1
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Zhang T, Jin Z, Zhao H, Lai C, Liu Z, Luo P, Dong Z, Wang F. Aqueous alkaline phosphate facilitates the non-exchangeable deuteration of peptides and proteins. RSC Adv 2024; 14:8075-8080. [PMID: 38464689 PMCID: PMC10921277 DOI: 10.1039/d3ra08636d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/29/2024] [Indexed: 03/12/2024] Open
Abstract
The incorporation of deuterium into peptides and proteins holds broad applications across various fields, such as drug development and structural characterization. Nevertheless, current methods for peptide/protein deuteration often target exchangeable labile sites or require harsh conditions for stable modification. In this study, we present a late-stage approach utilizing an alkaline phosphate solution to achieve deuteration of non-exchangeable backbone sites of peptides and proteins. The specific deuteration regions are identified through ultraviolet photodissociation (UVPD) and mass spectrometry analysis. This deuteration strategy demonstrates site and structure selectivity, with a notable affinity for labeling the α-helix regions of myoglobin. The deuterium method is particularly suitable for peptides and proteins that remain stable under high pH conditions.
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Affiliation(s)
- Tingting Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhixiong Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Heng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Can Lai
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Pan Luo
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- Institute of Advanced Science Facilities Shenzhen 518000 China
| | - Zhe Dong
- Shenzhen Grubbs Institute and Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology Shenzhen 518000 China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
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2
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Vallejo DD, Rojas Ramírez C, Parson KF, Han Y, Gadkari VV, Ruotolo BT. Mass Spectrometry Methods for Measuring Protein Stability. Chem Rev 2022; 122:7690-7719. [PMID: 35316030 DOI: 10.1021/acs.chemrev.1c00857] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Mass spectrometry is a central technology in the life sciences, providing our most comprehensive account of the molecular inventory of the cell. In parallel with developments in mass spectrometry technologies targeting such assessments of cellular composition, mass spectrometry tools have emerged as versatile probes of biomolecular stability. In this review, we cover recent advancements in this branch of mass spectrometry that target proteins, a centrally important class of macromolecules that accounts for most biochemical functions and drug targets. Our efforts cover tools such as hydrogen-deuterium exchange, chemical cross-linking, ion mobility, collision induced unfolding, and other techniques capable of stability assessments on a proteomic scale. In addition, we focus on a range of application areas where mass spectrometry-driven protein stability measurements have made notable impacts, including studies of membrane proteins, heat shock proteins, amyloidogenic proteins, and biotherapeutics. We conclude by briefly discussing the future of this vibrant and fast-moving area of research.
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Affiliation(s)
- Daniel D Vallejo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Carolina Rojas Ramírez
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kristine F Parson
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Yilin Han
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Varun V Gadkari
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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3
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Brodbelt JS, Morrison LJ, Santos I. Ultraviolet Photodissociation Mass Spectrometry for Analysis of Biological Molecules. Chem Rev 2020; 120:3328-3380. [PMID: 31851501 PMCID: PMC7145764 DOI: 10.1021/acs.chemrev.9b00440] [Citation(s) in RCA: 139] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The development of new ion-activation/dissociation methods continues to be one of the most active areas of mass spectrometry owing to the broad applications of tandem mass spectrometry in the identification and structural characterization of molecules. This Review will showcase the impact of ultraviolet photodissociation (UVPD) as a frontier strategy for generating informative fragmentation patterns of ions, especially for biological molecules whose complicated structures, subtle modifications, and large sizes often impede molecular characterization. UVPD energizes ions via absorption of high-energy photons, which allows access to new dissociation pathways relative to more conventional ion-activation methods. Applications of UVPD for the analysis of peptides, proteins, lipids, and other classes of biologically relevant molecules are emphasized in this Review.
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Affiliation(s)
- Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lindsay J. Morrison
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Inês Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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4
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Genereux JC. Mass spectrometric approaches for profiling protein folding and stability. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:111-144. [PMID: 31928723 DOI: 10.1016/bs.apcsb.2019.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein stability reports on protein homeostasis, function, and binding interactions, such as to other proteins, metabolites and drugs. As such, there is a pressing need for technologies that can report on protein stability. The ideal technique could be applied in vitro or in vivo systems, proteome-wide, independently of matrix, under native conditions, with residue-level resolution, and on protein at endogenous levels. Mass spectrometry has rapidly become a preferred technology for identifying and quantifying proteins. As such, it has been increasingly incorporated into methodologies for interrogating protein stability and folding. Although no single technology can satisfy all desired applications, several emerging approaches have shown outstanding success at providing biological insight into the stability of the proteome. This chapter outlines some of these recent emerging technologies.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA, United States
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5
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Mehaffey MR, Schardon CL, Novelli ET, Cammarata MB, Webb LJ, Fast W, Brodbelt JS. Investigation of GTP-dependent dimerization of G12X K-Ras variants using ultraviolet photodissociation mass spectrometry. Chem Sci 2019; 10:8025-8034. [PMID: 31853358 PMCID: PMC6837035 DOI: 10.1039/c9sc01032g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/14/2019] [Indexed: 12/14/2022] Open
Abstract
Mutations in the GTPase enzyme K-Ras, specifically at codon G12, remain the most common genetic alterations in human cancers. The mechanisms governing activation of downstream signaling pathways and how they relate back to the identity of the mutation have yet to be completely defined. Here we use native mass spectrometry (MS) combined with ultraviolet photodissociation (UVPD) to investigate the impact of three G12X mutations (G12C, G12V, G12S) on the homodimerization of K-Ras as well as heterodimerization with a downstream effector protein, Raf. Electrospray ionization (ESI) was used to transfer complexes of WT or G12X K-Ras bound to guanosine 5'-diphosphate (GDP) or GppNHp (non-hydrolyzable analogue of GTP) into the gas phase. Relative abundances of homo- or hetero-dimer complexes were estimated from ESI-MS spectra. K-Ras + Raf heterocomplexes were activated with UVPD to probe structural changes responsible for observed differences in the amount of heterocomplex formed for each variant. Holo (ligand-bound) fragment ions resulting from photodissociation suggest the G12X mutants bind Raf along the expected effector binding region (β-interface) but may interact with Raf via an alternative α-interface as well. Variations in backbone cleavage efficiencies during UV photoactivation of each variant were used to relate mutation identity to structural changes that might impact downstream signaling. Specifically, oncogenic upregulation for hydrogen-bonding amino acid substitutions (G12C, G12S) is achieved by stabilizing β-interface interactions with Raf, while a bulkier, hydrophobic G12V substitution leads to destabilization of this interface and instead increases the proximity of residues along the α-helical bundles. This study deciphers new pieces of the complex puzzle of how different K-Ras mutations exert influence in downstream signaling.
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Affiliation(s)
- M Rachel Mehaffey
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Christopher L Schardon
- Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy , University of Texas at Austin , Austin , TX 78712 , USA
| | - Elisa T Novelli
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Michael B Cammarata
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Lauren J Webb
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
| | - Walter Fast
- Division of Chemical Biology and Medicinal Chemistry , College of Pharmacy , University of Texas at Austin , Austin , TX 78712 , USA
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , TX 78712-0165 , USA . ; Tel: +1-512-471-0028
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6
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Zhao E, St-Jean F, Robinson SJ, Sirois LE, Pellett J, Al-Sayah MA. Identification of an acetonitrile addition impurity formed during peptide disulfide bond reduction using dithiothreitol and Tris(2-carboxyethyl)phosphine. J Pharm Biomed Anal 2019; 174:518-524. [DOI: 10.1016/j.jpba.2019.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 02/06/2023]
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7
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Stiving AQ, VanAernum ZL, Busch F, Harvey SR, Sarni SH, Wysocki VH. Surface-Induced Dissociation: An Effective Method for Characterization of Protein Quaternary Structure. Anal Chem 2019; 91:190-209. [PMID: 30412666 PMCID: PMC6571034 DOI: 10.1021/acs.analchem.8b05071] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Alyssa Q. Stiving
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Zachary L. VanAernum
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
| | - Florian Busch
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Sophie R. Harvey
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
| | - Samantha H. Sarni
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
| | - Vicki H. Wysocki
- Department of Chemistry and Biochemistry and Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210
- Campus Chemical Instrument Center, The Ohio State University, Columbus, OH 43210
- The Center for RNA Biology, The Ohio State University, Columbus, OH 43210
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8
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Limpikirati P, Liu T, Vachet RW. Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions. Methods 2018; 144:79-93. [PMID: 29630925 PMCID: PMC6051898 DOI: 10.1016/j.ymeth.2018.04.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
Using mass spectrometry (MS) to obtain information about a higher order structure of protein requires that a protein's structural properties are encoded into the mass of that protein. Covalent labeling (CL) with reagents that can irreversibly modify solvent accessible amino acid side chains is an effective way to encode structural information into the mass of a protein, as this information can be read-out in a straightforward manner using standard MS-based proteomics techniques. The differential reactivity of proteins under two or more conditions can be used to distinguish protein topologies, conformations, and/or binding sites. CL-MS methods have been effectively used for the structural analysis of proteins and protein complexes, particularly for systems that are difficult to study by other more traditional biochemical techniques. This review provides an overview of the non-specific CL approaches that have been combined with MS with a particular emphasis on the reagents that are commonly used, including hydroxyl radicals, carbenes, and diethylpyrocarbonate. We describe the reagent and protein factors that affect the reactivity of amino acid side chains. We also include details about experimental design and workflow, data analysis, recent applications, and some future prospects of CL-MS methods.
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Affiliation(s)
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, MA 01003, United States.
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9
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Holden DD, Sanders JD, Weisbrod CR, Mullen C, Schwartz JC, Brodbelt JS. Implementation of Fragment Ion Protection (FIP) during Ultraviolet Photodissociation (UVPD) Mass Spectrometry. Anal Chem 2018; 90:8583-8591. [PMID: 29927232 DOI: 10.1021/acs.analchem.8b01723] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ultraviolet photodissociation (UVPD) is a nonselective activation method in which both precursor and fragment ions may absorb photons and dissociate. Photoactivation of fragment ions may result in secondary or multiple generations of dissociation, which decreases the signal-to-noise ratio (S/N) of larger fragment ions owing to the prevalent subdivision of the ion current into many smaller, often less informative, fragment ions. Here we report the use of dipolar excitation waveforms to displace fragment ions out of the laser beam path, thus alleviating the extent of secondary dissociation during 193 nm UVPD. This fragment ion protection (FIP) strategy increases S/N of larger fragment ions and improves the sequence coverage obtained for proteins via retaining information deeper into the midsection of protein sequences.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - James D Sanders
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Chad R Weisbrod
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Christopher Mullen
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jae C Schwartz
- Thermo Fisher Scientific Inc. , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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10
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Brodie NI, Huguet R, Zhang T, Viner R, Zabrouskov V, Pan J, Petrotchenko EV, Borchers CH. Top-Down Hydrogen-Deuterium Exchange Analysis of Protein Structures Using Ultraviolet Photodissociation. Anal Chem 2018; 90:3079-3082. [PMID: 29336549 DOI: 10.1021/acs.analchem.7b03655] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Top-down hydrogen-deuterium exchange (HDX) analysis using electron capture or transfer dissociation Fourier transform mass spectrometry (FTMS) is a powerful method for the analysis of secondary structure of proteins in solution. The resolution of the method is a function of the degree of fragmentation of backbone bonds in the proteins. While fragmentation is usually extensive near the N- and C-termini, electron capture (ECD) or electron transfer dissociation (ETD) fragmentation methods sometimes lack good coverage of certain regions of the protein, most often in the middle of the sequence. Ultraviolet photodissociation (UVPD) is a recently developed fast-fragmentation technique, which provides extensive backbone fragmentation that can be complementary in sequence coverage to the aforementioned electron-based fragmentation techniques. Here, we explore the application of electrospray ionization (ESI)-UVPD FTMS on an Orbitrap Fusion Lumos Tribrid mass spectrometer to top-down HDX analysis of proteins. We have incorporated UVPD-specific fragment-ion types and fragment-ion mixtures into our isotopic envelope fitting software (HDX Match) for the top-down HDX analysis. We have shown that UVPD data is complementary to ETD, thus improving the overall resolution when used as a combined approach.
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Affiliation(s)
- Nicholas I Brodie
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Romain Huguet
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Terry Zhang
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Rosa Viner
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific , 355 River Oaks Parkway , San Jose , California 95134 , United States
| | - Jingxi Pan
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Evgeniy V Petrotchenko
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, Vancouver Island Technology Park , Victoria , British Columbia V8Z 7X8 , Canada
| | - Christoph H Borchers
- University of Victoria -Genome British Columbia Proteomics Centre , No. 3101-4464 Markham Street, 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 , Montreal , Quebec H3T 1E2 , Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital , McGill University , 3755 Côte Ste-Catherine Road , Montreal , Quebec H3T 1E2 , Canada
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11
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Mehaffey MR, Cammarata MB, Brodbelt JS. Tracking the Catalytic Cycle of Adenylate Kinase by Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2018; 90:839-846. [PMID: 29188992 PMCID: PMC5750083 DOI: 10.1021/acs.analchem.7b03591] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The complex interplay of dynamic protein plasticity and specific side-chain interactions with substrate molecules that allows enzymes to catalyze reactions has yet to be fully unraveled. Top-down ultraviolet photodissociation (UVPD) mass spectrometry is used to track snapshots of conformational fluctuations in the phosphotransferase adenylate kinase (AK) throughout its active reaction cycle by characterization of complexes containing AK and each of four different adenosine phosphate ligands. Variations in efficiencies of UVPD backbone cleavages were consistently observed for three α-helices and the adenosine binding regions for AK complexes representing different steps of the catalytic cycle, implying that these stretches of the protein sample various structural microstates as the enzyme undergoes global open-to-closed transitions. Focusing on the conformational impact of recruiting or releasing the Mg2+ cofactor highlights two loop regions for which fragmentation increases upon UVPD, signaling an increase in loop flexibility as the metal cation disrupts the loop interactions with the substrate ligands. Additionally, the observation of holo ions and variations in UVPD backbone cleavage efficiency at R138 implicate this conserved active site residue in stabilizing the donor phosphoryl group during catalysis. This study showcases the utility of UVPD-MS to provide insight into conformational fluctuations of single residues for active enzymes.
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Affiliation(s)
- M. Rachel Mehaffey
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712
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12
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Zerdane S, Collet E, Dong X, Matar SF, Wang HF, Desplanches C, Chastanet G, Chollet M, Glownia JM, Lemke HT, Lorenc M, Cammarata M. Electronic and Structural Dynamics During the Switching of the Photomagnetic Complex [Fe(L
222
N
5
)(CN)
2
]. Chemistry 2017; 24:5064-5069. [DOI: 10.1002/chem.201704746] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Serhane Zerdane
- Univ Rennes 1, CNRS Institut de Physique de Rennes, UMR 6251, UBL, F- 35042 Rennes France
| | - Eric Collet
- Univ Rennes 1, CNRS Institut de Physique de Rennes, UMR 6251, UBL, F- 35042 Rennes France
| | - Xu Dong
- Univ Rennes 1, CNRS Institut de Physique de Rennes, UMR 6251, UBL, F- 35042 Rennes France
| | - Samir F. Matar
- CNRS Université de Bordeaux ICMCB 87 avenue du Dr A. Schweitzer Pessac, F- 33608 France
- Lebanese German University (LGU) Sahel Alam Campus, P.O. BOX 206 Jounieh Lebanon
| | - Hong Feng Wang
- CNRS Université de Bordeaux ICMCB 87 avenue du Dr A. Schweitzer Pessac, F- 33608 France
| | - Cedric Desplanches
- CNRS Université de Bordeaux ICMCB 87 avenue du Dr A. Schweitzer Pessac, F- 33608 France
| | - Guillaume Chastanet
- CNRS Université de Bordeaux ICMCB 87 avenue du Dr A. Schweitzer Pessac, F- 33608 France
| | | | | | - Henrick T. Lemke
- LCLS SLAC National Laboratory Menlo Park 94025 CA USA
- SwissFEL Paul Scherrer Institut Villigen PSI 5232 Switzerland
| | - Maciej Lorenc
- Univ Rennes 1, CNRS Institut de Physique de Rennes, UMR 6251, UBL, F- 35042 Rennes France
| | - Marco Cammarata
- Univ Rennes 1, CNRS Institut de Physique de Rennes, UMR 6251, UBL, F- 35042 Rennes France
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13
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Greer SM, Holden DD, Fellers R, Kelleher NL, Brodbelt JS. Modulation of Protein Fragmentation Through Carbamylation of Primary Amines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1587-1599. [PMID: 28374316 PMCID: PMC5624212 DOI: 10.1007/s13361-017-1648-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 05/23/2023]
Abstract
We evaluate the impact of carbamylation of the primary amines of the side-chains of Lys and the N-termini on the fragmentation of intact protein ions and the chromatographic properties of a mixture of E. coli ribosomal proteins. The fragmentation patterns of the six unmodified and carbamylated proteins obtained by higher energy collision dissociation (HCD) and ultraviolet photodissociation (UVPD) were compared. Carbamylation significantly reduced the total number of protons retained by the protein owing to the conversion of basic primary amines to non-basic carbamates. Carbamylation caused a significant negative impact on fragmentation of the protein by HCD (i.e., reduced sequence coverage and fewer diagnostic fragment ions) consistent with the mobile proton model, which correlates peptide fragmentation with charge distribution and the opportunity for charge-directed pathways. In addition, fragmentation was enhanced near the N- and C-termini upon HCD of carbamylated proteins. For LCMS/MS analysis of E. coli ribosomal proteins, the retention times increased by 16 min on average upon carbamylation, an outcome attributed to the increased hydrophobicity of the proteins after carbamylation. As noted for both the six model proteins and the ribosomal proteins, carbamylation had relatively little impact on the distribution or types of fragment ions product by UVPD, supporting the proposition that the mechanism of UVPD for intact proteins does not reflect the mobile proton model. Graphical Abstract ᅟ.
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Affiliation(s)
- Sylvester M Greer
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Dustin D Holden
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ryan Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, 60208, USA
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, 60208, USA
- Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University, Evanston, IL, 60208, USA
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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14
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Li H, Sheng Y, McGee W, Cammarata M, Holden D, Loo JA. Structural Characterization of Native Proteins and Protein Complexes by Electron Ionization Dissociation-Mass Spectrometry. Anal Chem 2017; 89:2731-2738. [PMID: 28192979 DOI: 10.1021/acs.analchem.6b02377] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS) has played an increasingly important role in the identification and structural and functional characterization of proteins. In particular, the use of tandem mass spectrometry has afforded one of the most versatile methods to acquire structural information for proteins and protein complexes. The unique nature of electron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent interactions has made it especially suitable for the study of native protein structures. However, the intra- and intermolecular interactions stabilized by hydrogen bonds and salt bridges can hinder the separation of fragments even with preactivation, which has become particularly problematic for the study of large macromolecular proteins and protein complexes. Here, we describe the capabilities of another activation method, 30 eV electron ionization dissociation (EID), for the top-down MS characterization of native protein-ligand and protein-protein complexes. Rich structural information that cannot be delivered by ECD can be generated by EID. EID allowed for the comparison of the gas-phase and the solution-phase structural stability and unfolding process of human carbonic anhydrase I (HCA-I). In addition, the EID fragmentation patterns reflect the structural similarities and differences among apo-, Zn-, and Cu,Zn-superoxide dismutase (SOD1) dimers. In particular, the structural changes due to Cu-binding and a point mutation (G41D) were revealed by EID-MS. The performance of EID was also compared to that of 193 nm ultraviolet photodissociation (UVPD), which allowed us to explore their qualitative similarities and differences as potential valuable tools for the MS study of native proteins and protein complexes.
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Affiliation(s)
- Huilin Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States
| | - Yuewei Sheng
- Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
| | - William McGee
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michael Cammarata
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Dustin Holden
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Joseph A Loo
- Department of Biological Chemistry, David Geffen School of Medicine, University of California , Los Angeles, California 90095, United States.,Department of Chemistry and Biochemistry, UCLA/DOE Institute of Genomics and Proteomics, and UCLA Molecular Biology Institute, University of California , Los Angeles, California 90095, United States
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15
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Holden DD, Brodbelt JS. Improving Performance Metrics of Ultraviolet Photodissociation Mass Spectrometry by Selective Precursor Ejection. Anal Chem 2016; 89:837-846. [PMID: 28105830 DOI: 10.1021/acs.analchem.6b03777] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Confident protein identifications derived from high-throughput bottom-up and top-down proteomics workflows depend on acquisition of thousands of tandem mass spectrometry (MS/MS) spectra with adequate signal-to-noise and accurate mass assignments of the fragment ions. Ultraviolet photodissociation (UVPD) using 193 nm photons has proven to be well-suited for activation and fragmentation of peptides and proteins in ion trap mass spectrometers, but the spectral signal-to-noise ratio (S/N) is typically lower than that obtained from collisional activation methods. The lower S/N is attributed to the dispersion of ion current among numerous fragment ion channels (a,b,c,x,y,z ions). In addition, frequently UVPD is performed such that a relatively large population of precursor ions remains undissociated after the UV photoactivation period in order to prevent overdissociation into small uninformative or internal fragment ions. Here we report a method to improve spectral S/N and increase the accuracy of mass assignments of UVPD mass spectra via resonance ejection of undissociated precursor ions after photoactivation. This strategy, termed precursor ejection UVPD or PE-UVPD, allows the ion trap to be filled with more ions prior to UVPD while at the same time alleviating the space charge problems that would otherwise contribute to the skewing of mass assignments and reduction of S/N. Here we report the performance gains by implementation of PE-UVPD for peptide analysis in an ion trap mass spectrometer.
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Affiliation(s)
- Dustin D Holden
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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16
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Cammarata MB, Schardon CL, Mehaffey MR, Rosenberg J, Singleton J, Fast W, Brodbelt JS. Impact of G12 Mutations on the Structure of K-Ras Probed by Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2016; 138:13187-13196. [DOI: 10.1021/jacs.6b04474] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael B. Cammarata
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Christopher L. Schardon
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - M. Rachel Mehaffey
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jake Rosenberg
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jonathan Singleton
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Walter Fast
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S. Brodbelt
- Department of Chemistry, ‡Graduate Program in Biochemistry, and §Division of Chemical Biology and
Medicinal Chemistry, College of Pharmacy, University of Texas, Austin, Texas 78712, United States
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17
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Madsen JA, Yin Y, Qiao J, Gill V, Renganathan K, Fu WY, Smith S, Anderson J. Covalent Labeling Denaturation Mass Spectrometry for Sensitive Localized Higher Order Structure Comparisons. Anal Chem 2016; 88:2478-88. [PMID: 26750983 DOI: 10.1021/acs.analchem.5b04736] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein higher order structure (HOS) describes the three-dimensional folding arrangement of a given protein and plays critical roles in structure/function relationships. As such, it is a key product quality attribute that is monitored during biopharmaceutical development. Covalent labeling of surface residues, combined with mass spectrometry analysis, has increasingly played an important role in characterizing localized protein HOS. Since the label can potentially induce conformation changes, protocols generally use a small amount of label to ensure that the integrity of the protein HOS is not disturbed. The present study, however, describes a method that purposely uses high amounts of isobaric label (levels that induce denaturation) to enhance the sensitivity and resolution for detecting localized structural differences between two or more biological products. The method proved to be highly discriminative, detecting differences in HOS affecting as little as 2.5-5% of the molecular population, levels at which circular dichroism and nuclear magnetic resonance spectroscopy fingerprinting, both gold standard HOS techniques, were unable to adequately differentiate. The methodology was shown to have comparable sensitivity to differential scanning calorimetry for detecting HOS differences. In addition, the workflow presented herein can also quantify other product attributes such as post-translational modifications and site-specific glycosylation, using a single liquid chromatography-tandem mass spectrometry (LC-MS/MS) run with automated data analysis. We applied this technique to characterize a large (>90 kDa), multiply glycosylated therapeutic protein under different heat stress conditions and aggregation states.
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Affiliation(s)
- James A Madsen
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Yan Yin
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Jing Qiao
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Vanessa Gill
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | | | - Wing-Yee Fu
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - Stephen Smith
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
| | - James Anderson
- Momenta Pharmaceuticals, 675 West Kendall Street, Cambridge, Massachusetts 02142, United States
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18
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Affiliation(s)
- Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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19
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Quintyn RS, Zhou M, Yan J, Wysocki VH. Surface-Induced Dissociation Mass Spectra as a Tool for Distinguishing Different Structural Forms of Gas-Phase Multimeric Protein Complexes. Anal Chem 2015; 87:11879-86. [PMID: 26499904 DOI: 10.1021/acs.analchem.5b03441] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Royston S. Quintyn
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Mowei Zhou
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Jing Yan
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
| | - Vicki H. Wysocki
- Department of Chemistry and
Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, Ohio 43210, United States
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20
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Cammarata MB, Thyer R, Rosenberg J, Ellington A, Brodbelt JS. Structural Characterization of Dihydrofolate Reductase Complexes by Top-Down Ultraviolet Photodissociation Mass Spectrometry. J Am Chem Soc 2015; 137:9128-35. [PMID: 26125523 DOI: 10.1021/jacs.5b04628] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The stepwise reduction of dihydrofolate to tetrahydrofolate entails significant conformational changes of dihydrofolate reductase (DHFR). Binary and ternary complexes of DHFR containing cofactor NADPH, inhibitor methotrexate (MTX), or both NADPH and MTX were characterized by 193 nm ultraviolet photodissociation (UVPD) mass spectrometry. UVPD yielded over 80% sequence coverage of DHFR and resulted in production of fragment ions that revealed the interactions between DHFR and each ligand. UVPD of the binary DHFR·NADPH and DHFR·MTX complexes led to an unprecedented number of fragment ions containing either an N- or C-terminal protein fragment still bound to the ligand via retention of noncovalent interactions. In addition, holo-fragments retaining both ligands were observed upon UVPD of the ternary DHFR·NADPH·MTX complex. The combination of extensive holo and apo fragment ions allowed the locations of the NADPH and MTX ligands to be mapped, with NADPH associated with the adenosine binding domain of DHFR and MTX interacting with the loop domain. These findings are consistent with previous crystallographic evidence. Comparison of the backbone cleavage propensities for apo DHFR and its holo counterparts revealed significant variations in UVPD fragmentation in the regions expected to experience conformational changes upon binding NADPH, MTX, or both ligands. In particular, the subdomain rotation and loop movements, which are believed to occur upon formation of the transition state of the ternary complex, are reflected in the UVPD mass spectra. The UVPD spectra indicate enhanced backbone cleavages in regions that become more flexible or show suppressed backbone cleavages for those regions either shielded by the ligand or involved in new intramolecular interactions. This study corroborates the versatility of 193 nm UVPD mass spectrometry as a sensitive technique to track enzymatic cycles that involve conformational rearrangements.
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Affiliation(s)
- Michael B Cammarata
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ross Thyer
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jake Rosenberg
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew Ellington
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- †Department of Chemistry and ‡Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
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21
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Cammarata MB, Brodbelt JS. Structural characterization of holo- and apo-myoglobin in the gas phase by ultraviolet photodissociation mass spectrometry. Chem Sci 2015; 6:1324-1333. [PMID: 29560219 PMCID: PMC5811132 DOI: 10.1039/c4sc03200d] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Accepted: 11/26/2014] [Indexed: 01/18/2023] Open
Abstract
Ultraviolet photodissociation (UVPD) mass spectrometry is employed to investigate the structure of holo-myoglobin as well as its apo form transferred to the gas phase by native electrospray. UVPD provided insight into the stability of native structural elements of holo-myoglobin. The fragmentation yields from UVPD showed the greatest overall correlation with B-factors generated from the crystal structure of apo-myoglobin, particularly for the more disordered loop regions. Solvent accessibility measurements also showed some correlation with the UVPD fragmentation of holo-myoglobin. Comparison of UVPD of holo- and apo-myoglobin revealed similarities in fragmentation yields, particularly for the lower charge states (8 and 9+). Both holo- and apo-myoglobin exhibited low fragmentation yields for the AGH helical core, whereas regions known to interact with the heme show suppressed fragmentation for holo-myoglobin. The fragment yields from HCD showed the lowest correlation with B-factor values and rather reflected preferential charge-directed backbone cleavages.
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Affiliation(s)
- Michael B Cammarata
- Department of Chemistry , The University of Texas at Austin , 1 University Station A5300 , Austin , TX , USA 78712 .
| | - Jennifer S Brodbelt
- Department of Chemistry , The University of Texas at Austin , 1 University Station A5300 , Austin , TX , USA 78712 .
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22
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Wang D, Wynne C, Gu F, Becker C, Zhao J, Mueller HM, Li H, Shameem M, Liu YH. Characterization of Drug-Product-Related Impurities and Variants of a Therapeutic Monoclonal Antibody by Higher Energy C-Trap Dissociation Mass Spectrometry. Anal Chem 2015; 87:914-21. [DOI: 10.1021/ac503158g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Deyun Wang
- Eurofins-Lancaster Laboratories Inc., 2425
New Holland Pike, Lancaster, Pennsylvania 17601, United States
| | - Colin Wynne
- Eurofins-Lancaster Laboratories Inc., 2425
New Holland Pike, Lancaster, Pennsylvania 17601, United States
| | - Flora Gu
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Chris Becker
- Protein Metrics Inc., 1622 San
Carlos Avenue, Suite C, San Carlos, California 94070, United States
| | - Jia Zhao
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hans-Martin Mueller
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Huijuan Li
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mohammed Shameem
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yan-Hui Liu
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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23
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Li G, Yin Y, Huang G. Increased disulfide peptide sequence coverage via “cleavage ON/OFF” switch during nanoelectrospray. RSC Adv 2014. [DOI: 10.1039/c4ra12386g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Disulfide peptide sequence coverage could be increased via switching “cleavage ON/OFF” modes between conventional and induced nanoelectrospray MS within 1 min.
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Affiliation(s)
- Gongyu Li
- Department of Chemistry
- University of Science and Technology of China
- Hefei, P.R. China
| | - Yue Yin
- Department of Chemistry
- University of Science and Technology of China
- Hefei, P.R. China
| | - Guangming Huang
- Department of Chemistry
- University of Science and Technology of China
- Hefei, P.R. China
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