1
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Attanayake K, Mahmud S, Banerjee C, Sharif D, Rahman M, Majuta S, DeBastiani A, Sultana MN, Foroushani SH, Li C, Li P, Valentine SJ. Examining DNA Structures with In-droplet Hydrogen/Deuterium Exchange Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2024; 499:117231. [PMID: 38854816 PMCID: PMC11156224 DOI: 10.1016/j.ijms.2024.117231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Capillary vibrating sharp-edge spray ionization (cVSSI) combined with hydrogen/deuterium exchange-mass spectrometry (HDX-MS) has been utilized to characterize different solution-phase DNA conformers including DNA G-quadruplex topologies as well as triplex DNA and duplex DNA. In general, G-quadruplex DNA shows a wide range of protection of hydrogens extending from ~12% to ~21% deuterium incorporation. Additionally, the DNA sequences selected to represent parallel, antiparallel, and hybrid G-quadruplex topologies exhibit slight differences in deuterium uptake levels which appear to loosely relate to overall conformer stability. Notably, the exchange level for one of the hybrid sequence sub topologies of G-quadruplex DNA (24 TTG) is significantly different (compared with the others studied here) despite the DNA sequences being highly comparable. For the quadruplex-forming sequences, correlation analysis suggests protection of base hydrogens involved in tetrad hydrogen bonding. For duplex DNA ~19% deuterium incorporation is observed while only ~16% is observed for triplex DNA. This increased protection of hydrogens may be due to the added backbone scaffolding and Hoogsteen base pairing of the latter species. These experiments lay the groundwork for future studies aimed at determining the structural source of this protection as well as the applicability of the approach for ascertaining different oligonucleotide folds, co-existing conformations, and/or overall conformer flexibility.
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Affiliation(s)
- Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Chandrima Banerjee
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Sandra Majuta
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - Chong Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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2
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Wrigley MS, Blockinger H, Haque HME, Karunaratne SP, Weis DD. Optimization of a Hydrogen Exchange-Mass Spectrometry Robotic Liquid Handler Using Tracers. Anal Chem 2024; 96:1522-1529. [PMID: 38237105 DOI: 10.1021/acs.analchem.3c04186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Hydrogen exchange-mass spectrometry (HX-MS) is a valuable analytical technique that can provide insight into protein interactions and structure. The deuterium labeling necessary to gain this insight is affected by many physical and chemical factors, making it challenging to achieve high reproducibility. Poor precision during dispensing, transfer, and mixing of solutions during the experiment contributes substantially to the overall variability. While the use of a robotic liquid handler can potentially improve precision, its operation must be optimized. We observed poor precision in data collected using a robotic liquid handler to perform HX-MS. In this work, we describe how we were able to improve that system's precision considerably based on tracking performance using caffeine, caffeine-d3, and caffeine-d9 as tracers for the sample, label, and quench to report on each operation of the liquid handling workflow. The insights gained about liquid handler performance and the three-tracer approach can aid in optimizing HX-MS workflow operations, whether performed manually or when using a liquid handling system. Additionally, these tracers can be incorporated as internal tracers during an experiment to report on the labeling and quench operations of each sample throughout the run and, if desired, be used to implement an uptake correction described previously.
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Affiliation(s)
- Michael S Wrigley
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Hayley Blockinger
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - H M Emranul Haque
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - Sachini P Karunaratne
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
| | - David D Weis
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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3
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Anderson KW, Hudgens JW. Hydrophilic Interaction Liquid Chromatography at Subzero Temperature for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:2672-2679. [PMID: 37930109 PMCID: PMC10704588 DOI: 10.1021/jasms.3c00243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/26/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
Chromatographic separations at subzero temperature significantly improve the precision of back-exchange-corrected hydrogen-deuterium exchange mass spectrometry (HDX-MS) determinations. Our previously reported dual-enzyme HDX-MS analysis instrument used reversed phase liquid chromatography (RPLC) at -30 °C, but high backpressures limited flow rates and required materials and equipment rated for very high pressures. Here, we report the design and performance of a dual-enzyme HDX-MS analysis instrument comprising a RPLC trap column and a hydrophilic interaction liquid chromatography (HILIC) analytical column in a two-dimensional RPLC-HILIC configuration at subzero temperature. During operation at -30 °C, the HILIC column manifests greatly reduced backpressure, which enables faster analytical flow rates and the use of materials rated for lower maximum pressures. The average peptide eluted from a HILIC column during a 40 min gradient at -30 °C contained ≈13% more deuterium than peptides eluted from a tandem RPLC-RPLC apparatus using a conventional 8 min gradient at 0 °C. A subset of peptides eluted from the HILIC apparatus contained ≈24% more deuterium.
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Affiliation(s)
- Kyle W. Anderson
- Bioprocess
Measurements Group, Biomolecular Measurement 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
| | - Jeffrey W. Hudgens
- Bioprocess
Measurements Group, Biomolecular Measurement 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
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4
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Sharif D, Rahman M, Mahmud S, Sultana MN, Attanayake K, DeBastiani A, Foroushani SH, Li P, Valentine SJ. In-droplet hydrogen-deuterium exchange to examine protein/peptide solution conformer heterogeneity. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9593. [PMID: 37430450 DOI: 10.1002/rcm.9593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/25/2023] [Accepted: 05/22/2023] [Indexed: 07/12/2023]
Abstract
RATIONALE Many different structure analysis techniques are not capable of probing the heterogeneity of solution conformations. Here, we examine the ability of in-droplet hydrogen-deuterium exchange (HDX) to directly probe solution conformer heterogeneity of a protein with mass spectrometry (MS) detection. METHODS Two vibrating capillary vibrating sharp-edge spray ionization (cVSSI) devices have been arranged such that they generate microdroplet plumes of the analyte and D2 O reagent, which coalesce to form reaction droplets where HDX takes place in the solution environment. The native HDX-MS setup has been first explored for two model peptides that have distinct structural compositions in solution. The effectiveness of the multidevice cVSSI-HDX in illustrating structural details has been further exploited to investigate coexisting solution-phase conformations of the protein ubiquitin. RESULTS In-droplet HDX reveals decreased backbone exchange for a model peptide that has a greater helix-forming propensity. Differences in intrinsic rates of the alanine and serine residues may account for much of the observed protection. The data allow the first estimates of backbone exchange rates for peptides undergoing in-droplet HDX. That said, the approach may hold greater potential for investigating the tertiary structure and structural transitions of proteins. For ubiquitin protein, HDX reactivity differences suggest that multiple conformers are present in native solutions. The addition of methanol to buffered aqueous solutions of ubiquitin results in increased populations of solution conformers of higher reactivity. Data analysis suggests that partially folded conformers such as the A-state of ubiquitin increase with methanol content; the native state may be preserved to a limited degree even under stronger denaturation conditions. CONCLUSION The deuterium uptake after in-droplet HDX has been observed to correspond to some degree with peptide backbone hydrogen protection based on differences in intrinsic rates of exchange. The presence of coexisting protein solution structures under native and denaturing solution conditions has been distinguished by the isotopic distributions of deuterated ubiquitin ions.
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Affiliation(s)
- Daud Sharif
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mohammad Rahman
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Sultan Mahmud
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Mst Nigar Sultana
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Kushani Attanayake
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Anthony DeBastiani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Samira Hajian Foroushani
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
| | - Stephen J Valentine
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, West Virginia, USA
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Hatvany JB, Gallagher ES. Hydrogen/deuterium exchange for the analysis of carbohydrates. Carbohydr Res 2023; 530:108859. [PMID: 37290371 DOI: 10.1016/j.carres.2023.108859] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/10/2023]
Abstract
Carbohydrates and glycans are integral to many biological processes, including cell-cell recognition and energy storage. However, carbohydrates are often difficult to analyze due to the high degree of isomerism present. One method being developed to distinguish these isomeric species is hydrogen/deuterium exchange-mass spectrometry (HDX-MS). In HDX-MS, carbohydrates are exposed to a deuterated reagent and the functional groups with labile hydrogen atoms, including hydroxyls and amides, exchange with the 1 amu heavier isotope, deuterium. These labels can then be detected by MS, which monitors the mass increase with the addition of D-labels. The observed rate of exchange is dependent on the exchanging functional group, the accessibility of the exchanging functional group, and the presence of hydrogen bonds. Herein, we discuss how HDX has been applied in the solution-phase, gas-phase, and during MS ionization to label carbohydrates and glycans. Additionally, we compare differences in the conformations that are labeled, the labeling timeframes, and applications of each of these methods. Finally, we comment on future opportunities for development and use of HDX-MS to analyze glycans and glycoconjugates.
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Affiliation(s)
- Jacob B Hatvany
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA
| | - Elyssia S Gallagher
- Department of Chemistry and Biochemistry, Baylor University, One Bear Place #97348, Waco, TX, 76798, USA.
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6
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Kalaninová Z, Fojtík L, Chmelík J, Novák P, Volný M, Man P. Probing Antibody Structures by Hydrogen/Deuterium Exchange Mass Spectrometry. Methods Mol Biol 2023; 2718:303-334. [PMID: 37665467 DOI: 10.1007/978-1-0716-3457-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Hydrogen/deuterium exchange (HDX) followed by mass spectrometry detection (MS) provides a fast, reliable, and detailed solution for the assessment of a protein structure. It has been widely recognized as an indispensable tool and already approved by several regulatory agencies as a structural technique for the validation of protein biopharmaceuticals, including antibody-based drugs. Antibodies are of a key importance in life and medical sciences but considered to be challenging analytical targets because of their compact structure stabilized by disulfide bonds and due to the presence of glycosylation. Despite these difficulties, there are already numerous excellent studies describing MS-based antibody structure characterization. In this chapter, we describe a universal HDX-MS workflow. Deeper attention is paid to sample handling, optimization procedures, and feasibility stages, as these elements of the HDX experiment are crucial for obtaining reliable detailed and spatially well-resolved information.
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Affiliation(s)
- Zuzana Kalaninová
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lukáš Fojtík
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Josef Chmelík
- Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Novák
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Michael Volný
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic
| | - Petr Man
- BioCeV - Institute of Microbiology of the Czech Academy of Sciences, Vestec, Czech Republic.
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7
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Anderson KW, Hudgens JW. Chromatography at -30 °C for Reduced Back-Exchange, Reduced Carryover, and Improved Dynamic Range for Hydrogen-Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1282-1292. [PMID: 35732031 PMCID: PMC9264389 DOI: 10.1021/jasms.2c00096] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
For hydrogen-deuterium exchange mass spectrometry (HDX-MS) to have an increased role in quality control of biopharmaceuticals, H for D back-exchange occurring during protein analyses should be minimized to promote greater reproducibility. Standard HDX-MS analysis systems that digest proteins and separate peptides at pH 2.7 and 0 °C can lose >30% of the deuterium marker within 15 min of sample injection. This report describes the architecture and performance of a dual-enzyme, HDX-MS instrument that conducts liquid chromatography (LC) separations at subzero temperature, thereby reducing back-exchange and supporting longer LC separations with improved chromatographic resolution. LC separations of perdeuterated, fully reduced, iodoacetamide-treated BSA protein digest standard peptides were performed at 0, -10, -20, and -30 °C in ethylene glycol (EG)/H2O mixtures. Analyses conducted at -20 and -30 °C produced similar results. After subtracting for deuterium retained in arginine side chains, the average peptide eluted during a 40 min gradient contained ≈16% more deuterium than peptides eluted with a conventional 8 min gradient at 0 °C. A subset of peptides exhibited ≈26% more deuterium. Although chromatographic peaks shift with EG concentration and temperature, the apparatus elutes unbroadened LC peaks. Electrospray ion intensity does not decline with increasing EG fraction. To minimize bias from sample carryover, the fluidic circuits allow flush and backflush cleaning of all enzyme and LC columns. The system can perform LC separations and clean enzyme columns simultaneously. Temperature zones are controlled ±0.058 °C. The potential of increased sensitivity by mixing acetonitrile with the analytical column effluent was also examined.
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Affiliation(s)
- Kyle W. Anderson
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Jeffrey W. Hudgens
- National
Institute of Standards and Technology, Bioprocess
Measurement Group, Biomolecular Measurements Division, Rockville, Maryland 20850, United States
- Institute
for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
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8
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Anderson KW, Bergonzo C, Scott K, Karageorgos IL, Gallagher ES, Tayi VS, Butler M, Hudgens JW. HDX-MS and MD Simulations Provide Evidence for Stabilization of the IgG1-FcγRIa (CD64a) Immune Complex Through Intermolecular Glycoprotein Bonds. J Mol Biol 2021; 434:167391. [PMID: 34890647 DOI: 10.1016/j.jmb.2021.167391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/05/2021] [Accepted: 11/29/2021] [Indexed: 11/19/2022]
Abstract
Previous reports present different models for the stabilization of the Fc-FcγRI immune complex. Although accord exists on the importance of L235 in IgG1 and some hydrophobic contacts for complex stabilization, discord exists regarding the existence of stabilizing glycoprotein contacts between glycans of IgG1 and a conserved FG-loop (171MGKHRY176) of FcγRIa. Complexes formed from the FcγRIa receptor and IgG1s containing biantennary glycans with N-acetylglucosamine, galactose, and α2,6-N-acetylneuraminic terminations were measured by hydrogen-deuterium exchange mass spectrometry (HDX-MS), classified for dissimilarity with Welch's ANOVA and Games-Howell post hoc procedures, and modeled with molecular dynamics (MD) simulations. For each glycoform of the IgG1-FcγRIa complex peptic peptides of Fab, Fc and FcγRIa report distinct H/D exchange rates. MD simulations corroborate the differences in the peptide deuterium content through calculation of the percent of time that transient glycan-peptide bonds exist. These results indicate that stability of IgG1-FcγRIa complexes correlate with the presence of intermolecular glycoprotein interactions between the IgG1 glycans and the 173KHR175 motif within the FG-loop of FcγRIa. The results also indicate that intramolecular glycan-protein bonds stabilize the Fc region in isolated and complexed IgG1. Moreover, HDX-MS data evince that the Fab domain has glycan-protein binding contacts within the IgG1-FcγRI complex.
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Affiliation(s)
- Kyle W Anderson
- National Institute of Standards and Technology, Bioprocess Measurements Group, Biomolecular Measurement Division, 9600 Gudelsky Drive, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Christina Bergonzo
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA; National Institute of Standards and Technology, Biomolecular Structure and Function Group, Biomolecular Measurement Division, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Kerry Scott
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA; National Institute of Standards and Technology, Bioanalytical Science Group, Biomolecular Measurement Division, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Ioannis L Karageorgos
- National Institute of Standards and Technology, Bioprocess Measurements Group, Biomolecular Measurement Division, 9600 Gudelsky Drive, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Elyssia S Gallagher
- National Institute of Standards and Technology, Bioprocess Measurements Group, Biomolecular Measurement Division, 9600 Gudelsky Drive, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
| | - Venkata S Tayi
- University of Manitoba, Department of Microbiology, Winnipeg, MB R3T 2N2, Canada.
| | - Michael Butler
- University of Manitoba, Department of Microbiology, Winnipeg, MB R3T 2N2, Canada; National Institute for Bioprocessing Research and Training, 26 Foster's Ave, Belfield, Blackrock, Co. Dublin A94 F5D5, Ireland.
| | - Jeffrey W Hudgens
- National Institute of Standards and Technology, Bioprocess Measurements Group, Biomolecular Measurement Division, 9600 Gudelsky Drive, Rockville, MD 20850, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA.
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9
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Hamuro Y. Quantitative Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:2711-2727. [PMID: 34749499 DOI: 10.1021/jasms.1c00216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
This Account describes considerations for the data generation, data analysis, and data interpretation of a hydrogen/deuterium exchange-mass spectrometry (HDX-MS) experiment to have a quantitative argument. Although HDX-MS has gained its popularity as a biophysical tool, the argument from its data often remains qualitative. To generate HDX-MS data that are more suitable for a quantitative argument, the sequence coverage and sequence resolution should be optimized during the feasibility stage, and the time window coverage and time window resolution should be improved during the HDX stage. To extract biophysically meaningful values for a certain perturbation from medium-resolution HDX-MS data, there are two major ways: (i) estimating the area between the two deuterium buildup curves using centroid values with and without the perturbation when plotted against log time scale and (ii) dissecting into multiple single-exponential curves using the isotope envelopes. To have more accurate arguments for an HDX-MS perturbation study, (i) false negatives due to sequence coverage, (ii) false negatives due to time window coverage, (iii) false positives due to sequence resolution, and (iv) false positives due to allosteric effects should be carefully examined.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation, 11 Deer Park Drive, Suite 103, Monmouth Junction, New Jersey 08852, United States
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10
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James EI, Murphree TA, Vorauer C, Engen JR, Guttman M. Advances in Hydrogen/Deuterium Exchange Mass Spectrometry and the Pursuit of Challenging Biological Systems. Chem Rev 2021; 122:7562-7623. [PMID: 34493042 PMCID: PMC9053315 DOI: 10.1021/acs.chemrev.1c00279] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Solution-phase hydrogen/deuterium
exchange (HDX) coupled to mass
spectrometry (MS) is a widespread tool for structural analysis across
academia and the biopharmaceutical industry. By monitoring the exchangeability
of backbone amide protons, HDX-MS can reveal information about higher-order
structure and dynamics throughout a protein, can track protein folding
pathways, map interaction sites, and assess conformational states
of protein samples. The combination of the versatility of the hydrogen/deuterium
exchange reaction with the sensitivity of mass spectrometry has enabled
the study of extremely challenging protein systems, some of which
cannot be suitably studied using other techniques. Improvements over
the past three decades have continually increased throughput, robustness,
and expanded the limits of what is feasible for HDX-MS investigations.
To provide an overview for researchers seeking to utilize and derive
the most from HDX-MS for protein structural analysis, we summarize
the fundamental principles, basic methodology, strengths and weaknesses,
and the established applications of HDX-MS while highlighting new
developments and applications.
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Affiliation(s)
- Ellie I James
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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11
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Weis DD. Recommendations for the Propagation of Uncertainty in Hydrogen Exchange-Mass Spectrometric Measurements. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1610-1617. [PMID: 33764776 DOI: 10.1021/jasms.0c00475] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Hydrogen exchange-mass spectrometry (HX-MS) is used widely to characterize higher-order protein structure and to locate changes in protein structure and dynamics that accompany, for example, ligand binding and protein-protein interactions. Quantitative differences in the amount of hydrogen exchange between two states (i.e., differential HX) are taken as evidence of significant differences in higher-order structure or dynamics. The quantitative measures range from simple mass differences at one HX labeling time to differences averaged across an HX time course with correction for deuterium recovery. This work applies the principles of uncertainty propagation to differential HX measurements to facilitate the identification of significant differences. Furthermore, it is shown that pooled estimates of experimental uncertainty result in a lower false positive rate than estimates of uncertainty based on individual standard deviations.
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Affiliation(s)
- David D Weis
- Department of Chemistry, The University of Kansas, 1567 Irving Hill Road, Lawrence, Kansas 66045, United States
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12
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Anderson KW, Scott K, Karageorgos IL, Gallagher ES, Tayi VS, Butler M, Hudgens JW. Dataset from HDX-MS Studies of IgG1 Glycoforms and Their Interactions with the FcγRIa (CD64) Receptor. JOURNAL OF RESEARCH OF THE NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY 2021; vol:126010. [PMID: 36474595 PMCID: PMC9681196 DOI: 10.6028/jres.126.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 05/17/2023]
Abstract
This document presents hydrogen-deuterium exchange mass spectrometry (HDX-MS) data from measurements of three purified IgG1 glycoform samples, predominantly G0F, G2F, and SAF, in isolation and in complexation with the high-affinity receptor, FcγRIa (CD64). The IgG1 antibody used in this study, aIL8hFc, is a murine-human chimeric IgG1, which inhibits IL-8 binding to human neutrophils.
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Affiliation(s)
- Kyle W. Anderson
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Kerry Scott
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Ioannis L. Karageorgos
- National Institute of Standards and Technology, 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, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
| | - Venkata S. Tayi
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2,
Canada
| | - Michael Butler
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2,
Canada
- National Institute for Bioprocessing Research and Training, Foster Avenue, Mount Merrion, Blackrock, Co. Dublin,
Ireland
| | - Jeffrey W. Hudgens
- National Institute of Standards and Technology, Gaithersburg, MD 20899,
USA
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850,
USA
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13
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Murphree TA, Vorauer C, Brzoska M, Guttman M. Imidazolium Compounds as Internal Exchange Reporters for Hydrogen/Deuterium Exchange by Mass Spectrometry. Anal Chem 2020; 92:9830-9837. [PMID: 32569457 DOI: 10.1021/acs.analchem.0c01328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is a powerful tool for protein structure analysis that is well suited for biotherapeutic development and characterization. Because HDX is strongly dependent on solution conditions, even small variations in temperature or pH can have a pronounced effect on the observed kinetics that can manifest in significant run-to-run variability and compromise reproducibility. Recent attention has been given to the development of internal exchange reporters (IERs), which directly monitor changes to exchange reaction conditions. However, the currently available small peptide IERs are only capable of sampling a very narrow temporal window and are understood to exhibit complex solution dependent exchange behavior. Here we demonstrate the use of imidazolium carbon acids as superior IERs for HDX-MS. These compounds exhibit predictable exchange behavior under a wide variety of reaction conditions, are highly stable, and can be readily modified to exchange over a broad temporal window. The use of these compounds as IERs for solution based HDX-MS could considerably extend the utility of the technique by allowing for more robust empirical exchange correction, thereby improving reproducibility.
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Affiliation(s)
- Taylor A Murphree
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Clint Vorauer
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Marie Brzoska
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195, United States
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14
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Liu H, Wang D, Zhang Q, Zhao Y, Mamonova T, Wang L, Zhang C, Li S, Friedman PA, Xiao K. Parallel Post-Translational Modification Scanning Enhancing Hydrogen-Deuterium Exchange-Mass Spectrometry Coverage of Key Structural Regions. Anal Chem 2019; 91:6976-6980. [PMID: 31082219 DOI: 10.1021/acs.analchem.9b01410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen-deuterium exchange-mass spectrometry (HDXMS) is a powerful technology to characterize conformations and conformational dynamics of proteins and protein complexes. HDXMS has been widely used in the field of therapeutics for the development of protein drugs. Although sufficient sequence coverage is critical to the success of HDXMS, it is sometimes difficult to achieve. In this study, we developed a HDXMS data analysis strategy that includes parallel post-translational modification (PTM) scanning in HDXMS analysis. Using a membrane-delimited G protein-coupled receptor (vasopressin type 2 receptor; V2R) and a cytosolic protein (Na+/H+ exchanger regulatory factor-1; NHERF1) as examples, we demonstrate that this strategy substantially improves protein sequence coverage, especially in key structural regions likely including PTMs themselves that play important roles in protein conformational dynamics and function.
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Affiliation(s)
| | | | | | | | | | | | | | - Sheng Li
- Department of Medicine , University of California San Diego , La Jolla , California 92093 , United States
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15
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Kratochvil I, Hofmann T, Rother S, Schlichting R, Moretti R, Scharnweber D, Hintze V, Escher BI, Meiler J, Kalkhof S, von Bergen M. Mono(2-ethylhexyl) phthalate (MEHP) and mono(2-ethyl-5-oxohexyl) phthalate (MEOHP) but not di(2-ethylhexyl) phthalate (DEHP) bind productively to the peroxisome proliferator-activated receptor γ. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33 Suppl 1:75-85. [PMID: 30085373 PMCID: PMC6367069 DOI: 10.1002/rcm.8258] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 06/18/2018] [Accepted: 07/29/2018] [Indexed: 05/09/2023]
Abstract
RATIONALE The most frequently occurring phthalate, di(2-ethylhexyl) phthalate (DEHP), causes adverse effects on glucose homeostasis and insulin sensitivity in several cell models and epidemiological studies. However, thus far, there is no information available on the molecular interaction of phthalates and one of the key regulators of the metabolism, the peroxisome proliferator-activated receptor gamma (PPARγ). Since the endogenous ligand of PPARγ, 15-deoxy-delta-12,14-prostaglandin J2 (15Δ-PGJ2 ), features structural similarity to DEHP and its main metabolites produced in human hepatic metabolism, mono(2-ethylhexyl) phthalate (MEHP) and mono(2-ethyl-5-oxohexyl) phthalate (MEOHP), we tested the hypothesis of direct interactions between PPARγ and DEHP or its transformation products. METHODS Hydrogen/deuterium exchange mass spectrometry (HDX-MS) and docking were conducted to obtain structural insights into the interactions and surface plasmon resonance (SPR) analysis to reveal information about binding levels. To confirm the activation of PPARγ upon ligand binding on the cellular level, the GeneBLAzer® bioassay was performed. RESULTS HDX-MS and SPR analyses demonstrated that the metabolites MEHP and MEOHP, but not DEHP itself, bind to the ligand binding pocket of PPARγ. This binding leads to typical activation-associated conformational changes, as observed with its endogenous ligand 15Δ-PGJ2 . Furthermore, the reporter gene assay confirmed productive interaction. DEHP was inactive up to a concentration of 14 μM, while the metabolites MEHP and MEOHP were active at low micromolar concentrations. CONCLUSIONS In summary, this study gives structural insights into the direct interaction of PPARγ with MEHP and MEOHP and shows that the DEHP transformation products may modulate the lipid metabolism through PPARγ pathways.
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Affiliation(s)
- Isabel Kratochvil
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Tommy Hofmann
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Sandra Rother
- Institute of Materials Science, Max Bergmann Center of Biomaterials, TU Dresden, Budapester Straße 27, 01069 Dresden, Germany
| | - Rita Schlichting
- Department of Cell Toxicology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Rocco Moretti
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - Dieter Scharnweber
- Institute of Materials Science, Max Bergmann Center of Biomaterials, TU Dresden, Budapester Straße 27, 01069 Dresden, Germany
| | - Vera Hintze
- Institute of Materials Science, Max Bergmann Center of Biomaterials, TU Dresden, Budapester Straße 27, 01069 Dresden, Germany
| | - Beate I. Escher
- Department of Cell Toxicology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37212, USA
| | - Stefan Kalkhof
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany
- Institute of Biochemistry, Leipzig University, Brüderstraße 34, 04103 Leipzig, Germany
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16
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MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals. Methods 2018; 144:134-151. [PMID: 29678586 DOI: 10.1016/j.ymeth.2018.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 01/18/2023] Open
Abstract
Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of protein therapeutics.
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17
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Hamuro Y, Coales SJ. Optimization of Feasibility Stage for Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:623-629. [PMID: 29299838 DOI: 10.1007/s13361-017-1860-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 05/12/2023]
Abstract
The practice of HDX-MS remains somewhat difficult, not only for newcomers but also for veterans, despite its increasing popularity. While a typical HDX-MS project starts with a feasibility stage where the experimental conditions are optimized and the peptide map is generated prior to the HDX study stage, the literature usually reports only the HDX study stage. In this protocol, we describe a few considerations for the initial feasibility stage, more specifically, how to optimize quench conditions, how to tackle the carryover issue, and how to apply the pepsin specificity rule. Two sets of quench conditions are described depending on the presence of disulfide bonds to facilitate the quench condition optimization process. Four protocols are outlined to minimize carryover during the feasibility stage: (1) addition of a detergent to the quench buffer, (2) injection of a detergent or chaotrope to the protease column after each sample injection, (3) back-flushing of the trap column and the analytical column with a new plumbing configuration, and (4) use of PEEK (or PEEK coated) frits instead of stainless steel frits for the columns. The application of the pepsin specificity rule after peptide map generation and not before peptide map generation is suggested. The rule can be used not only to remove falsely identified peptides, but also to check the sample purity. A well-optimized HDX-MS feasibility stage makes subsequent HDX study stage smoother and the resulting HDX data more reliable. Graphical Abstract ᅟ.
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Affiliation(s)
- Yoshitomo Hamuro
- ExSAR Corporation (scientifically co-founded by Professor Virgil Woods and now dissolved), Monmouth Junction, NJ, USA.
- SGS Life North America, 606 Brandywine Parkway, West Chester, PA, 19380, USA.
| | - Stephen J Coales
- ExSAR Corporation (scientifically co-founded by Professor Virgil Woods and now dissolved), Monmouth Junction, NJ, USA
- LEAP Technologies, 1015 Aviation Parkway, Suite 1000, Morrisville, NC, 27560, USA
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18
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Mohtar MA, Hernychova L, O'Neill JR, Lawrence ML, Murray E, Vojtesek B, Hupp TR. The Sequence-specific Peptide-binding Activity of the Protein Sulfide Isomerase AGR2 Directs Its Stable Binding to the Oncogenic Receptor EpCAM. Mol Cell Proteomics 2018; 17:737-763. [PMID: 29339412 PMCID: PMC5880107 DOI: 10.1074/mcp.ra118.000573] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Indexed: 12/30/2022] Open
Abstract
AGR2 is an oncogenic endoplasmic reticulum (ER)-resident protein disulfide isomerase. AGR2 protein has a relatively unique property for a chaperone in that it can bind sequence-specifically to a specific peptide motif (TTIYY). A synthetic TTIYY-containing peptide column was used to affinity-purify AGR2 from crude lysates highlighting peptide selectivity in complex mixtures. Hydrogen-deuterium exchange mass spectrometry localized the dominant region in AGR2 that interacts with the TTIYY peptide to within a structural loop from amino acids 131–135 (VDPSL). A peptide binding site consensus of Tx[IL][YF][YF] was developed for AGR2 by measuring its activity against a mutant peptide library. Screening the human proteome for proteins harboring this motif revealed an enrichment in transmembrane proteins and we focused on validating EpCAM as a potential AGR2-interacting protein. AGR2 and EpCAM proteins formed a dose-dependent protein-protein interaction in vitro. Proximity ligation assays demonstrated that endogenous AGR2 and EpCAM protein associate in cells. Introducing a single alanine mutation in EpCAM at Tyr251 attenuated its binding to AGR2 in vitro and in cells. Hydrogen-deuterium exchange mass spectrometry was used to identify a stable binding site for AGR2 on EpCAM, adjacent to the TLIYY motif and surrounding EpCAM's detergent binding site. These data define a dominant site on AGR2 that mediates its specific peptide-binding function. EpCAM forms a model client protein for AGR2 to study how an ER-resident chaperone can dock specifically to a peptide motif and regulate the trafficking a protein destined for the secretory pathway.
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Affiliation(s)
- M Aiman Mohtar
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR.,§National University of Malaysia, UKM Medical Molecular Biology Institute (UMBI), 56000 Kuala Lumpur, Malaysia
| | - Lenka Hernychova
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - J Robert O'Neill
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR
| | - Melanie L Lawrence
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR
| | - Euan Murray
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR.,¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Borek Vojtesek
- ¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic
| | - Ted R Hupp
- From the ‡University of Edinburgh, Institute of Genetics and Molecular Medicine, Edinburgh, Scotland, United Kingdom, EH4 2XR; .,¶Regional Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, 656 53 Brno, Czech Republic.,‖University of Gdansk, International Centre for Cancer Vaccine Science, ul. Wita Stwosza 63, 80-308 Gdansk, Poland
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19
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Masson GR, Jenkins ML, Burke JE. An overview of hydrogen deuterium exchange mass spectrometry (HDX-MS) in drug discovery. Expert Opin Drug Discov 2017; 12:981-994. [PMID: 28770632 DOI: 10.1080/17460441.2017.1363734] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Hydrogen deuterium exchange mass spectrometry (HDX-MS) is a powerful methodology to study protein dynamics, protein folding, protein-protein interactions, and protein small molecule interactions. The development of novel methodologies and technical advancements in mass spectrometers has greatly expanded the accessibility and acceptance of this technique within both academia and industry. Areas covered: This review examines the theoretical basis of how amide exchange occurs, how different mass spectrometer approaches can be used for HDX-MS experiments, as well as the use of HDX-MS in drug development, specifically focusing on how HDX-MS is used to characterize bio-therapeutics, and its use in examining protein-protein and protein small molecule interactions. Expert opinion: HDX-MS has been widely accepted within the pharmaceutical industry for the characterization of bio-therapeutics as well as in the mapping of antibody drug epitopes. However, there is room for this technique to be more widely used in the drug discovery process. This is particularly true in the use of HDX-MS as a complement to other high-resolution structural approaches, as well as in the development of small molecule therapeutics that can target both active-site and allosteric binding sites.
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Affiliation(s)
- Glenn R Masson
- a Protein and Nucleic Acid Chemistry Division , MRC Laboratory of Molecular Biology , Cambridge , UK
| | - Meredith L Jenkins
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
| | - John E Burke
- b Department of Biochemistry and Microbiology , University of Victoria , Victoria , Canada
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20
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Cummins DJ, Espada A, Novick SJ, Molina-Martin M, Stites RE, Espinosa JF, Broughton H, Goswami D, Pascal BD, Dodge JA, Chalmers MJ, Griffin PR. Two-Site Evaluation of the Repeatability and Precision of an Automated Dual-Column Hydrogen/Deuterium Exchange Mass Spectrometry Platform. Anal Chem 2016; 88:6607-14. [PMID: 27224086 DOI: 10.1021/acs.analchem.6b01650] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) is an information-rich biophysical method for the characterization of protein dynamics. Successful applications of differential HDX-MS include the characterization of protein-ligand binding. A single differential HDX-MS data set (protein ± ligand) is often comprised of more than 40 individual HDX-MS experiments. To eliminate laborious manual processing of samples, and to minimize random and gross errors, automated systems for HDX-MS analysis have become routine in many laboratories. However, an automated system, while less prone to random errors introduced by human operators, may have systematic errors that go unnoticed without proper detection. Although the application of automated (and manual) HDX-MS has become common, there are only a handful of studies reporting the systematic evaluation of the performance of HDX-MS experiments, and no reports have been published describing a cross-site comparison of HDX-MS experiments. Here, we describe an automated HDX-MS platform that operates with a parallel, two-trap, two-column configuration that has been installed in two remote laboratories. To understand the performance of the system both within and between laboratories, we have designed and completed a test-retest repeatability study for differential HDX-MS experiments implemented at each of two laboratories, one in Florida and the other in Spain. This study provided sufficient data to do both within and between laboratory variability assessments. Initial results revealed a systematic run-order effect within one of the two systems. Therefore, the study was repeated, and this time the conclusion was that the experimental conditions were successfully replicated with minimal systematic error.
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Affiliation(s)
- David J Cummins
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Alfonso Espada
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Scott J Novick
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Manuel Molina-Martin
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Ryan E Stites
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Juan Felix Espinosa
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Howard Broughton
- Analytical Technologies Department, Centro de Investigación Lilly, SA , Avenida de la Industria 30, 28108 Alcobendas, Spain
| | - Devrishi Goswami
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Bruce D Pascal
- The Scripps Research institute, Informatics Core, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Jeffrey A Dodge
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Michael J Chalmers
- Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Patrick R Griffin
- The Scripps Research Institute , Department of Molecular Therapeutics, 130 Scripps Way, Jupiter, Florida 33458, United States
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21
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Gallagher ES, Hudgens JW. Mapping Protein–Ligand Interactions with Proteolytic Fragmentation, Hydrogen/Deuterium Exchange-Mass Spectrometry. Methods Enzymol 2016; 566:357-404. [DOI: 10.1016/bs.mie.2015.08.010] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Abstract
The structural analysis of viruses is often a complex task. In many cases, the details of the viral architecture, especially for enveloped viruses, are limited to low-resolution techniques such as electron microscopy. These structural proteins and assemblies of viruses often populate multiple conformational states and undergo dramatic structural changes, making them difficult to study by most structural methods. They also frequently include highly dynamic regions that are of key functional importance. Many viruses present large surface glycoproteins, which have also proved to be challenging for structural biology due to the intrinsic flexibility and heterogeneity of the glycan decorations. Over the past two decades, hydrogen deuterium exchange coupled to mass spectrometry (HDX-MS) has provided a wealth of information on many diverse viral proteins, glycoproteins, and complexes, in many cases, in multiple conformational states. Here, we describe the methodology for using HDX-MS to investigate the rich structural dynamics of viral systems, and we briefly review the type of systems that have been examined through this type of approach. Though the technique is relatively simple, several potential pitfalls exist at both the sample preparation and the data analysis stage that investigators should be aware of for obtaining reliable data.
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Affiliation(s)
- Miklos Guttman
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA.
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23
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Yang M, Hoeppner M, Rey M, Kadek A, Man P, Schriemer DC. Recombinant Nepenthesin II for Hydrogen/Deuterium Exchange Mass Spectrometry. Anal Chem 2015; 87:6681-7. [DOI: 10.1021/acs.analchem.5b00831] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Menglin Yang
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Morgan Hoeppner
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Martial Rey
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Alan Kadek
- Institute
of Microbiology, Academy of Sciences of the Czech Republic, 117
20 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 116
36 Prague, Czech Republic
| | - Petr Man
- Institute
of Microbiology, Academy of Sciences of the Czech Republic, 117
20 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles University in Prague, 116
36 Prague, Czech Republic
| | - David C. Schriemer
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Alberta, Canada T2N 1N4
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24
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Affiliation(s)
- Gregory
F. Pirrone
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - Roxana E. Iacob
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
| | - John R. Engen
- Department of Chemistry and
Chemical Biology, Northeastern University, 360 Huntington Ave., Boston, Massachusetts 02115 United States
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25
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Arndt JR, Brown RJ, Burke KA, Legleiter J, Valentine SJ. Lysine residues in the N-terminal huntingtin amphipathic α-helix play a key role in peptide aggregation. JOURNAL OF MASS SPECTROMETRY : JMS 2015; 50:117-126. [PMID: 25601683 DOI: 10.1002/jms.3504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 08/27/2014] [Accepted: 09/05/2014] [Indexed: 06/04/2023]
Abstract
Huntington's disease is a genetic neurodegenerative disorder caused by an expansion in a polyglutamine domain near the N-terminus of the huntingtin (htt) protein that results in the formation of protein aggregates. Here, htt aggregate structure has been examined using hydrogen-deuterium exchange techniques coupled with tandem mass spectrometry. The focus of the study is on the 17-residue N-terminal flanking region of the peptide that has been shown to alter htt aggregation kinetics and morphology. A top-down sequencing strategy employing electron transfer dissociation is utilized to determine the location of accessible and protected hydrogens. In these experiments, peptides aggregate in a deuterium-rich solvent at neutral pH and are subsequently subjected to deuterium-hydrogen back-exchange followed by rapid quenching, disaggregation, and tandem mass spectrometry analysis. Electrospray ionization of the peptide solution produces the [M + 5H](5+) to [M + 10H](10+) charge states and reveals the presence of multiple peptide sequences differing by single glutamine residues. The [M + 7H](7+) to [M + 9](9+) charge states corresponding to the full peptide are used in the electron transfer dissociation analyses. Evidence for protected residues is observed in the 17-residue N-terminal tract and specifically points to lysine residues as potentially playing a significant role in htt aggregation.
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Affiliation(s)
- James R Arndt
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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26
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Rey M, Sarpe V, Burns KM, Buse J, Baker CAH, van Dijk M, Wordeman L, Bonvin AMJJ, Schriemer DC. Mass spec studio for integrative structural biology. Structure 2014; 22:1538-48. [PMID: 25242457 DOI: 10.1016/j.str.2014.08.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/30/2014] [Accepted: 08/06/2014] [Indexed: 02/01/2023]
Abstract
The integration of biophysical data from multiple sources is critical for developing accurate structural models of large multiprotein systems and their regulators. Mass spectrometry (MS) can be used to measure the insertion location for a wide range of topographically sensitive chemical probes, and such insertion data provide a rich, but disparate set of modeling restraints. We have developed a software platform that integrates the analysis of label-based MS and tandem MS (MS(2)) data with protein modeling activities (Mass Spec Studio). Analysis packages can mine any labeling data from any mass spectrometer in a proteomics-grade manner, and link labeling methods with data-directed protein interaction modeling using HADDOCK. Support is provided for hydrogen/deuterium exchange (HX) and covalent labeling chemistries, including novel acquisition strategies such as targeted HX-MS(2) and data-independent HX-MS(2). The latter permits the modeling of highly complex systems, which we demonstrate by the analysis of microtubule interactions.
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Affiliation(s)
- Martial Rey
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Vladimir Sarpe
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Kyle M Burns
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Joshua Buse
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | - Marc van Dijk
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht CH 3584, the Netherlands
| | - Linda Wordeman
- Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA 98195-7290, USA
| | - Alexandre M J J Bonvin
- Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht CH 3584, the Netherlands
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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27
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Nucleotide exchange in dimeric MCAK induces longitudinal and lateral stress at microtubule ends to support depolymerization. Structure 2014; 22:1173-1183. [PMID: 25066134 DOI: 10.1016/j.str.2014.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 10/25/2022]
Abstract
Members of the kinesin-13 subfamily use motor domains in an unconventional fashion to initiate microtubule (MT) depolymerization at MT ends, suggesting unique conformational transitions for lattice engagement, end adaptation, or both. Using hydrogen-deuterium exchange and electron microscopy, we explored conformational changes in free dimeric mitotic centromere-associated kinesin (MCAK) and when bound to a depolymerization intermediate. ATP hydrolysis relaxes the conformation of the dimer, notably in the neck and N-terminal domain. Exchanging ADP in dimeric MCAK with ATP at the MT plus end induces outward curvature in α/β-tubulin, accompanied by a restructuring of the MCAK neck and N terminus, as it returns to a closed state. Reestablishing a closed dimer induces lateral separation of paired tubulin dimers, which may assist in depolymerization. Thus, full-length ADP-MCAK transitions from an open diffusion-competent configuration to a closed state upon plus end-mediated nucleotide exchange, which is mediated by conformational changes in the N-terminal domains of the dimer.
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Lindner R, Lou X, Reinstein J, Shoeman RL, Hamprecht FA, Winkler A. Hexicon 2: automated processing of hydrogen-deuterium exchange mass spectrometry data with improved deuteration distribution estimation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1018-28. [PMID: 24676893 PMCID: PMC4018513 DOI: 10.1007/s13361-014-0850-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/05/2014] [Accepted: 02/05/2014] [Indexed: 05/12/2023]
Abstract
Hydrogen-deuterium exchange (HDX) experiments analyzed by mass spectrometry (MS) provide information about the dynamics and the solvent accessibility of protein backbone amide hydrogen atoms. Continuous improvement of MS instrumentation has contributed to the increasing popularity of this method; however, comprehensive automated data analysis is only beginning to mature. We present Hexicon 2, an automated pipeline for data analysis and visualization based on the previously published program Hexicon (Lou et al. 2010). Hexicon 2 employs the sensitive NITPICK peak detection algorithm of its predecessor in a divide-and-conquer strategy and adds new features, such as chromatogram alignment and improved peptide sequence assignment. The unique feature of deuteration distribution estimation was retained in Hexicon 2 and improved using an iterative deconvolution algorithm that is robust even to noisy data. In addition, Hexicon 2 provides a data browser that facilitates quality control and provides convenient access to common data visualization tasks. Analysis of a benchmark dataset demonstrates superior performance of Hexicon 2 compared with its predecessor in terms of deuteration centroid recovery and deuteration distribution estimation. Hexicon 2 greatly reduces data analysis time compared with manual analysis, whereas the increased number of peptides provides redundant coverage of the entire protein sequence. Hexicon 2 is a standalone application available free of charge under http://hx2.mpimf-heidelberg.mpg.de.
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Affiliation(s)
- Robert Lindner
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Xinghua Lou
- Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg, Heidelberg, Germany
| | - Jochen Reinstein
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Robert L Shoeman
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Fred A Hamprecht
- Heidelberg Collaboratory for Image Processing (HCI), University of Heidelberg, Heidelberg, Germany
| | - Andreas Winkler
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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Konermann L, Vahidi S, Sowole MA. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal Chem 2013; 86:213-32. [DOI: 10.1021/ac4039306] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
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Huang RYC, Hudgens JW. Effects of desialylation on human α1-acid glycoprotein-ligand interactions. Biochemistry 2013; 52:7127-36. [PMID: 24041412 DOI: 10.1021/bi4011094] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human α1-acid glycoprotein (AGP), an acute-phase glycoprotein, exists predominantly in blood. With its ability to bind basic, lipophilic, and acidic drugs, AGP has served as a drug carrier. It has been shown that the carbohydrate composition of AGP changes in response to tissue injury, inflammation, or infection and can have a great impact on AGP's drug binding activities. The molecular-level details of the effects of desialylation on the AGP conformation and AGP-ligand interactions, however, are unknown. Here we report the use of hydrogen-deuterium exchange coupled with mass spectrometry (HDX-MS) to reveal the changes in AGP conformational dynamics induced by the removal of terminal sialic acid. HDX-MS also reveals the changes in the conformational dynamics of sialylated and unsialylated AGP upon formation of complexes of holo-AGP with progesterone or propranolol. Our HDX-MS results demonstrate that desialylation stabilizes two loop regions that are exterior to the β-sheet barrel in AGP, and this stabilization minimizes the conformational changes of AGP upon binding with progesterone or propranolol.
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Affiliation(s)
- Richard Y-C Huang
- Bioprocess Measurements Group, Biomolecular Measurement Division, National Institute of Standards and Technology , Gaithersburg, Maryland 20899, United States
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31
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Sheff JG, Rey M, Schriemer DC. Peptide-column interactions and their influence on back exchange rates in hydrogen/deuterium exchange-MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1006-15. [PMID: 23649779 DOI: 10.1007/s13361-013-0639-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 04/04/2013] [Accepted: 04/05/2013] [Indexed: 05/11/2023]
Abstract
Hydrogen/deuterium exchange (HDX) methods generate useful information on protein structure and dynamics, ideally at the individual residue level. Most MS-based HDX methods involve a rapid proteolytic digestion followed by LC/MS analysis, with exchange kinetics monitored at the peptide level. Localizing specific sites of HDX is usually restricted to a resolution the size of the host peptide because gas-phase processes can scramble deuterium throughout the peptide. Subtractive methods may improve resolution, where deuterium levels of overlapping and nested peptides are used in a subtractive manner to localize exchange to smaller segments. In this study, we explore the underlying assumption of the subtractive method, namely, that the measured back exchange kinetics of a given residue is independent of its host peptide. Using a series of deuterated peptides, we show that secondary structure can be partially retained under quenched conditions, and that interactions between peptides and reversed-phase LC columns may both accelerate and decelerate residue HDX, depending upon peptide sequence and length. Secondary structure is induced through column interactions in peptides with a solution-phase propensity for structure, which has the effect of slowing HDX rates relative to predicted random coil values. Conversely, column interactions can orient random-coil peptide conformers to accelerate HDX, the degree to which correlates with peptide charge in solution, and which can be reversed by using stronger ion pairing reagents. The dependency of these effects on sequence and length suggest that subtractive methods for improving structural resolution in HDX-MS will not offer a straightforward solution for increasing exchange site resolution.
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Affiliation(s)
- Joey G Sheff
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
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Demartini DR, Pasquali G, Carlini CR. An overview of proteomics approaches applied to biopharmaceuticals and cyclotides research. J Proteomics 2013; 93:224-33. [PMID: 23777896 DOI: 10.1016/j.jprot.2013.06.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 06/03/2013] [Accepted: 06/06/2013] [Indexed: 01/22/2023]
Abstract
The evolution in proteomics approaches is notable, including quantitative proteomics and strategies for elucidation of post-translational modifications. Faster and more accurate mass spectrometers as well as cleverer bioinformatics tolls are making the difference in such advancement. Among the wide range of research in plant proteomics, biopharmaceutical production using plants as "biofactories" and the screening of new activities of new molecules, in this case, peptides, are quite important regarding translational proteomics. The present review is focused on "recombinant proteins and bioactive peptides", with biopharmaceuticals and cyclotides chosen as examples. Their application and challenges are focused on a "translational proteomics" point of view, in order to exemplify some new areas of research based on proteomics strategies. This article is part of a Special Issue entitled: Translational Plant Proteomics.
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Affiliation(s)
- Diogo Ribeiro Demartini
- Center of Biotechnology, Universidade Federal do Rio Grande do Sul., Av. Bento Gonçalves 9500, Prédio 43431, Sala 214, Porto Alegre, RS 91501-970, Brazil.
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