Vestec , Czech Republic
| | - Francis J O'Reilly
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany
| | - Matthias Pelzing
- Analytical Biochemistry, CSL Limited , Bio21 Institute , 30 Flemington Road , 3010 Parkville, Melbourne , Australia
| | - Evgeniy Petrotchenko
- University of Victoria-Genome British Columbia Proteomics Centre , Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Lolita Piersimoni
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Manolo Plasencia
- Departments of Biological Chemistry, Bioinformatics, and Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Tara Pukala
- Discipline of Chemistry, Faculty of Sciences , University of Adelaide , North Terrace, Adelaide , South Australia 5005 , Australia
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Juri Rappsilber
- Chair of Bioanalytics, Institute of Biotechnology Technische Universität Berlin , 13355 Berlin , Germany.,Wellcome Trust Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , EH9 3BF Edinburgh , U.K
| | - Dana Reichmann
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Carolin Sailer
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Chris P Sarnowski
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland.,PhD Program in Systems Biology , University of Zurich and ETH Zurich , 8092 Zurich , Switzerland
| | - Richard A Scheltema
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences , University of Utrecht and Netherlands Proteomics Centre , Padualaan 8 , 3584 CH Utrecht , The Netherlands
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Institute for Biochemistry and Biotechnology, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Yi Shi
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Moriya Slavin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Safra Campus Givat Ram , The Hebrew University of Jerusalem , Jerusalem 91904 , Israel
| | - Frank Sobott
- Department of Chemistry , University of Antwerp , Groenenborgerlaan 171 , 2020 Antwerp , Belgium.,The Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology , University of Leeds , LS2 9JT Leeds , U.K
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Faculty of Chemistry and Pharmacy , Ludwig Maximilians University of Munich , Feodor-Lynen-Strasse 25 , 81377 Munich , Germany
| | - Heike Stephanowitz
- Leibniz Institute of Molecular Pharmacology (FMP) , Robert-Rössle-Strasse 10 , 13125 Berlin , Germany
| | - Florian Stengel
- University of Konstanz , Department of Biology , Universitätsstrasse 10 , 78457 Konstanz , Germany
| | - Christian E Stieger
- Protein Chemistry Facility, Research Institute of Molecular Pathology (IMP) and Institute of Molecular Biotechnology (IMBA) , Vienna Biocenter (VBC) , Dr. Bohr-Gasse 3 , 1030 Vienna , Austria
| | - Esben Trabjerg
- Department of Pharmacy , University of Copenhagen , 2100 Copenhagen , Denmark
| | - Michael Trnka
- UCSF Mass Spectrometry Facility , Genentech Hall, 600 16th Street , San Francisco , California 94158 , United States
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology (BIST) , Baldiri Reixac 10 , 08028 Barcelona , Spain
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Yufei Xiang
- Department of Cell Biology , University of Pittsburgh, School of Medicine , Pittsburgh , Pennsylvania 15213 , United States
| | - Sule Yilmaz
- Computational Systems Biochemistry Research Group , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , 82152 Martinsried , Germany
| | - Alex Zelter
- Department of Biochemistry , University of Washington , Seattle , Washington 98195 , United States
| | - Daniel Ziemianowicz
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre , University of Calgary , 3330 Hospital Drive North West , Calgary , Alberta T2N 4N1 , Canada
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology , ETH Zurich , Otto-Stern-Weg 3 , 8093 Zurich , Switzerland
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Charles Tanford Protein Center , Martin Luther University Halle-Wittenberg , Kurt-Mothes-Strasse 3a , 06120 Halle/Saale , Germany
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21
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Filliben JJ, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb. Anal Chem 2019; 91:7336-7345. [PMID: 31045344 DOI: 10.1021/acs.analchem.9b01100] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ sLab⟩ ≤ (0.15 ± 0.01) Da (1σx̅). All laboratories achieved ⟨sLab⟩ ≤ 0.4 Da. For immersions of protein at THDX = (3.6 to 25) °C and for D2O exchange times of tHDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σreproducibility15 Laboratories( tHDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at THDX = 25 °C exhibited reproducibility of σreproducibility25C cohort( tHDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.
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Affiliation(s)
- Jeffrey W Hudgens
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Elyssia S Gallagher
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Ioannis Karageorgos
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - Kyle W Anderson
- Bioprocess Measurement Group, Biomolecular Measurements Division , National Institute of Standards and Technology , Rockville , Maryland 20850 , United States.,Institute for Bioscience and Biotechnology Research , 9600 Gudelsky Drive , Rockville , Maryland 20850 , United States
| | - James J Filliben
- Statistical Engineering Division , National Institute of Standards and Technology , Gaithersburg , Maryland 20899 , United States
| | - Richard Y-C Huang
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - Guodong Chen
- Pharmaceutical Candidate Optimization, Research and Development , Bristol-Myers Squibb Company , Princeton , New Jersey 08540 , United States
| | - George M Bou-Assaf
- Analytical Development , Biogen Inc. , 225 Binney Street , Cambridge , Massachusetts 02142 , United States
| | - Alfonso Espada
- Centro de Investigación Lilly S.A. , 28108 Alcobendas , Spain
| | - Michael J Chalmers
- Lilly Research Laboratories , Eli Lilly and Company , Indianapolis , Indiana 46285 , United States
| | | | - Hui-Min Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Benjamin T Walters
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - Jennifer Zhang
- Protein Analytical Chemistry , Genentech, Inc. , 1 DNA Way , South San Francisco , California 94080 , United States
| | - John Venable
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States.,Joint Center for Structural Genomics , La Jolla , California 92037 , United States
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation , 10675 John Jay Hopkins Drive , San Diego , California 92121 , United States
| | - Xiaojun Lu
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Ratnesh Pandey
- MedImmune LLC , One MedImmune Way , Gaithersburg , Maryland 20878 , United States
| | - Arun Chandramohan
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Ganesh Srinivasan Anand
- Department of Biological Sciences , National University of Singapore , 14, Science Drive 4 , Singapore 117543
| | - Sasidhar N Nirudodhi
- Vaccine R&D , Pfizer Inc. , 401 N Middletown Rd , Pearl River, New York 10965 , United States
| | - Justin B Sperry
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Jason C Rouse
- Analytical R&D , Pfizer Inc. , 1 Burtt Road , Andover , Massachusetts 01810 , United States
| | - James A Carroll
- Analytical R&D , Pfizer Inc. , 700 Chesterfield Parkway West , Chesterfield , Missouri 63017 , United States
| | - Kasper D Rand
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - Ulrike Leurs
- Department of Pharmacy , University of Copenhagen , Universitetsparken 2 , DK-2100 Copenhagen , Denmark
| | - David D Weis
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Mohammed A Al-Naqshabandi
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States.,Department of General Science , Soran University , Kawa Street , Soran , Kurdistan Region, Iraq
| | - Tyler S Hageman
- Department of Chemistry , University of Kansas , 1567 Irving Hill Road , Lawrence , Kansas 66045 , United States
| | - Daniel Deredge
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Patrick L Wintrode
- Department of Pharmaceutical Sciences , University of Maryland, Baltimore, School of Pharmacy , 20 North Pine Street , Baltimore , Maryland 21201 , United States
| | - Malvina Papanastasiou
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - John D Lambris
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Laboratories , University of Pennsylvania , 422 Curie Boulevard , Philadelphia , Pennsylvania 19104 , United States
| | - Sheng Li
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
| | - Sarah Urata
- Department of Medicine , University of California, San Diego , 9500 Gilman Drive , La Jolla , California 92093 , United States
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22
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Hudgens JW, Gallagher ES, Karageorgos I, Anderson KW, Huang RYC, Chen G, Bou-Assaf GM, Espada A, Chalmers MJ, Harguindey E, Zhang HM, Walters BT, Zhang J, Venable J, Steckler C, Park I, Brock A, Lu X, Pandey R, Chandramohan A, Anand GS, Nirudodhi SN, Sperry JB, Rouse JC, Carroll JA, Rand KD, Leurs U, Weis DD, Al-Naqshabandi MA, Hageman TS, Deredge D, Wintrode PL, Papanastasiou M, Lambris JD, Li S, Urata S. Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb. J Res Natl Inst Stand Technol 2019; 124:1-7. [PMID: 34877153 PMCID: PMC7339623 DOI: 10.6028/jres.124.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/10/2019] [Indexed: 06/13/2023]
Abstract
The spreadsheet file reported herein provides centroid data, descriptive of
deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as
measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS)
method. The protein sample was incubated in deuterium-rich solutions under uniform
pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging
over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic
peptide fragments were measured by mass spectrometry. These data were reported by
fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass
spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide
sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage.
In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide
sequences of the Fc fragment. The instrumentation and physical and chemical
conditions under which these data were acquired are documented.
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Affiliation(s)
- Jeffrey W Hudgens
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Elyssia S Gallagher
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Ioannis Karageorgos
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Kyle W Anderson
- National Institute of Standards and Technology, Bioprocess Measurement Group, Biomolecular Measurements Division, Gaithersburg, MD 20899, USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Richard Y-C Huang
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - Guodong Chen
- Bristol-Myers Squibb Company, Pharmaceutical Candidate Optimization, Research and Development, Princeton, NJ 08540, USA
| | - George M Bou-Assaf
- Biogen Inc., Analytical Development, 225 Binney Street, Cambridge, MA 02142, USA
| | - Alfonso Espada
- Centro de Investigación Lilly S.A., 28108-Alcobendas, Spain
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN 46285, USA
| | | | - Hui-Min Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Benjamin T Walters
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jennifer Zhang
- Genentech, Inc. Protein Analytical Chemistry, 1 DNA Way, South San Francisco, CA 94080, USA
| | - John Venable
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Caitlin Steckler
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
- Joint Center for Structural Genomics, La Jolla, CA 92037, USA
| | - Inhee Park
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Ansgar Brock
- Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA 92121, USA
| | - Xiaojun Lu
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Ratnesh Pandey
- MedImmune LLC, One MedImmune Way, Gaithersburg, MD 20878, USA
| | - Arun Chandramohan
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | - Ganesh Srinivasan Anand
- National University of Singapore, Department of Biological Sciences, 14, Science Drive 4, Singapore 117543
| | | | - Justin B Sperry
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Jason C Rouse
- Pfizer Inc., Analytical R&D, 1 Burtt Road, Andover, MA 01810, USA
| | - James A Carroll
- Pfizer Inc., Analytical R&D, 700 Chesterfield Parkway West, Chesterfield, MO 63017, USA
| | - Kasper D Rand
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Ulrike Leurs
- University of Copenhagen, Department of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - David D Weis
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Mohammed A Al-Naqshabandi
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
- Soran University, Department of General Science, Kawa Street, Soran, Kurdistan Region, Iraq
| | - Tyler S Hageman
- University of Kansas, Department of Chemistry, 1251 Wescoe Hall Drive, Lawrence, KS 66045, USA
| | - Daniel Deredge
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Patrick L Wintrode
- University of Maryland, Baltimore, School of Pharmacy, Department of Pharmaceutical Sciences, 20 North Pine Street, Baltimore, MD 21201, USA
| | - Malvina Papanastasiou
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - John D Lambris
- University of Pennsylvania, Department of Pathology & Laboratory Medicine, Perelman School of Medicine, 402 Stellar-Chance Labs, 422 Curie Boulevard, Philadelphia, PA 19104-6100, USA
| | - Sheng Li
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Sarah Urata
- University of Southern California, Department of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA
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23
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Möller IR, Slivacka M, Nielsen AK, Rasmussen SGF, Gether U, Loland CJ, Rand KD. Conformational dynamics of the human serotonin transporter during substrate and drug binding. Nat Commun 2019; 10:1687. [PMID: 30976000 PMCID: PMC6459873 DOI: 10.1038/s41467-019-09675-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 03/22/2019] [Indexed: 12/24/2022] Open
Abstract
The serotonin transporter (SERT), a member of the neurotransmitter:sodium symporter family, is responsible for termination of serotonergic signaling by re-uptake of serotonin (5-HT) into the presynaptic neuron. Its key role in synaptic transmission makes it a major drug target, e.g. for the treatment of depression, anxiety and post-traumatic stress. Here, we apply hydrogen-deuterium exchange mass spectrometry to probe the conformational dynamics of human SERT in the absence and presence of known substrates and targeted drugs. Our results reveal significant changes in dynamics in regions TM1, EL3, EL4, and TM12 upon binding co-transported ions (Na+/K+) and ligand-mediated changes in TM1, EL3 and EL4 upon binding 5-HT, the drugs S-citalopram, cocaine and ibogaine. Our results provide a comprehensive direct view of the conformational response of SERT upon binding both biologically relevant substrate/ions and ligands of pharmaceutical interest, thus advancing our understanding of the structure-function relationship in SERT.
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Affiliation(s)
- Ingvar R Möller
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Marika Slivacka
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anne Kathrine Nielsen
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Ulrik Gether
- Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Claus J Loland
- Laboratory for Membrane Protein Dynamics, Department of Neuroscience, University of Copenhagen, Copenhagen, 2200, Denmark.
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen, 2100, Denmark.
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24
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Dorosz J, Kristensen LH, Aduri NG, Mirza O, Lousen R, Bucciarelli S, Mehta V, Sellés-Baiget S, Solbak SMØ, Bach A, Mesa P, Hernandez PA, Montoya G, Nguyen TTTN, Rand KD, Boesen T, Gajhede M. Molecular architecture of the Jumonji C family histone demethylase KDM5B. Sci Rep 2019; 9:4019. [PMID: 30858420 PMCID: PMC6411775 DOI: 10.1038/s41598-019-40573-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/19/2019] [Indexed: 12/02/2022] Open
Abstract
The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level.
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Affiliation(s)
- Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Line Hyltoft Kristensen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Nanda G Aduri
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Osman Mirza
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Rikke Lousen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Saskia Bucciarelli
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Ved Mehta
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Selene Sellés-Baiget
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Sara Marie Øie Solbak
- Medicinal Chemistry Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Anders Bach
- Medicinal Chemistry Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Pablo Mesa
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Pablo Alcon Hernandez
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Guillermo Montoya
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark.
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25
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Jensen PF, Kadziola A, Comamala G, Segura DR, Anderson L, Poulsen JCN, Rasmussen KK, Agarwal S, Sainathan RK, Monrad RN, Svendsen A, Nielsen JE, Lo Leggio L, Rand KD. Structure and Dynamics of a Promiscuous Xanthan Lyase from Paenibacillus nanensis and the Design of Variants with Increased Stability and Activity. Cell Chem Biol 2019; 26:191-202.e6. [DOI: 10.1016/j.chembiol.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/14/2018] [Accepted: 10/19/2018] [Indexed: 10/27/2022]
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26
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Kathrine Nielsen A, Möller IR, Rasmussen SG, Rand KD, Loland CJ. Substrate-Induced Conformational Dynamics of the Dopamine Transporter. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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27
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Mistarz UH, Chandler SA, Brown JM, Benesch JLP, Rand KD. Probing the Dissociation of Protein Complexes by Means of Gas-Phase H/D Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2019; 30:45-57. [PMID: 30460642 DOI: 10.1007/s13361-018-2064-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 05/16/2023]
Abstract
Gas-phase hydrogen/deuterium exchange measured by mass spectrometry (gas-phase HDX-MS) is a fast method to probe the conformation of protein ions. The use of gas-phase HDX-MS to investigate the structure and interactions of protein complexes is however mostly unharnessed. Ionizing proteins under conditions that maximize preservation of their native structure (native MS) enables the study of solution-like conformation for milliseconds after electrospray ionization (ESI), which enables the use of ND3-gas inside the mass spectrometer to rapidly deuterate heteroatom-bound non-amide hydrogens. Here, we explored the utility of gas-phase HDX-MS to examine protein-protein complexes and inform on their binding surface and the structural consequences of gas-phase dissociation. Protein complexes ranging from 24 kDa dimers to 395 kDa 24mers were analyzed by gas-phase HDX-MS with subsequent collision-induced dissociation (CID). The number of exchangeable sites involved in complex formation could, therefore, be estimated. For instance, dimers of cytochrome c or α-lactalbumin incorporated less deuterium/subunit than their unbound monomer counterparts, providing a measure of the number of heteroatom-bound side-chain hydrogens involved in complex formation. We furthermore studied if asymmetric charge-partitioning upon dissociation of protein complexes caused intermolecular H/D migration. In larger multimeric protein complexes, the dissociated monomer showed a significant increase in deuterium. This indicates that intermolecular H/D migration occurs as part of the asymmetric partitioning of charge during CID. We discuss several models that may explain this increase deuterium content and find that a model where only deuterium involved in migrating charge can account for most of the deuterium enrichment observed on the ejected monomer. In summary, the deuterium content of the ejected subunit can be used to estimate that of the intact complex with deviations observed for large complexes accounted for by charge migration. Graphical abstract ᅟ.
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Affiliation(s)
- Ulrik H Mistarz
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Shane A Chandler
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Jeffery M Brown
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK.
| | - Kasper D Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark.
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28
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Svejdal RR, Dickinson ER, Sticker D, Kutter JP, Rand KD. Thiol-ene Microfluidic Chip for Performing Hydrogen/Deuterium Exchange of Proteins at Subsecond Time Scales. Anal Chem 2018; 91:1309-1317. [DOI: 10.1021/acs.analchem.8b03050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rasmus R. Svejdal
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Eleanor R. Dickinson
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Drago Sticker
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jörg P. Kutter
- Microscale Analytical Systems Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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29
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Trabjerg E, Nazari ZE, Rand KD. Conformational analysis of complex protein states by hydrogen/deuterium exchange mass spectrometry (HDX-MS): Challenges and emerging solutions. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.06.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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30
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Przygońska K, Poznański J, Mistarz UH, Rand KD, Dadlez M. Side-chain moieties from the N-terminal region of Aβ are Involved in an oligomer-stabilizing network of interactions. PLoS One 2018; 13:e0201761. [PMID: 30080867 PMCID: PMC6078298 DOI: 10.1371/journal.pone.0201761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/20/2018] [Indexed: 12/31/2022] Open
Abstract
Oligomeric forms of the Aβ peptide represent the most probable neurotoxic agent in Alzheimer’s disease. The dynamic and heterogeneous character of these oligomers makes their structural characterization by classic methods difficult. Native mass spectrometry, when supported by additional gas phase techniques, like ion mobility separation and hydrogen-deuterium exchange (IM-HDX-MS), enable analysis of different oligomers coexisting in the sample and may provide species-specific structural information for each oligomeric form populated in the gas phase. Here, we have combined these three techniques to obtain insight into the structural properties of oligomers of Aβ1–40 and two variants with scrambled sequences. Gas-phase HDX-MS revealed a sequence-specific engagement of the side-chains of residues located at the N-terminal part of the peptide in a network of oligomer-stabilizing interactions. Oligomer-specific interactions were no longer observed in the case of the fully scrambled sequence. Also, the ability to form alternative structures, observed for WT Aβ peptide, was lost upon scrambling. Our data underscore a role for the N-terminal residues in shaping the equilibria of oligomeric forms. Although the peptide lacking the N-terminal 1–16 residues (p3 peptide) is thought to be benign, the role of the N-terminus has not been sufficiently characterized yet. We speculate that the interaction networks revealed here may be crucial for enabling structural transitions necessary to obtain mature parallel cross-β structures from smaller antiparallel oligomers. We provide a hypothetical molecular model of the trajectory that allows a gradual conversion from antiparallel to parallel oligomers without decomposition of oligomers. Oligomer-defining interactions involving the Aβ peptide N-terminus may be important in production of the neurotoxic forms and thus should not be neglected.
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Affiliation(s)
- Kaja Przygońska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ulrik H. Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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31
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Mistarz UH, Rand KD. Installation, validation, and application examples of two instrumental setups for gas-phase HDX-MS analysis of peptides and proteins. Methods 2018; 144:113-124. [PMID: 29753788 DOI: 10.1016/j.ymeth.2018.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/17/2018] [Accepted: 05/04/2018] [Indexed: 01/15/2023] Open
Abstract
Gas-phase hydrogen/deuterium exchange measured by mass spectrometry in a millisecond timeframe after ESI (gas-phase HDX-MS) is a fast and sensitive, yet unharnessed method to analyze the primary- and higher-order structure, intramolecular and intermolecular interactions, surface properties, and charge location of peptides and proteins. During a gas-phase HDX-MS experiment, heteroatom-bound non-amide hydrogens are made to exchange with deuterium during a millisecond timespan after electrospray ionization (ESI) by reaction with the highly basic reagent ND3, enabling conformational analysis of protein states that are pertinent to the native solution-phase. Here, we describe two different instrumental approaches to enable gas-phase HDX-MS for analysis of peptides and proteins on high-resolution Q-TOF mass spectrometers. We include a description of the procedure and equipment required for successful installation as well as suggested procedures for testing, validation, and troubleshooting of a gas-phase HDX-MS setup. In the two described approaches, gas-phase HDX-MS are performed either immediately after ESI in the cone exit region by leading N2-gas over a deuterated ND3/D2O solution, or by leading purified ND3-gas into different traveling wave ion guides (TWIG) of the mass spectrometer. We envision that a detailed description of the two gas-phase HDX-MS setups and their practical implementation and validation can pave the way for gas-phase HDX-MS to become a more routinely used MS technique for structural analysis of peptides and proteins.
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Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark.
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32
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Moroz OV, Jensen PF, McDonald SP, McGregor N, Blagova E, Comamala G, Segura DR, Anderson L, Vasu SM, Rao VP, Giger L, Sørensen TH, Monrad RN, Svendsen A, Nielsen JE, Henrissat B, Davies GJ, Brumer H, Rand KD, Wilson KS. Structural Dynamics and Catalytic Properties of a Multimodular Xanthanase. ACS Catal 2018. [DOI: 10.1021/acscatal.8b00666] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Olga V. Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Pernille F. Jensen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Sean P. McDonald
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Nicholas McGregor
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Gerard Comamala
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | | | - Lars Anderson
- Novozymes A/S, Krogshojvej 36, DK-2880 Bagsvard, Denmark
| | | | | | - Lars Giger
- Novozymes A/S, Krogshojvej 36, DK-2880 Bagsvard, Denmark
| | - Trine Holst Sørensen
- Department of Science and Environment, INM, Roskilde University, 1 Universitetsvej, DK-4000 Roskilde, Denmark
| | | | - Allan Svendsen
- Novozymes A/S, Krogshojvej 36, DK-2880 Bagsvard, Denmark
| | | | - Bernard Henrissat
- Institut National de la Recherche Agronomique, USC 1408, Architecture et Fonction des Macromolecules Biologiques, F-13288, UMR 7857 CNRS, Aix-Marseille University, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Gideon J. Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
| | - Harry Brumer
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Keith S. Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, United Kingdom
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33
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Merkle PS, Gotfryd K, Cuendet MA, Leth-Espensen KZ, Gether U, Loland CJ, Rand KD. Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT. Sci Adv 2018; 4:eaar6179. [PMID: 29756037 PMCID: PMC5947982 DOI: 10.1126/sciadv.aar6179] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
LeuT, a prokaryotic member of the neurotransmitter:sodium symporter (NSS) family, is an established structural model for mammalian NSS counterparts. We investigate the substrate translocation mechanism of LeuT by measuring the solution-phase structural dynamics of the transporter in distinct functional states by hydrogen/deuterium exchange mass spectrometry (HDX-MS). Our HDX-MS data pinpoint LeuT segments involved in substrate transport and reveal for the first time a comprehensive and detailed view of the dynamics associated with transition of the transporter between outward- and inward-facing configurations in a Na+- and K+-dependent manner. The results suggest that partial unwinding of transmembrane helices 1/5/6/7 drives LeuT from a substrate-bound, outward-facing occluded conformation toward an inward-facing open state. These hitherto unknown, large-scale conformational changes in functionally important transmembrane segments, observed for LeuT in detergent-solubilized form and when embedded in a native-like phospholipid bilayer, could be of physiological relevance for the translocation process.
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Affiliation(s)
- Patrick S. Merkle
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Kamil Gotfryd
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Michel A. Cuendet
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Katrine Z. Leth-Espensen
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
| | - Ulrik Gether
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Claus J. Loland
- Department of Neuroscience, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Kasper D. Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, 2100 Copenhagen O, Denmark
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34
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Högel P, Götz A, Kuhne F, Ebert M, Stelzer W, Rand KD, Scharnagl C, Langosch D. Glycine Perturbs Local and Global Conformational Flexibility of a Transmembrane Helix. Biochemistry 2018; 57:1326-1337. [DOI: 10.1021/acs.biochem.7b01197] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Philipp Högel
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Alexander Götz
- Physics
of Synthetic Biological Systems (E14), Technical University of Munich, Maximus-von-Imhof Forum 4, 85354 Freising, Germany
| | - Felix Kuhne
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Maximilian Ebert
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Walter Stelzer
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Christina Scharnagl
- Physics
of Synthetic Biological Systems (E14), Technical University of Munich, Maximus-von-Imhof Forum 4, 85354 Freising, Germany
| | - Dieter Langosch
- Center
for Integrated Protein Science Munich (CIPSM) at the Lehrstuhl Chemie
der Biopolymere, Technical University of Munich, Weihenstephaner
Berg 3, 85354 Freising, Germany
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35
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Mistarz UH, Bellina B, Jensen PF, Brown JM, Barran PE, Rand KD. UV Photodissociation Mass Spectrometry Accurately Localize Sites of Backbone Deuteration in Peptides. Anal Chem 2017; 90:1077-1080. [DOI: 10.1021/acs.analchem.7b04683] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ulrik H. Mistarz
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Bruno Bellina
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Pernille F. Jensen
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Jeffery M. Brown
- Waters Corporation, Stamford
Avenue, Altrincham Road, Wilmslow, SK9 4AX, United Kingdom
| | - Perdita E. Barran
- Michael
Barber Centre for Collaborative Mass Spectrometry, Manchester Institute
of Biotechnology, and Photon Science Institute, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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36
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Trabjerg E, Kartberg F, Christensen S, Rand KD. Conformational characterization of nerve growth factor-β reveals that its regulatory pro-part domain stabilizes three loop regions in its mature part. J Biol Chem 2017; 292:16665-16676. [PMID: 28798232 DOI: 10.1074/jbc.m117.803320] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 08/07/2017] [Indexed: 11/06/2022] Open
Abstract
Nerve growth factor-β (NGF) is essential for the correct development of the nervous system. NGF exists in both a mature form and a pro-form (proNGF). The two forms have opposing effects on neurons: NGF induces proliferation, whereas proNGF induces apoptosis via binding to a receptor complex of the common neurotrophin receptor (p75NTR) and sortilin. The overexpression of both proNGF and sortilin has been associated with several neurodegenerative diseases. Insights into the conformational differences between proNGF and NGF are central to a better understanding of the opposing mechanisms of action of NGF and proNGF on neurons. However, whereas the structure of NGF has been determined by X-ray crystallography, the structural details for proNGF remain elusive. Here, using a sensitive MS-based analytical method to measure the hydrogen/deuterium exchange of proteins in solution, we analyzed the conformational properties of proNGF and NGF. We detected the presence of a localized higher-order structure motif in the pro-part of proNGF. Furthermore, by comparing the hydrogen/deuterium exchange in the mature part of NGF and proNGF, we found that the presence of the pro-part in proNGF causes a structural stabilization of three loop regions in the mature part, possibly through a direct molecular interaction. Moreover, using tandem MS analyses, we identified two N-linked and two O-linked glycosylations in the pro-part of proNGF. These results advance our knowledge of the conformational properties of proNGF and NGF and help provide a rationale for the diverse biological effects of NGF and proNGF at the molecular level.
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Affiliation(s)
- Esben Trabjerg
- From the Department of Pharmacy, University of Copenhagen, 2100 Copenhagen E, Denmark and.,the Department of Biologics, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Fredrik Kartberg
- the Department of Biologics, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Søren Christensen
- the Department of Biologics, H. Lundbeck A/S, Ottiliavej 9, 2500 Valby, Denmark
| | - Kasper D Rand
- From the Department of Pharmacy, University of Copenhagen, 2100 Copenhagen E, Denmark and
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37
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Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites. Biochemistry 2017; 56:3945-3961. [DOI: 10.1021/acs.biochem.7b00385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Patrick S. Merkle
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Melita Irving
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Song Hongjian
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Mathias Ferber
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Thomas J. D. Jørgensen
- Department
of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | - Kirsten Scholten
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Immanuel Luescher
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - George Coukos
- Ludwig
Branch for Cancer Research, University of Lausanne, 1015 Lausanne, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Michel A. Cuendet
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
- Department
of Physiology and Biophysics, Weill Cornell Medical College, 1300
York Avenue, New York, New
York 10065, United States
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Bâtiment Génopode, UNIL Sorge, 1015 Lausanne, Switzerland
| | - Kasper D. Rand
- Department
of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark
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38
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Stiefler-Jensen D, Schwarz-Linnet T, de Lichtenberg C, Nguyen TTTN, Rand KD, Huang L, She Q, Teilum K. The extraordinary thermal stability of EstA from S. islandicus is independent of post translational modifications. Protein Sci 2017; 26:1819-1827. [PMID: 28681456 DOI: 10.1002/pro.3220] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/09/2017] [Accepted: 06/21/2017] [Indexed: 12/20/2022]
Abstract
Enzymes from thermophilic and hyper-thermophilic organisms have an intrinsic high stability. Understanding the mechanisms behind their high stability will be important knowledge for the engineering of novel enzymes with high stability. Lysine methylation of proteins is prevalent in Sulfolobus, a genus of hyperthermophilic and acidophilic archaea. Both unspecific and temperature dependent lysine methylations are seen, but the significance of this post-translational modification has not been investigated. Here, we test the effect of eliminating in vivo lysine methylation on the stability of an esterase (EstA). The enzyme was purified from the native host S. islandicus as well as expressed as a recombinant protein in E. coli, a mesophilic host that does not code for any machinery for in vivo lysine methylation. We find that lysine mono methylation indeed has a positive effect on the stability of EstA, but the effect is small. The effect of the lysine methylation on protein stability is secondary to that of protein expression in E. coli, as the E. coli recombinant enzyme is compromised both on stability and activity. We conclude that these differences are not attributed to any covalent difference between the protein expressed in hyperthermophilic versus mesophilic hosts.
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Affiliation(s)
| | - Troels Schwarz-Linnet
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Casper de Lichtenberg
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacology, University of Copenhagen, København, Denmark
| | - Kasper D Rand
- Department of Pharmacology, University of Copenhagen, København, Denmark
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Qunxin She
- Archaea Centre, Department of Biology, University of Copenhagen, København, Denmark
| | - Kaare Teilum
- Structural Biology and NMR Laboratory and The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, København, Denmark
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39
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Mistarz UH, Singh SK, Nguyen TTTN, Roeffen W, Yang F, Lissau C, Madsen SM, Vrang A, Tiendrebeogo RW, Kana IH, Sauerwein RW, Theisen M, Rand KD. Expression, Purification and Characterization of GMZ2'.10C, a Complex Disulphide-Bonded Fusion Protein Vaccine Candidate against the Asexual and Sexual Life-Stages of the Malaria-Causing Plasmodium falciparum Parasite. Pharm Res 2017. [PMID: 28646324 DOI: 10.1007/s11095-017-2208-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE Production and characterization of a chimeric fusion protein (GMZ2'.10C) which combines epitopes of key malaria parasite antigens: glutamate-rich protein (GLURP), merozoite surface protein 3 (MSP3), and the highly disulphide bonded Pfs48/45 (10C). GMZ2'.10C is a potential candidate for a multi-stage malaria vaccine that targets both transmission and asexual life-cycle stages of the parasite. METHODS GMZ2'.10C was produced in Lactococcus lactis and purified using either an immunoaffinity purification (IP) or a conventional purification (CP) method. Protein purity and stability was analysed by RP-HPLC, SEC-HPLC, 2-site ELISA, gel-electrophoresis and Western blotting. Structural characterization (mass analysis, peptide mapping and cysteine connectivity mapping) was performed by LC-MS/MS. RESULTS CP-GMZ2'.10C resulted in similar purity, yield, structure and stability as compared to IP-GMZ2'.10C. CP-GMZ2'.10C and IP-GMZ2'.10C both elicited a high titer of transmission blocking (TB) antibodies in rodents. The intricate disulphide-bond connectivity of C-terminus Pfs48/45 was analysed by tandem mass spectrometry and was established for GMZ2'.10C and two reference fusion proteins encompassing similar parts of Pfs48/45. CONCLUSION GMZ2'.10C, combining GMZ2' and correctly-folded Pfs48/45 can be produced by the Lactoccus lactis P170 based expression system in purity and quality for pharmaceutical development and elicit high level of TB antibodies. The cysteine connectivity for the 10C region of Pfs48/45 was revealed experimentally, providing an important guideline for employing the Pfs48/45 antigen in vaccine design.
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Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark
| | - Susheel K Singh
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, Copenhagen, Denmark.,Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark
| | - Will Roeffen
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Fen Yang
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark
| | - Casper Lissau
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark
| | | | | | - Régis W Tiendrebeogo
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, Copenhagen, Denmark.,Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Ikhlaq H Kana
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, Copenhagen, Denmark.,Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, Copenhagen, Denmark. .,Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark. .,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark.
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40
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Singh SK, Roeffen W, Mistarz UH, Chourasia BK, Yang F, Rand KD, Sauerwein RW, Theisen M. Construct design, production, and characterization of Plasmodium falciparum 48/45 R0.6C subunit protein produced in Lactococcus lactis as candidate vaccine. Microb Cell Fact 2017; 16:97. [PMID: 28569168 PMCID: PMC5452637 DOI: 10.1186/s12934-017-0710-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 05/26/2017] [Indexed: 01/10/2023] Open
Abstract
Background The sexual stages of Plasmodium falciparum are responsible for the spread of the parasite in malaria endemic areas. The cysteine-rich Pfs48/45 protein, exposed on the surface of sexual stages, is one of the most advanced antigens for inclusion into a vaccine that will block transmission. However, clinical Pfs48/45 sub-unit vaccine development has been hampered by the inability to produce high yields of recombinant protein as the native structure is required for the induction of functional transmission-blocking (TB) antibodies. We have investigated a downstream purification process of a sub-unit (R0.6C) fragment representing the C-terminal 6-Cys domain of Pfs48/45 (6C) genetically fused to the R0 region (R0) of asexual stage Glutamate Rich Protein expressed in Lactococcus lactis. Results A series of R0.6C fusion proteins containing features, which aim to increase expression levels or to facilitate protein purification, were evaluated at small scale. None of these modifications affected the overall yield of recombinant protein. Consequently, R0.6C with a C-terminal his tag was used for upstream and downstream process development. A simple work-flow was developed consisting of batch fermentation followed by two purification steps. As such, the recombinant protein was purified to homogeneity. The composition of the final product was verified by HPLC, mass spectrometry, SDS-PAGE and Western blotting with conformation dependent antibodies against Pfs48/45. The recombinant protein induced high levels of functional TB antibodies in rats. Conclusions The established production and purification process of the R0.6C fusion protein provide a strong basis for further clinical development of this candidate transmission blocking malaria vaccine. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0710-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susheel K Singh
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Will Roeffen
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Bishwanath Kumar Chourasia
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Fen Yang
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Robert W Sauerwein
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark. .,Department of International Health, Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark. .,Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.
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41
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Jönsson A, Svejdal RR, Bøgelund N, Nguyen TTTN, Flindt H, Kutter JP, Rand KD, Lafleur JP. Thiol-ene Monolithic Pepsin Microreactor with a 3D-Printed Interface for Efficient UPLC-MS Peptide Mapping Analyses. Anal Chem 2017; 89:4573-4580. [PMID: 28322047 DOI: 10.1021/acs.analchem.6b05103] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
To improve the sample handling, and reduce cost and preparation time, of peptide mapping LC-MS workflows in protein analytical research, we here investigate the possibility of replacing conventional enzymatic digestion methods with a polymer microfluidic chip based enzyme reactor. Off-stoichiometric thiol-ene is utilized as both bulk material and as a monolithic stationary phase for immobilization of the proteolytic enzyme pepsin. The digestion efficiency of the, thiol-ene based, immobilized enzyme reactor (IMER) is compared to that of a conventional, agarose packed bed, pepsin IMER column commonly used in LC-MS based protein analyses. The chip IMER is found to rival the conventional column in terms of digestion efficiency at comparable residence time and, using a 3D-printed interface, be directly interfaceable with LC-MS.
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Affiliation(s)
- Alexander Jönsson
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Rasmus R Svejdal
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Nanna Bøgelund
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Henrik Flindt
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Jörg P Kutter
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Kasper D Rand
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
| | - Josiane P Lafleur
- Department of Pharmacy, Copenhagen University , Universitetsparken 2, Copenhagen E DK-2100, Denmark
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42
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E. Nazari Z, van de Weert M, Bou-Assaf G, Houde D, Weiskopf A, D. Rand K. Rapid Conformational Analysis of Protein Drugs in Formulation by Hydrogen/Deuterium Exchange Mass Spectrometry. J Pharm Sci 2016; 105:3269-3277. [DOI: 10.1016/j.xphs.2016.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Revised: 06/29/2016] [Accepted: 07/12/2016] [Indexed: 01/21/2023]
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43
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Stelzer W, Scharnagl C, Leurs U, Rand KD, Langosch D. The Impact of the ‘Austrian’ Mutation of the Amyloid Precursor Protein Transmembrane Helix is Communicated to the Hinge Region. ChemistrySelect 2016. [DOI: 10.1002/slct.201601090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Walter Stelzer
- Lehrstuhl Chemie der Biopolymere; Technical University of Munich and Munich Center for Integrated Protein Science (CIPS ); Weihenstephaner Berg 3 85354 Freising Germany
| | - Christina Scharnagl
- Fakultät für Physik E14; Technical University of Munich; Maximus-von-Imhof-Forum 4 85354 Freising Germany
| | - Ulrike Leurs
- Department of Pharmacy; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Kasper D. Rand
- Department of Pharmacy; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Dieter Langosch
- Lehrstuhl Chemie der Biopolymere; Technical University of Munich and Munich Center for Integrated Protein Science (CIPS ); Weihenstephaner Berg 3 85354 Freising Germany
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44
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Fuchs D, Pedersen-Bjergaard S, Jensen H, Rand KD, Honoré Hansen S, Petersen NJ. Fully Automated Electro Membrane Extraction Autosampler for LC–MS Systems Allowing Soft Extractions for High-Throughput Applications. Anal Chem 2016; 88:6797-804. [DOI: 10.1021/acs.analchem.6b01243] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- David Fuchs
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Stig Pedersen-Bjergaard
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- School
of Pharmacy, University of Oslo, P.O. Box 1068 Blindern, 0316 Oslo, Norway
| | - Henrik Jensen
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Kasper D. Rand
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Steen Honoré Hansen
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Nickolaj Jacob Petersen
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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45
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Houde D, Nazari ZE, Bou-Assaf GM, Weiskopf AS, Rand KD. Conformational Analysis of Proteins in Highly Concentrated Solutions by Dialysis-Coupled Hydrogen/Deuterium Exchange Mass Spectrometry. J Am Soc Mass Spectrom 2016; 27:669-676. [PMID: 26860088 DOI: 10.1007/s13361-015-1331-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 12/18/2015] [Accepted: 12/24/2015] [Indexed: 06/05/2023]
Abstract
When highly concentrated, an antibody solution can exhibit unusual behaviors, which can lead to unwanted properties, such as increased levels of protein aggregation and unusually high viscosity. Molecular modeling, along with many indirect biophysical measurements, has suggested that the cause for these phenomena can be due to short range electrostatic and/or hydrophobic protein-protein interactions. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a useful tool for investigating protein conformation, dynamics, and interactions. However, "traditional" continuous dilution labeling HDX-MS experiments have limited utility for the direct analysis of solutions with high concentrations of protein. Here, we present a dialysis-based HDX-MS (di-HDX-MS) method as an alternative HDX-MS labeling format, which takes advantage of passive dialysis rather than the classic dilution workflow. We applied this approach to a highly concentrated antibody solution without dilution or significant sample manipulation, prior to analysis. Such a method could pave the way for a deeper understanding of the unusual behavior of proteins at high concentrations, which is highly relevant for development of biopharmaceuticals in industry. Graphical Abstract ᅟ.
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Affiliation(s)
- Damian Houde
- Protein Pharmaceutical Development, Biogen, Cambridge, MA, 02142, USA.
| | - Zeinab E Nazari
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrew S Weiskopf
- Protein Pharmaceutical Development, Biogen, Cambridge, MA, 02142, USA
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
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46
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Danwen Q, Code C, Quan C, Gong BJ, Arndt J, Pepinsky B, Rand KD, Houde D. Investigating the Role of Artemin Glycosylation. Pharm Res 2016; 33:1383-98. [DOI: 10.1007/s11095-016-1880-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/11/2016] [Indexed: 11/24/2022]
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47
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Fuchs D, Gabel-Jensen C, Jensen H, Rand KD, Pedersen-Bjergaard S, Hansen SH, Petersen NJ. Direct coupling of a flow–flow electromembrane extraction probe to LC-MS. Anal Chim Acta 2016; 905:93-9. [DOI: 10.1016/j.aca.2015.12.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 10/22/2015] [Accepted: 12/01/2015] [Indexed: 12/01/2022]
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48
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Mistarz UH, Brown JM, Haselmann KF, Rand KD. Probing the Binding Interfaces of Protein Complexes Using Gas-Phase H/D Exchange Mass Spectrometry. Structure 2015; 24:310-8. [PMID: 26749447 DOI: 10.1016/j.str.2015.11.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022]
Abstract
Fast gas-phase hydrogen/deuterium exchange mediated by ND3 gas and measured by mass spectrometry (gas-phase HDX-MS) is a largely unharnessed, fast, and sensitive method for probing primary- and higher-order polypeptide structure. Labeling of heteroatom-bound non-amide hydrogens in a sub-millisecond time span after electrospray ionization by ND3 gas can provide structural insights into protein conformers present in solution. Here, we have explored the use of gas-phase HDX-MS for probing the higher-order structure and binding interfaces of protein complexes originating from native solution conditions. Lysozyme ions bound by an oligosaccharide incorporated less deuterium than the unbound ion. Similarly, trypsin ions showed reduced deuterium uptake when bound by the peptide ligand vasopressin. Our results are in good agreement with crystal structures of the native protein complexes, and illustrate that gas-phase HDX-MS can provide a sensitive and simple approach to measure the number of heteroatom-bound non-amide side-chain hydrogens involved in the binding interface of biologically relevant protein complexes.
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Affiliation(s)
- Ulrik H Mistarz
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Jeffery M Brown
- Waters MS Technologies Centre, Waters Corporation, Altrincham Road, Wilmslow SK9 4AX, UK
| | - Kim F Haselmann
- Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park 1, Måløv 2670, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark.
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Walters BT, Jensen PF, Larraillet V, Lin K, Patapoff T, Schlothauer T, Rand KD, Zhang J. Conformational Destabilization of Immunoglobulin G Increases the Low pH Binding Affinity with the Neonatal Fc Receptor. J Biol Chem 2015; 291:1817-1825. [PMID: 26627822 DOI: 10.1074/jbc.m115.691568] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Indexed: 11/06/2022] Open
Abstract
Crystallographic evidence suggests that the pH-dependent affinity of IgG molecules for the neonatal Fc receptor (FcRn) receptor primarily arises from salt bridges involving IgG histidine residues, resulting in moderate affinity at mildly acidic conditions. However, this view does not explain the diversity in affinity found in IgG variants, such as the YTE mutant (M252Y,S254T,T256E), which increases affinity to FcRn by up to 10×. Here we compare hydrogen exchange measurements at pH 7.0 and pH 5.5 with and without FcRn bound with surface plasmon resonance estimates of dissociation constants and FcRn affinity chromatography. The combination of experimental results demonstrates that differences between an IgG and its cognate YTE mutant vary with their pH-sensitive dynamics prior to binding FcRn. The conformational dynamics of these two molecules are nearly indistinguishable upon binding FcRn. We present evidence that pH-induced destabilization in the CH2/3 domain interface of IgG increases binding affinity by breaking intramolecular H-bonds and increases side-chain adaptability in sites that form intermolecular contacts with FcRn. Our results provide new insights into the mechanism of pH-dependent affinity in IgG-FcRn interactions and exemplify the important and often ignored role of intrinsic conformational dynamics in a protein ligand, to dictate affinity for biologically important receptors.
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Affiliation(s)
- Benjamin T Walters
- From the Departments of Protein Analytical Chemistry,; Early Stage Pharmaceutical Development, and.
| | - Pernille F Jensen
- the Department of Pharmacy, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Vincent Larraillet
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center, DE-82377 Penzberg, Germany, and
| | - Kevin Lin
- Analytical Operations, Genentech Inc., South San Francisco, California 94080-4990
| | | | - Tilman Schlothauer
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center, DE-82377 Penzberg, Germany, and
| | - Kasper D Rand
- the Department of Pharmacy, University of Copenhagen, 1165 Copenhagen, Denmark
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Trabjerg E, Jakobsen RU, Mysling S, Christensen S, Jørgensen TJD, Rand KD. Conformational analysis of large and highly disulfide-stabilized proteins by integrating online electrochemical reduction into an optimized H/D exchange mass spectrometry workflow. Anal Chem 2015; 87:8880-8. [PMID: 26249042 DOI: 10.1021/acs.analchem.5b01996] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of disulfide-bonded proteins by hydrogen/deuterium exchange mass spectrometry (HDX-MS) requires effective and rapid reduction of disulfide bonds before enzymatic digestion in order to increase sequence coverage. In a conventional HDX-MS workflow, disulfide bonds are reduced chemically by addition of a reducing agent to the quench solution (e.g., tris(2-carboxyethyl)phosphine (TCEP)). The chemical reduction, however, is severely limited under quenched conditions due to a narrow time window as well as low pH and temperature. Here, we demonstrate the real-world applicability of integrating electrochemical reduction into an online HDX-MS workflow. We have optimized the electrochemical reduction efficiency during HDX-MS analysis of two particularly challenging disulfide stabilized proteins: a therapeutic IgG1-antibody and nerve growth factor-β (NGF). Several different parameters (flow rate and applied square wave potential, as well as the type of labeling and quench buffer) were investigated, and the optimized workflow increased the sequence coverage of NGF from 46% with chemical reduction to 99%, when electrochemical reduction was applied. Additionally, the optimized workflow also enabled a similar high sequence coverage of 96% and 87% for the heavy and light chain of the IgG1-antibody, respectively. The presented results demonstrate the successful electrochemical reduction during HDX-MS analysis of both a small exceptional tightly disulfide-bonded protein (NGF) as well as the largest protein attempted to date (IgG1-antibody). We envision that online electrochemical reduction is poised to decrease the complexity of sample handling and increase the versatility of the HDX-MS technique.
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Affiliation(s)
- Esben Trabjerg
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, Copenhagen E, DK-2100, Denmark.,Department of Biologics, H. Lundbeck A/S , Ottiliavej 9, Valby, DK-2500, Denmark
| | - Rasmus U Jakobsen
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, Copenhagen E, DK-2100, Denmark
| | - Simon Mysling
- Finsen Laboratory, Rigshospitalet and Biotech Research and Innovation Centre (BRIC), Copenhagen Biocenter , Ole Maaløes vej 5, Copenhagen N, DK-2200, Denmark
| | - Søren Christensen
- Department of Biologics, H. Lundbeck A/S , Ottiliavej 9, Valby, DK-2500, Denmark
| | - Thomas J D Jørgensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campuvej 55, Odense, DK-5230, Denmark
| | - Kasper D Rand
- Department of Pharmacy, University of Copenhagen , Universitetsparken 2, Copenhagen E, DK-2100, Denmark
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