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Pan X, Vachet RW. MEMBRANE PROTEIN STRUCTURES AND INTERACTIONS FROM COVALENT LABELING COUPLED WITH MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2022; 41:51-69. [PMID: 33145813 PMCID: PMC8093322 DOI: 10.1002/mas.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/31/2023]
Abstract
Membrane proteins are incredibly important biomolecules because they mediate interactions between a cell's external and internal environment. Obtaining information about membrane protein structure and interactions is thus important for understanding these essential biomolecules. Compared with the analyses of water-soluble proteins, the structural analysis of membrane proteins is more challenging owing to their unique chemical properties and the presence of lipid components that are necessary to solubilize them. The combination of covalent labeling (CL) and mass spectrometry (MS) has recently been applied with great success to study membrane protein structure and interactions. These studies have demonstrated the many advantages that CL-MS methods have over other traditional biophysical techniques. In this review, we discuss both amino acid-specific and non-specific labeling approaches and the special considerations needed to address the unique challenges associated with interrogating membrane proteins. This review highlights the aspects of this approach that require special care to be applied correctly and provides a comprehensive review of the membrane protein systems that have been studied by CL-MS. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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2
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Chiu D, Pan L, Fay L, Eakin C, Valliere-Douglass J. Structural characterization of a monomethylauristatin-E based ADC that contains 8 drugs conjugated at interchain cysteine residues. J Pharm Biomed Anal 2021; 205:114309. [PMID: 34403866 DOI: 10.1016/j.jpba.2021.114309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/31/2021] [Accepted: 08/04/2021] [Indexed: 10/20/2022]
Abstract
Antibody-drug conjugates (ADCs) with a drug-to-antibody ratio (DAR) of 8 are attractive as therapeutic anti-cancer agents due to the higher levels of cytotoxic payload delivered to tumors. Biophysical characterization of a DAR 8 ADC fully conjugated at all interchain cysteine residues was carried out to determine if IgG1 interchain disulfide reduction and conjugation led to structural perturbations that impacted product stability. Comparisons between the DAR 8 ADC and the unconjugated parent antibody identified minor tertiary and quaternary structural changes localized to the CL, CH1, and CH2 domains and CH2-CH3 domain interface. Stability studies of the DAR 8 ADC indicated that the structural changes had minimal impacts to product stability as demonstrated by low levels of fragmentation and aggregation under nominal storage and temperature stress stability conditions. Additionally, no detectable higher order structural changes were observed by CD or DSC in the DAR 8 ADC after 3 months at (25 °C) stability conditions. The structural and stability results support the developability of DAR 8 ADCs fully conjugated to interchain cysteines residues with an optimized and clinically relevant second generation monomethylauristatin-E (MMAE) drug-linker.
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Affiliation(s)
- David Chiu
- Quality Control, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - Lucy Pan
- Quality Control, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - Lindsay Fay
- Pharmaceutical Sciences, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - Catherine Eakin
- Analytical Sciences, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
| | - John Valliere-Douglass
- Analytical Sciences, Seagen Inc., 21823 30th Drive Southeast, Bothell, WA, 98021, United States.
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3
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Na S, Paek E. Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions. Comput Struct Biotechnol J 2020; 18:1391-1402. [PMID: 32637038 PMCID: PMC7322682 DOI: 10.1016/j.csbj.2020.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/01/2020] [Accepted: 06/01/2020] [Indexed: 12/28/2022] Open
Abstract
Mass spectrometry (MS) has made enormous contributions to comprehensive protein identification and quantification in proteomics. MS is also gaining momentum for structural biology in a variety of ways, complementing conventional structural biology techniques. Here, we will review how MS-based techniques, such as hydrogen/deuterium exchange, covalent labeling, and chemical cross-linking, enable the characterization of protein structure, dynamics, and interactions, especially from a perspective of their data analyses. Structural information encoded by chemical probes in intact proteins is decoded by interpreting MS data at a peptide level, i.e., revealing conformational and dynamic changes in local regions of proteins. The structural MS data are not amenable to data analyses in traditional proteomics workflow, requiring dedicated software for each type of data. We first provide basic principles of data interpretation, including isotopic distribution and peptide sequencing. We then focus particularly on computational methods for structural MS data analyses and discuss outstanding challenges in a proteome-wide large scale analysis.
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Affiliation(s)
- Seungjin Na
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
| | - Eunok Paek
- Dept. of Computer Science, Hanyang University, Seoul 04763, Republic of Korea
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4
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Crittenden CM, Novelli ET, Mehaffey MR, Xu GN, Giles DH, Fies WA, Dalby KN, Webb LJ, Brodbelt JS. Structural Evaluation of Protein/Metal Complexes via Native Electrospray Ultraviolet Photodissociation Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1140-1150. [PMID: 32275426 PMCID: PMC7386362 DOI: 10.1021/jasms.0c00066] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultraviolet photodissociation (UVPD) has emerged as a promising tool to characterize proteins with regard to not only their primary sequences and post-translational modifications, but also their tertiary structures. In this study, three metal-binding proteins, Staphylococcal nuclease, azurin, and calmodulin, are used to demonstrate the use of UVPD to elucidate metal-binding regions via comparisons between the fragmentation patterns of apo (metal-free) and holo (metal-bound) proteins. The binding of staphylococcal nuclease to calcium was evaluated, in addition to a series of lanthanide(III) ions which are expected to bind in a similar manner as calcium. On the basis of comparative analysis of the UVPD spectra, the binding region for calcium and the lanthanide ions was determined to extend from residues 40-50, aligning with the known crystal structure. Similar analysis was performed for both azurin (interrogating copper and silver binding) and calmodulin (four calcium binding sites). This work demonstrates the utility of UVPD methods for determining and analyzing the metal binding sites of a variety of classes of proteins.
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Affiliation(s)
| | - Elisa T Novelli
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - M Rachel Mehaffey
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Gulan N Xu
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - David H Giles
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Whitney A Fies
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, University of Texas, Austin, Texas 78712, United States
- Graduate Program in Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
| | - Lauren J Webb
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
- Institute for Cell and Molecular Biology, University of Texas, Austin, Texas 78712, United States
- Texas Materials Institute, University of Texas, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas, Austin, Texas 78712, United States
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5
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Kaltashov IA, Bobst CE, Pawlowski J, Wang G. Mass spectrometry-based methods in characterization of the higher order structure of protein therapeutics. J Pharm Biomed Anal 2020; 184:113169. [PMID: 32092629 DOI: 10.1016/j.jpba.2020.113169] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/31/2022]
Abstract
Higher order structure of protein therapeutics is an important quality attribute, which dictates both potency and safety. While modern experimental biophysics offers an impressive arsenal of state-of-the-art tools that can be used for the characterization of higher order structure, many of them are poorly suited for the characterization of biopharmaceutical products. As a result, these analyses were traditionally carried out using classical techniques that provide relatively low information content. Over the past decade, mass spectrometry made a dramatic debut in this field, enabling the characterization of higher order structure of biopharmaceuticals as complex as monoclonal antibodies at a level of detail that was previously unattainable. At present, mass spectrometry is an integral part of the analytical toolbox across the industry, which is critical not only for quality control efforts, but also for discovery and development.
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Affiliation(s)
- Igor A Kaltashov
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA.
| | - Cedric E Bobst
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Jake Pawlowski
- Department of Chemistry, University of Massachusetts-Amherst, Amherst, MA, USA
| | - Guanbo Wang
- School of Chemistry and Materials Science, Nanjing Normal University, Nanjing, Jiangsu Province, PR China
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6
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Martens C, Shekhar M, Lau AM, Tajkhorshid E, Politis A. Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. Nat Protoc 2019; 14:3183-3204. [PMID: 31605097 PMCID: PMC7058097 DOI: 10.1038/s41596-019-0219-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 06/20/2019] [Indexed: 12/20/2022]
Abstract
Biological membranes define the boundaries of cells and are composed primarily of phospholipids and membrane proteins. It has become increasingly evident that direct interactions of membrane proteins with their surrounding lipids play key roles in regulating both protein conformations and function. However, the exact nature and structural consequences of these interactions remain difficult to track at the molecular level. Here, we present a protocol that specifically addresses this challenge. First, hydrogen-deuterium exchange mass spectrometry (HDX-MS) of membrane proteins incorporated into nanodiscs of controlled lipid composition is used to obtain information on the lipid species that are involved in modulating the conformational changes in the membrane protein. Then molecular dynamics (MD) simulations in lipid bilayers are used to pinpoint likely lipid-protein interactions, which can be tested experimentally using HDX-MS. By bringing together the MD predictions with the conformational readouts from HDX-MS, we have uncovered key lipid-protein interactions implicated in stabilizing important functional conformations. This protocol can be applied to virtually any integral membrane protein amenable to classic biophysical studies and for which a near-atomic-resolution structure or homology model is available. This protocol takes ~4 d to complete, excluding the time for data analysis and MD simulations, which depends on the size of the protein under investigation.
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Affiliation(s)
- Chloe Martens
- Department of Chemistry, King's College London, London, UK
- Department of Chemistry, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium
| | - Mrinal Shekhar
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Andy M Lau
- Department of Chemistry, King's College London, London, UK
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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7
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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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8
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Wang H, Yong G, Brown SL, Lee HE, Zenaidee MA, Supuran CT, Donald WA. Supercharging protein ions in native mass spectrometry using theta capillary nanoelectrospray ionization mass spectrometry and cyclic alkylcarbonates. Anal Chim Acta 2018; 1003:1-9. [DOI: 10.1016/j.aca.2017.11.075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/22/2017] [Accepted: 11/25/2017] [Indexed: 12/27/2022]
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9
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Tian Y, Ruotolo BT. The growing role of structural mass spectrometry in the discovery and development of therapeutic antibodies. Analyst 2018; 143:2459-2468. [DOI: 10.1039/c8an00295a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The comprehensive structural characterization of therapeutic antibodies is of critical importance for the successful discovery and development of such biopharmaceuticals, yet poses many challenges to modern measurement science. Here, we review the current state-of-the-art mass spectrometry technologies focusing on the characterization of antibody-based therapeutics.
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Affiliation(s)
- Yuwei Tian
- Department of Chemistry
- University of Michigan
- Ann Arbor
- USA
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10
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Li J, Wei H, Krystek SR, Bond D, Brender TM, Cohen D, Feiner J, Hamacher N, Harshman J, Huang RYC, Julien SH, Lin Z, Moore K, Mueller L, Noriega C, Sejwal P, Sheppard P, Stevens B, Chen G, Tymiak AA, Gross ML, Schneeweis LA. Mapping the Energetic Epitope of an Antibody/Interleukin-23 Interaction with Hydrogen/Deuterium Exchange, Fast Photochemical Oxidation of Proteins Mass Spectrometry, and Alanine Shave Mutagenesis. Anal Chem 2017; 89:2250-2258. [PMID: 28193005 PMCID: PMC5347259 DOI: 10.1021/acs.analchem.6b03058] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epitope mapping the specific residues of an antibody/antigen interaction can be used to support mechanistic interpretation, antibody optimization, and epitope novelty assessment. Thus, there is a strong need for mapping methods, particularly integrative ones. Here, we report the identification of an energetic epitope by determining the interfacial hot-spot that dominates the binding affinity for an anti-interleukin-23 (anti-IL-23) antibody by using the complementary approaches of hydrogen/deuterium exchange mass spectrometry (HDX-MS), fast photochemical oxidation of proteins (FPOP), alanine shave mutagenesis, and binding analytics. Five peptide regions on IL-23 with reduced backbone amide solvent accessibility upon antibody binding were identified by HDX-MS, and five different peptides over the same three regions were identified by FPOP. In addition, FPOP analysis at the residue level reveals potentially key interacting residues. Mutants with 3-5 residues changed to alanine have no measurable differences from wild-type IL-23 except for binding of and signaling blockade by the 7B7 anti-IL-23 antibody. The M5 IL-23 mutant differs from wild-type by five alanine substitutions and represents the dominant energetic epitope of 7B7. M5 shows a dramatic decrease in binding to BMS-986010 (which contains the 7B7 Fab, where Fab is fragment antigen-binding region of an antibody), yet it maintains functional activity, binding to p40 and p19 specific reagents, and maintains biophysical properties similar to wild-type IL-23 (monomeric state, thermal stability, and secondary structural features).
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Affiliation(s)
- Jing Li
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130-4889, USA
| | - Hui Wei
- Biologics Development, Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534
| | - Stanley R. Krystek
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Derek Bond
- Process Development, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Ty M. Brender
- Discovery Biology, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Daniel Cohen
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Jena Feiner
- Applied Genomics, Bristol-Myers Squibb, 311 Pennington-Rocky Hill Road, Pennington, NJ 08534
| | - Nels Hamacher
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Johanna Harshman
- Molecular Structure & Design, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Richard Y.-C. Huang
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Susan H. Julien
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Zheng Lin
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Kristina Moore
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Luciano Mueller
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Claire Noriega
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Preeti Sejwal
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Paul Sheppard
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Brenda Stevens
- Protein Engineering, Bristol-Myers Squibb, 1201 Eastlake Ave E., Seattle WA 98102
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Adrienne A. Tymiak
- Bioanalytical and Discovery Analytical Sciences, Research and Development, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130-4889, USA
| | - Lumelle A. Schneeweis
- Protein Science, Bristol-Myers Squibb, Rt. 206 & Province Line Rd, Princeton, NJ 08543
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11
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Kathiresan M, English AM. LC-MS/MS suggests that hole hopping in cytochrome c peroxidase protects its heme from oxidative modification by excess H 2O 2. Chem Sci 2017; 8:1152-1162. [PMID: 28451256 PMCID: PMC5369544 DOI: 10.1039/c6sc03125k] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 09/06/2016] [Indexed: 12/20/2022] Open
Abstract
We recently reported that cytochrome c peroxidase (Ccp1) functions as a H2O2 sensor protein when H2O2 levels rise in respiring yeast. The availability of its reducing substrate, ferrocytochrome c (CycII), determines whether Ccp1 acts as a H2O2 sensor or peroxidase. For H2O2 to serve as a signal it must modify its receptor so we employed high-performance LC-MS/MS to investigate in detail the oxidation of Ccp1 by 1, 5 and 10 M eq. of H2O2 in the absence of CycII to prevent peroxidase activity. We observe strictly heme-mediated oxidation, implicating sequential cycles of binding and reduction of H2O2 at Ccp1's heme. This results in the incorporation of ∼20 oxygen atoms predominantly at methionine and tryptophan residues. Extensive intramolecular dityrosine crosslinking involving neighboring residues was uncovered by LC-MS/MS sequencing of the crosslinked peptides. The proximal heme ligand, H175, is converted to oxo-histidine, which labilizes the heme but irreversible heme oxidation is avoided by hole hopping to the polypeptide until oxidation of the catalytic distal H52 in Ccp1 treated with 10 M eq. of H2O2 shuts down heterolytic cleavage of H2O2 at the heme. Mapping of the 24 oxidized residues in Ccp1 reveals that hole hopping from the heme is directed to three polypeptide zones rich in redox-active residues. This unprecedented analysis unveils the remarkable capacity of a polypeptide to direct hole hopping away from its active site, consistent with heme labilization being a key outcome of Ccp1-mediated H2O2 signaling. LC-MS/MS identification of the oxidized residues also exposes the bias of electron paramagnetic resonance (EPR) detection toward transient radicals with low O2 reactivity.
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Affiliation(s)
- Meena Kathiresan
- Concordia University Faculty of Arts and Science, and PROTEOhttp://www.proteo.ca/index.html , Chemistry and Biochemistry , Montreal , Canada .
| | - Ann M English
- Concordia University Faculty of Arts and Science, and PROTEOhttp://www.proteo.ca/index.html , Chemistry and Biochemistry , Montreal , Canada .
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12
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Pan LY, Salas-Solano O, Valliere-Douglass JF. Localized conformational interrogation of antibody and antibody-drug conjugates by site-specific carboxyl group footprinting. MAbs 2016; 9:307-318. [PMID: 27929747 DOI: 10.1080/19420862.2016.1268306] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains. Our results for two case studies are shown here. The first study was aimed at defining the conformational changes of mAbs induced by deglycosylation. We found that two residues in CH2 domain (D268 and E297) show significantly enhanced side chain accessibility upon deglycosylation. This site-specific result highlighted the advantage of monitoring the labeling kinetics at the amino acid level as opposed to the peptide level, which would result in averaging out of highly localized conformational differences. The second study was designed to assess conformational effects brought on by conjugation of mAbs with drug-linkers. All 59 monitored carboxyl residues displayed similar solvent-accessibility between the ADC and mAb under native conditions, which suggests the ADC and mAb share similar side chain conformation. The findings are well correlated and complementary with results from other assays. This work illustrated that site-specific CGF is capable of pinpointing local conformational changes in mAbs or ADCs that might arise during development and manufacturing. The methodology can be readily implemented within the industry to provide comprehensive conformational assessment of these molecules.
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13
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Chan CP. Forced degradation studies: current trends and future perspectives for protein-based therapeutics. Expert Rev Proteomics 2016; 13:651-8. [DOI: 10.1080/14789450.2016.1200469] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Christine P. Chan
- Global Manufacturing Science & Technology, Specialty Care Operations, Sanofi, Framingham, MA, USA
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14
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Ren J, Tian Y, Hossain E, Connolly MD. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:646-661. [PMID: 26832347 DOI: 10.1007/s13361-016-1341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/07/2016] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry. Graphical Abstract ᅟ.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
| | - Yuan Tian
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ekram Hossain
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael D Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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15
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Rinas A, Espino JA, Jones LM. An efficient quantitation strategy for hydroxyl radical-mediated protein footprinting using Proteome Discoverer. Anal Bioanal Chem 2016; 408:3021-31. [PMID: 26873216 DOI: 10.1007/s00216-016-9369-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 01/17/2016] [Accepted: 01/27/2016] [Indexed: 01/12/2023]
Abstract
Hydroxyl radical protein footprinting coupled with mass spectrometry has become an invaluable technique for protein structural characterization. In this method, hydroxyl radicals react with solvent exposed amino acid side chains producing stable, covalently attached labels. Although this technique yields beneficial information, the extensive list of known oxidation products produced make the identification and quantitation process considerably complex. Currently, the methods available for analysis either involve manual analysis steps, or limit the amount of searchable modifications or the size of sequence database. This creates a bottleneck which can result in a long and arduous analysis process, which is further compounded in a complex sample. Here, we report the use of a new footprinting analysis method for both peptide and residue-level analysis, demonstrated on the GCaMP2 synthetic construct in calcium free and calcium bound states. This method utilizes a customized multi-search node workflow developed for an on-market search platform in conjunction with a quantitation platform developed using a free Excel add-in. Moreover, the method expedites the analysis process, requiring only two post-search hours to complete quantitation, regardless of the size of the experiment or the sample complexity.
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Affiliation(s)
- Aimee Rinas
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St LD326, Indianapolis, IN, 46202, USA
| | - Jessica A Espino
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St LD326, Indianapolis, IN, 46202, USA
| | - Lisa M Jones
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St LD326, Indianapolis, IN, 46202, USA.
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16
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Abstract
Specific conformations of signaling proteins can serve as “signals” in signal transduction by being recognized by receptors.
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Affiliation(s)
- Peter Tompa
- VIB Structural Biology Research Center (SBRC)
- Brussels
- Belgium
- Vrije Universiteit Brussel
- Brussels
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17
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Protein Structural Analysis via Mass Spectrometry-Based Proteomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:397-431. [PMID: 27975228 DOI: 10.1007/978-3-319-41448-5_19] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Modern mass spectrometry (MS) technologies have provided a versatile platform that can be combined with a large number of techniques to analyze protein structure and dynamics. These techniques include the three detailed in this chapter: (1) hydrogen/deuterium exchange (HDX), (2) limited proteolysis, and (3) chemical crosslinking (CX). HDX relies on the change in mass of a protein upon its dilution into deuterated buffer, which results in varied deuterium content within its backbone amides. Structural information on surface exposed, flexible or disordered linker regions of proteins can be achieved through limited proteolysis, using a variety of proteases and only small extents of digestion. CX refers to the covalent coupling of distinct chemical species and has been used to analyze the structure, function and interactions of proteins by identifying crosslinking sites that are formed by small multi-functional reagents, termed crosslinkers. Each of these MS applications is capable of revealing structural information for proteins when used either with or without other typical high resolution techniques, including NMR and X-ray crystallography.
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18
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Pancsa R, Varadi M, Tompa P, Vranken WF. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. Nucleic Acids Res 2015; 44:D429-34. [PMID: 26582925 PMCID: PMC4702845 DOI: 10.1093/nar/gkv1185] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/24/2015] [Indexed: 01/02/2023] Open
Abstract
Proteins fulfil a wide range of tasks in cells; understanding how they fold into complex three-dimensional (3D) structures and how these structures remain stable while retaining sufficient dynamics for functionality is essential for the interpretation of overall protein behaviour. Since the 1950's, solvent exchange-based methods have been the most powerful experimental means to obtain information on the folding and stability of proteins. Considerable expertise and care were required to obtain the resulting datasets, which, despite their importance and intrinsic value, have never been collected, curated and classified. Start2Fold is an openly accessible database (http://start2fold.eu) of carefully curated hydrogen/deuterium exchange (HDX) data extracted from the literature that is open for new submissions from the community. The database entries contain (i) information on the proteins investigated and the underlying experimental procedures and (ii) the classification of the residues based on their exchange protection levels, also allowing for the instant visualization of the relevant residue groups on the 3D structures of the corresponding proteins. By providing a clear hierarchical framework for the easy sharing, comparison and (re-)interpretation of HDX data, Start2Fold intends to promote a better understanding of how the protein sequence encodes folding and structure as well as the development of new computational methods predicting protein folding and stability.
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Affiliation(s)
- Rita Pancsa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium
| | - Mihaly Varadi
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium
| | - Peter Tompa
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium Interuniversity Institute of Bioinformatics in Brussels (IB), ULB-VUB, Brussels 1050, Belgium Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1113, Hungary
| | - Wim F Vranken
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels 1050, Belgium Structural Biology Research Center (IB), VIB, Brussels 1050, Belgium Interuniversity Institute of Bioinformatics in Brussels (IB), ULB-VUB, Brussels 1050, Belgium
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19
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Borotto NB, Zhou Y, Hollingsworth SR, Hale JE, Graban EM, Vaughan RC, Vachet RW. Investigating Therapeutic Protein Structure with Diethylpyrocarbonate Labeling and Mass Spectrometry. Anal Chem 2015; 87:10627-34. [PMID: 26399599 DOI: 10.1021/acs.analchem.5b03180] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein therapeutics are rapidly transforming the pharmaceutical industry. Unlike for small molecule therapeutics, current technologies are challenged to provide the rapid, high-resolution analyses of protein higher order structures needed to ensure drug efficacy and safety. Consequently, significant attention has turned to developing new methods that can quickly, accurately, and reproducibly characterize the three-dimensional structure of protein therapeutics. In this work, we describe a method that uses diethylpyrocarbonate (DEPC) labeling and mass spectrometry to detect three-dimensional structural changes in therapeutic proteins that have been exposed to degrading conditions. Using β2-microglobulin, immunoglobulin G1, and human growth hormone as model systems, we demonstrate that DEPC labeling can identify both specific protein regions that mediate aggregation and those regions that undergo more subtle structural changes upon mishandling of these proteins. Importantly, DEPC labeling is able to provide information for up to 30% of the surface residues in a given protein, thereby providing excellent structural resolution. Given the simplicity of the DEPC labeling chemistry and the relatively straightforward mass spectral analysis of DEPC-labeled proteins, we expect this method should be amenable to a wide range of protein therapeutics and their different formulations.
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Affiliation(s)
- Nicholas B Borotto
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Yuping Zhou
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
| | - Stephen R Hollingsworth
- Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - John E Hale
- QuarryBio , Bloomington, Indiana 47404, United States
| | - Eric M Graban
- QuarryBio , Bloomington, Indiana 47404, United States
| | - Robert C Vaughan
- Department of Molecular and Cellular Biochemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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20
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Farrokhi V, Bajrami B, Nemati R, McShane AJ, Rueckert F, Wells B, Yao X. Development of Structural Marker Peptides for Cystic Fibrosis Transmembrane Conductance Regulator in Cell Plasma Membrane by Reversed-Footprinting Mass Spectrometry. Anal Chem 2015; 87:8603-7. [DOI: 10.1021/acs.analchem.5b01962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | | | | | | | - Franz Rueckert
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Barrett Wells
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
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21
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Venable JD, Steckler C, Ou W, Grünewald J, Agarwalla S, Brock A. Isotope-Coded Labeling for Accelerated Protein Interaction Profiling Using MS. Anal Chem 2015; 87:7540-4. [PMID: 26151661 DOI: 10.1021/acs.analchem.5b01410] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein interaction surface mapping using MS is widely applied but comparatively resource-intensive. Here, a workflow adaptation for use of isotope-coded tandem mass tags for the purpose is reported. The key benefit of improved throughput derived from sample acquisition multiplexing and automated analysis is shown to be maintained in the new application. Mapping of the epitopes of two monoclonal antibodies on their respective targets serves to illustrate the novel approach. We conclude that the approach enables mapping of interactions by MS at significantly larger scales than hereto possible.
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Affiliation(s)
- John D Venable
- †Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Caitlin Steckler
- †Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States.,‡Joint Center for Structural Genomics, La Jolla, California 92037, United States, http://www.jcsg.org
| | - Weijia Ou
- †Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Jan Grünewald
- †Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Sanjay Agarwalla
- †Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Ansgar Brock
- †Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
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22
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Espino JA, Mali VS, Jones LM. In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells. Anal Chem 2015; 87:7971-8. [DOI: 10.1021/acs.analchem.5b01888] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jessica A. Espino
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46204, United States
| | | | - Lisa M. Jones
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46204, United States
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23
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Paleček E, Tkáč J, Bartošík M, Bertók T, Ostatná V, Paleček J. Electrochemistry of nonconjugated proteins and glycoproteins. Toward sensors for biomedicine and glycomics. Chem Rev 2015; 115:2045-108. [PMID: 25659975 PMCID: PMC4360380 DOI: 10.1021/cr500279h] [Citation(s) in RCA: 209] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Indexed: 02/07/2023]
Affiliation(s)
- Emil Paleček
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Tkáč
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Martin Bartošík
- Regional
Centre for Applied Molecular Oncology, Masaryk
Memorial Cancer Institute, Žlutý kopec 7, 656 53 Brno, Czech Republic
| | - Tomáš Bertók
- Institute
of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Veronika Ostatná
- Institute
of Biophysics Academy of Science of the Czech Republic, v.v.i., Královopolská
135, 612 65 Brno, Czech Republic
| | - Jan Paleček
- Central
European Institute of Technology, Masaryk
University, Kamenice
5, 625 00 Brno, Czech Republic
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24
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Wang L, Chance MR. Detection of structural waters and their role in structural dynamics of rhodopsin activation. Methods Mol Biol 2015; 1271:97-111. [PMID: 25697519 DOI: 10.1007/978-1-4939-2330-4_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Conserved structural waters trapped within GPCRs may form water networks indispensable for GPCR's signaling functions. Radiolysis-based hydroxyl radical footprinting (HRF) strategies coupled to mass spectrometry have been used to explore the structural waters within rhodopsin in multiple signaling states. These approaches, combined with (18)O labeling, can be used to identify the locations of structural waters in the transmembrane region and measure rates of water exchange with bulk solvent. Reorganizations of structural waters upon activation of signaling can be explicitly observed with this approach, and this provides a unique look at the structural modules driving the signaling process.
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Affiliation(s)
- Liwen Wang
- Case center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
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25
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Zhou X, Mester C, Stemmer PM, Reid GE. Oxidation-induced conformational changes in calcineurin determined by covalent labeling and tandem mass spectrometry. Biochemistry 2014; 53:6754-65. [PMID: 25286016 PMCID: PMC4222536 DOI: 10.1021/bi5009744] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The Ca2+/calmodulin activated
phosphatase, calcineurin,
is inactivated by H2O2 or superoxide-induced
oxidation, both in vivo and in vitro. However, the potential for global and/or local conformation changes
occurring within calcineurin as a function of oxidative modification,
that may play a role in the inactivation process, has not been examined.
Here, the susceptibility of calcineurin methionine residues toward
H2O2-induced oxidation were determined using
a multienzyme digestion strategy coupled with capillary HPLC–electrospray
ionization mass spectrometry and tandem mass spectrometry analysis.
Then, regions within the protein complex that underwent significant
conformational perturbation upon oxidative modification were identified
by monitoring changes in the modification rates of accessible lysine
residues between native and oxidized forms of calcineurin, using an
amine-specific covalent labeling reagent, S,S′-dimethylthiobutanoylhydroxysuccinimide ester (DMBNHS),
and tandem mass spectrometry. Importantly, methionine residues found
to be highly susceptible toward oxidation, and the lysine residues
exhibiting large increases in accessibility upon oxidation, were all
located in calcineurin functional domains involved in Ca2+/CaM binding regulated calcineurin stimulation. These findings therefore
provide initial support for the novel mechanistic hypothesis that
oxidation-induced global and/or local conformational changes within
calcineurin contribute to inactivation via (i) impairing the interaction
between calcineurin A and calcineurin B, (ii) altering the low-affinity
Ca2+ binding site in calcineurin B, (iii) inhibiting calmodulin
binding to calcineurin A, and/or (iv) by altering the affinity between
the calcineurin A autoinhibitory domain and the catalytic center.
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Affiliation(s)
- Xiao Zhou
- Department of Chemistry, and §Department of Biochemistry and Molecular Biology, Michigan State University , East Lansing, Michigan 48824, United States
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26
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Zhou M, Robinson CV. Flexible membrane proteins: functional dynamics captured by mass spectrometry. Curr Opin Struct Biol 2014; 28:122-30. [DOI: 10.1016/j.sbi.2014.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Revised: 07/23/2014] [Accepted: 08/13/2014] [Indexed: 10/24/2022]
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27
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Borotto NB, Degraan-Weber N, Zhou Y, Vachet RW. Label scrambling during CID of covalently labeled peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1739-46. [PMID: 25056863 PMCID: PMC4163129 DOI: 10.1007/s13361-014-0962-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 06/26/2014] [Accepted: 07/01/2014] [Indexed: 05/14/2023]
Abstract
Covalent labeling along with mass spectrometry is finding more use as a means of studying the higher order structure of proteins and protein complexes. Diethylpyrocarbonate (DEPC) is an increasingly used reagent for these labeling experiments because it is capable of modifying multiple residues at the same time. Pinpointing DEPC-labeled sites on proteins is typically needed to obtain more resolved structural information, and tandem mass spectrometry after protein proteolysis is often used for this purpose. In this work, we demonstrate that in certain instances, scrambling of the DEPC label from one residue to another can occur during collision-induced dissociation (CID) of labeled peptide ions, resulting in ambiguity in label site identity. From a preliminary study of over 30 labeled peptides, we find that scrambling occurs in about 25% of the peptides and most commonly occurs when histidine residues are labeled. Moreover, this scrambling appears to occur more readily under non-mobile proton conditions, meaning that low charge-state peptide ions are more prone to this reaction. For all peptides, we find that scrambling does not occur during electron transfer dissociation, which suggests that this dissociation technique is a safe alternative to CID for correct label site identification.
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Affiliation(s)
| | | | | | - Richard W. Vachet
- Corresponding author; address reprint requests to: Richard Vachet, Department of Chemistry, Life Sciences Laboratory, 240 Thatcher Way, University of Massachusetts, Amherst, MA 01003,
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28
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Liuni P, Zhu S, Wilson DJ. Oxidative protein labeling with analysis by mass spectrometry for the study of structure, folding, and dynamics. Antioxid Redox Signal 2014; 21:497-510. [PMID: 24512178 DOI: 10.1089/ars.2014.5850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SIGNIFICANCE Analytical approaches that can provide insights into the mechanistic processes underlying protein folding and dynamics are few since the target analytes-high-energy structural intermediates-are short lived and often difficult to distinguish from coexisting structures. Folding "intermediates" can be populated at equilibrium using weakly denaturing solvents, but it is not clear that these species are identical to those that are transiently populated during folding under "native" conditions. Oxidative labeling with mass spectrometric analysis is a powerful alternative for structural characterization of proteins and transient protein species based on solvent exposure at specific sites. RECENT ADVANCES Oxidative labeling is increasingly used with exceedingly short (μs) labeling pulses, both to minimize the occurrence of artifactual structural changes due to the incorporation of label and to detect short-lived species. The recent introduction of facile photolytic approaches for producing reactive oxygen species is an important technological advance that will enable more widespread adoption of the technique. CRITICAL ISSUES The most common critique of oxidative labeling data is that even with brief labeling pulses, covalent modification of the protein may cause significant artifactual structural changes. FUTURE DIRECTIONS While the oxidative labeling with the analysis by mass spectrometry is mature enough that most basic methodological issues have been addressed, a complete systematic understanding of side chain reactivity in the context of intact proteins is an avenue for future work. Specifically, there remain issues around the impact of primary sequence and side chain interactions on the reactivity of "solvent-exposed" residues. Due to its analytical power, wide range of applications, and relative ease of implementation, oxidative labeling is an increasingly important technique in the bioanalytical toolbox.
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Affiliation(s)
- Peter Liuni
- 1 Department of Chemistry, York University , Toronto, Canada
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29
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Bogdanov B, Zhao X, Robinson DB, Ren J. Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1202-1216. [PMID: 24845348 DOI: 10.1007/s13361-014-0869-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.
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Affiliation(s)
- Bogdan Bogdanov
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
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30
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Lysine-specific chemical cross-linking of protein complexes and identification of cross-linking sites using LC-MS/MS and the xQuest/xProphet software pipeline. Nat Protoc 2013; 9:120-37. [DOI: 10.1038/nprot.2013.168] [Citation(s) in RCA: 200] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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31
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Khemchyan LL, Khokhlova EA, Seitkalieva MM, Ananikov VP. Efficient Sustainable Tool for Monitoring Chemical Reactions and Structure Determination in Ionic Liquids by ESI-MS. ChemistryOpen 2013; 2:208-14. [PMID: 24551568 PMCID: PMC3892193 DOI: 10.1002/open.201300022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Indexed: 01/28/2023] Open
Abstract
An easy and convenient procedure is described for monitoring chemical reactions and characterization of compounds dissolved in ionic liquids using the well-known tandem mass spectrometry (MS/MS) technique. Generation of wastes was avoided by utilizing an easy procedure for analysis of ionic liquid systems without preliminary isolation and purification. The described procedure also decreased the risk of plausible contamination and damage of the ESI-MS hardware and increased sensitivity and accuracy of the measurements. ESI-MS detection in MS/MS mode was shown to be efficient in ionic liquids systems for structural and mechanistic studies, which are rather difficult otherwise. The developed ESI-MS/MS approach was applied to study samples corresponding to peptide systems in ionic liquids and to platform chemical directed biomass conversion in ionic liquids.
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Affiliation(s)
- Levon L Khemchyan
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47, Moscow 119991 (Russia) E-mail:
| | - Elena A Khokhlova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47, Moscow 119991 (Russia) E-mail:
| | - Marina M Seitkalieva
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47, Moscow 119991 (Russia) E-mail:
| | - Valentine P Ananikov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences Leninsky Prospect 47, Moscow 119991 (Russia) E-mail:
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32
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Zhong Y, Feng J, Ruotolo BT. Robotically assisted titration coupled to ion mobility-mass spectrometry reveals the interface structures and analysis parameters critical for multiprotein topology mapping. Anal Chem 2013; 85:11360-8. [PMID: 24164205 DOI: 10.1021/ac402276k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Multiprotein complexes have three-dimensional shapes and dynamic functions that impact almost every aspect of biochemistry. Despite this, our ability to rapidly assess the structures of such macromolecules lags significantly behind high-throughput efforts to identify their function, especially in the context of human disease. Here, we describe results obtained by coupling ion mobility-mass spectrometry with automated robotic sampling of different solvent compositions. This combination of technologies has allowed us to explore an extensive set of solution conditions for a group of eight protein homotetramers, representing a broad sample of protein structure and stability space. We find that altering solution ionic strength in concert with dimethylsulfoxide content is sufficient to disrupt the protein-protein interfaces of all of the complexes studied here. Ion mobility measurements captured for both intact assemblies and subcomplexes match expected values from available X-ray structures in all cases save two. For these exceptions, we find that distorted subcomplexes result from extreme disruption conditions, and are accompanied by small shifts in intact tetramers size, thus enabling the removal of distorted subcomplex data in downstream models. Furthermore, we find strong correlations between the relative intensities of disrupted protein tetramers and the relative number and type of interactions present at interfaces as a function of disrupting agent added. In most cases, this correlation appears strong enough to quantify various types of protein interfacial interactions within unknown proteins following appropriate calibration.
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Affiliation(s)
- Yueyang Zhong
- Department of Chemistry, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109, United States
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33
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Affiliation(s)
- Shengwen Shen
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - Xing-Fang Li
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
| | - William R. Cullen
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver,
British Columbia, Canada, V6T 1Z1
| | - Michael Weinfeld
- Department of Oncology, Cross
Cancer Institute, University of Alberta, 11560 University Avenue, Edmonton, Alberta, Canada, T6G 1Z2
| | - X. Chris Le
- Department
of Laboratory Medicine
and Pathology, 10-102 Clinical Sciences Building, University
of Alberta, Edmonton, Alberta, Canada, T6G 2G3
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34
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Zhou Y, Vachet RW. Covalent labeling with isotopically encoded reagents for faster structural analysis of proteins by mass spectrometry. Anal Chem 2013; 85:9664-70. [PMID: 24010814 DOI: 10.1021/ac401978w] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covalent labeling and mass spectrometry (MS) are increasingly being used to obtain higher-order structure of proteins and protein complexes. Because most covalent labels are relatively large, steps must be taken to ensure the structural integrity of the modified protein during the labeling reactions so that correct structural information can be obtained. Measuring labeling kinetics is a reliable way to ensure that a given labeling reagent does not perturb a protein's structure, but obtaining such kinetic information is time and sample intensive because it requires multiple liquid chromatography (LC)-MS experiments. Here we present a new strategy that uses isotopically encoded labeling reagents to measure labeling kinetics in a single LC-MS experiment. We illustrate this new strategy by labeling solvent-exposed lysine residues with commercially available tandem mass tags. After tandem MS experiments, these tags allow the simultaneous identification of modified sites and determination of the reaction rates at each site in a way that is just as reliable as experiments that involve multiple LC-MS measurements.
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Affiliation(s)
- Yuping Zhou
- Department of Chemistry, University of Massachusetts , Amherst, Massachusetts 01003, United States
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Optimal cleavage and oxidative folding of α-conotoxin TxIB as a therapeutic candidate peptide. Mar Drugs 2013; 11:3537-53. [PMID: 24048271 PMCID: PMC3806463 DOI: 10.3390/md11093537] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/19/2022] Open
Abstract
Alpha6beta2 nicotinic acetylcholine receptors (nAChRs) are potential therapeutic targets for the treatment of several neuropsychiatric diseases, including addiction and Parkinson’s disease. Alpha-conotoxin (α-CTx) TxIB is a uniquely selective ligand, which blocks α6/α3β2β3 nAChRs only, but does not block the other subtypes. Therefore, α-CTx TxIB is a valuable therapeutic candidate peptide. Synthesizing enough α-CTx TxIB with high yield production is required for conducting wide-range testing of its potential medicinal applications. The current study optimized the cleavage of synthesized α-CTx TxIB resin-bounded peptide and folding of the cleaved linear peptide. Key parameters influencing cleavage and oxidative folding of α-CTx TxIB were examined, such as buffer, redox agents, pH, salt, co-solvent and temperature. Twelve conditions were used for cleavage optimization. Fifty-four kinds of one-step oxidative solution were used to assess their effects on each α-CTx TxIB isomers’ yield. The result indicated that co-solvent choices were particularly important. Completely oxidative folding of globular isomer was achieved when the NH4HCO3 or Tris-HCl folding buffer at 4 °C contained 40% of co-solvent DMSO, and GSH:GSSG (2:1) or GSH only with pH 8~8.7.
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Pilau EJ, Iglesias AH, Gozzo FC. A new label-free approach for the determination of reaction rates in oxidative footprinting experiments. Anal Bioanal Chem 2013; 405:7679-86. [DOI: 10.1007/s00216-013-7247-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 07/08/2013] [Accepted: 07/10/2013] [Indexed: 11/29/2022]
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Kaltashov IA, Bobst CE, Nguyen SN, Wang S. Emerging mass spectrometry-based approaches to probe protein-receptor interactions: focus on overcoming physiological barriers. Adv Drug Deliv Rev 2013; 65:1020-30. [PMID: 23624418 DOI: 10.1016/j.addr.2013.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 04/15/2013] [Accepted: 04/17/2013] [Indexed: 01/10/2023]
Abstract
Physiological barriers, such as the blood-brain barrier and intestinal epithelial barrier, remain significant obstacles towards wider utilization of biopharmaceutical products. Receptor-mediated transcytosis has long been viewed as an attractive means of crossing such barriers, but successful exploitation of this route requires better understanding of the interactions between the receptors and protein-based therapeutics. Detailed characterization of such processes at the molecular level is challenging due to the very large physical size and heterogeneity of these species, which makes use of many state-of-the art analytical techniques, such as high-resolution NMR and X-ray crystallography impractical. Mass spectrometry has emerged in the past decade as a powerful tool to study protein-receptor interactions, although its applications to investigate interaction of biopharmaceuticals with their physiological partners are still limited. We highlight the potential of this technique by considering several recent examples where it had been instrumental for understanding molecular mechanisms critical for receptor-mediated transcytosis of transferrin-based therapeutics.
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38
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Monroe EB, Heien ML. Electrochemical generation of hydroxyl radicals for examining protein structure. Anal Chem 2013; 85:6185-9. [PMID: 23777226 DOI: 10.1021/ac400107c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of hydroxyl radicals to covalently label the solvent-exposed surface of proteins has been shown to be a powerful tool to examine the structure of proteins and intermolecular interfaces. Current methods to generate hydroxyl radicals for footprinting experiments rely on the laser photolysis of H2O2 or the synchrotron radiolysis of water, which adds significant costs and/or complexity to the experiments. In this work, we develop the electro-Fenton reaction as a means to generate hydroxyl radicals for structural footprinting mass spectrometry experiments to complement current laser and synchrotron-based methods, while reducing the costs and complexity of initiating such experiments. The use of an electrochemical flow cell also enables control of the timing and extent of the radical generation process, while reducing the complexity typically associated with radical footprinting experiments. Ubiquitin, a model protein, was labeled with electro-Fenton generated hydroxyl radicals and top-down proteomics was used to verify oxidation sites on the protein surface.
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Affiliation(s)
- Eric B Monroe
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, USA
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Resetca D, Wilson DJ. Characterizing rapid, activity-linked conformational transitions in proteins via sub-second hydrogen deuterium exchange mass spectrometry. FEBS J 2013; 280:5616-25. [DOI: 10.1111/febs.12332] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/26/2013] [Accepted: 05/01/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Diana Resetca
- Department of Chemistry; York University; Toronto Ontario Canada
| | - Derek J. Wilson
- Department of Chemistry; York University; Toronto Ontario Canada
- Center for Research in Mass Spectrometry; Department of Chemistry; York University; Toronto Ontario Canada
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Zhang Y, Romsted LS, Zhuang L, de Jong S. Simultaneous determination of interfacial molarities of amide bonds, carboxylate groups, and water by chemical trapping in micelles of amphiphiles containing peptide bond models. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:534-544. [PMID: 23237147 DOI: 10.1021/la3040819] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Chemical trapping is a powerful approach for obtaining experimental estimates of interfacial molarities of weakly basic nucleophiles in the interfacial regions of amphiphile aggregates. Here, we demonstrate that the chemical probe 4-hexadecyl-2,6-dimethylbenzenediazonium ion (16-ArN(2)(+)) reacts competitively with interfacial water, with the amide carbonyl followed by cleavage of the headgroups from the tail at the amide oxygen, and with the terminal carboxylate groups in micelles of two N-acyl amino-acid amphiphiles, sodium N-lauroylsarcosinate (SLS) and sodium N-lauroylglycinate (SLG), simple peptide bond model amphiphiles. Interfacial molarities (in moles per liter of interfacial volume) of these three groups were obtained from product yields, assuming that selectivity toward a particular nucleophile compared to water is the same in an aqueous reference solution and in the interfacial region. Interfacial carboxylate group molarities are ~1.5 M in both SLS and SLG micelles, but the concentration of the amide carbonyl for SLS micelles is ~4.6-5 times less (ca. 0.7 M) than that of SLG micelles (~3 M). The proton on the secondary N of SLG helps solubilize the amide bond in the aqueous region, but the methyl on the tertiary N of SLS helps solubilize the amide bond in the micellar core, reducing its reaction with 16-ArN(2)(+). Application of chemical trapping to proteins in membrane mimetic interfaces should provide insight into the topology of the protein within the interface because trapping of the amide carbonyl and cleavage at the C-N bond occurs only within the interface, and fragment characterization marks those peptide bonds located within the interface.
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Affiliation(s)
- Yongliang Zhang
- Department of Chemistry and Chemical Biology, Wright-Rieman Laboratories, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08903, United States
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41
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Konijnenberg A, Butterer A, Sobott F. Native ion mobility-mass spectrometry and related methods in structural biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:1239-56. [PMID: 23246828 DOI: 10.1016/j.bbapap.2012.11.013] [Citation(s) in RCA: 186] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Revised: 11/19/2012] [Accepted: 11/29/2012] [Indexed: 12/12/2022]
Abstract
Mass spectrometry-based methods have become increasingly important in structural biology - in particular for large and dynamic, even heterogeneous assemblies of biomolecules. Native electrospray ionization coupled to ion mobility-mass spectrometry provides access to stoichiometry, size and architecture of noncovalent assemblies; while non-native approaches such as covalent labeling and H/D exchange can highlight dynamic details of protein structures and capture intermediate states. In this overview article we will describe these methods and highlight some recent applications for proteins and protein complexes, with particular emphasis on native MS analysis. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
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Lauber MA, Rappsilber J, Reilly JP. Dynamics of ribosomal protein S1 on a bacterial ribosome with cross-linking and mass spectrometry. Mol Cell Proteomics 2012; 11:1965-76. [PMID: 23033476 PMCID: PMC3518124 DOI: 10.1074/mcp.m112.019562] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 09/19/2012] [Indexed: 11/23/2022] Open
Abstract
Ribosomal protein S1 has been shown to be a significant effector of prokaryotic translation. The protein is in fact capable of efficiently initiating translation, regardless of the presence of a Shine-Dalgarno sequence in mRNA. Structural insights into this process have remained elusive, as S1 is recalcitrant to traditional techniques of structural analysis, such as x-ray crystallography. Through the application of protein cross-linking and high resolution mass spectrometry, we have detailed the ribosomal binding site of S1 and have observed evidence of its dynamics. Our results support a previous hypothesis that S1 acts as the mRNA catching arm of the prokaryotic ribosome. We also demonstrate that in solution the major domains of the 30S subunit are remarkably flexible, capable of moving 30-50Å with respect to one another.
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Affiliation(s)
- Matthew A. Lauber
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Juri Rappsilber
- §Wellcome Trust Centre for Cell Biology, Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, UK and Institut für Biotechnologie, Technische Universität Berlin, 13353 Berlin, Germany
| | - James P. Reilly
- From the ‡Department of Chemistry, Indiana University, Bloomington, Indiana 47405
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43
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Hyung SJ, Ruotolo BT. Integrating mass spectrometry of intact protein complexes into structural proteomics. Proteomics 2012; 12:1547-64. [PMID: 22611037 DOI: 10.1002/pmic.201100520] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MS analysis of intact protein complexes has emerged as an established technology for assessing the composition and connectivity within dynamic, heterogeneous multiprotein complexes at low concentrations and in the context of mixtures. As this technology continues to move forward, one of the main challenges is to integrate the information content of such intact protein complex measurements with other MS approaches in structural biology. Methods such as H/D exchange, oxidative foot-printing, chemical cross-linking, affinity purification, and ion mobility separation add complementary information that allows access to every level of protein structure and organization. Here, we survey the structural information that can be retrieved by such experiments, demonstrate the applicability of integrative MS approaches in structural proteomics, and look to the future to explore upcoming innovations in this rapidly advancing area.
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Affiliation(s)
- Suk-Joon Hyung
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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Chen J, Cui W, Giblin D, Gross ML. New protein footprinting: fast photochemical iodination combined with top-down and bottom-up mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1306-18. [PMID: 22669760 PMCID: PMC3630512 DOI: 10.1007/s13361-012-0403-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 04/25/2012] [Accepted: 04/25/2012] [Indexed: 05/02/2023]
Abstract
We report a new approach for the fast photochemical oxidation of proteins (FPOP) whereby iodine species are used as the modifying reagent. We generate the radicals by photolysis of iodobenzoic acid at 248 nm; the putative iodine radical then rapidly modifies the target protein. This iodine-radical labeling is sensitive, tunable, and site-specific, modifying only histidine and tyrosine residues in contrast to OH radicals that modify 14 amino-acid side chains. We iodinated myoglobin (Mb) and apomyoglobin (aMb) in their native states and analyzed the outcome by both top-down and bottom-up proteomic strategies. Top-down sequencing selects a certain level (addition of one I, two I's) of modification and determines the major components produced in the modification reaction, whereas bottom-up reveals details for each modification site. Tyr146 is found to be modified for aMb but less so for Mb. His82, His93, and His97 are at least 10 times more modified for aMb than for Mb, in agreement with NMR studies. For carbonic anhydrase and its apo form, there are no significant differences of the modification extents, indicating their similarity in conformation and providing a control for this approach. For lispro insulin, insulin-EDTA, and insulin complexed with zinc, iodination yields are sensitive to differences in insulin oligomerization state. The iodine radical labeling is a promising addition to protein footprinting methods, offering higher specificity and lower reactivity than ∙OH and SO(4)(-∙), two other radicals already employed in FPOP.
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Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis, MO 63130, USA
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45
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Zhou Y, Vachet RW. Diethylpyrocarbonate labeling for the structural analysis of proteins: label scrambling in solution and how to avoid it. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:899-907. [PMID: 22351293 PMCID: PMC3324597 DOI: 10.1007/s13361-012-0349-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/20/2012] [Accepted: 01/23/2012] [Indexed: 05/11/2023]
Abstract
Covalent labeling along with mass spectrometry is a method that is increasingly used to study protein structure. Recently, it has been shown that diethylpyrocarbonate (DEPC) is a powerful labeling reagent because it can modify up to 30% of the residues in the average protein, including the N-terminus, His, Lys, Tyr, Ser, Thr, and Cys residues. We recently discovered, however, that Cys residues that form disulfide bonds appear to be modified by DEPC as well. In this work, we demonstrate that disulfide linked Cys residues are not actually reactive with DEPC but, instead, once reduced, free Cys residues can capture a carbethoxy group from other modified amino acids via a solution-phase reaction that can occur during the protein digestion step. This "scrambling" of carbethoxy groups decreases the amount of modification observed at other residues and can potentially provide incorrect protein structural information. Fortunately, label scrambling can be completely avoided by alkylating the free thiols after disulfide reduction.
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Affiliation(s)
| | - Richard W. Vachet
- Corresponding Author, Department of Chemistry, LGRT 104, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003,
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46
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Zhou Y, Vachet RW. Increased protein structural resolution from diethylpyrocarbonate-based covalent labeling and mass spectrometric detection. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:708-17. [PMID: 22298289 PMCID: PMC3334416 DOI: 10.1007/s13361-011-0332-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 12/21/2011] [Accepted: 12/28/2011] [Indexed: 05/03/2023]
Abstract
Covalent labeling and mass spectrometry are seeing increased use together as a way to obtain insight into the 3-dimensional structure of proteins and protein complexes. Several amino acid specific (e.g., diethylpyrocarbonate) and non-specific (e.g., hydroxyl radicals) labeling reagents are available for this purpose. Diethylpyrocarbonate (DEPC) is a promising labeling reagent because it can potentially probe up to 30% of the residues in the average protein and gives only one reaction product, thereby facilitating mass spectrometric analysis. It was recently reported, though, that DEPC modifications are labile for some amino acids. Here, we show that label loss is more significant and widespread than previously thought, especially for Ser, Thr, Tyr, and His residues, when relatively long protein digestion times are used. Such label loss ultimately decreases the amount of protein structural information that is obtainable with this reagent. We find, however, that the number of DEPC modified residues and, thus, protein structural information, can be significantly increased by decreasing the time between the covalent labeling reaction and the mass spectrometric analysis. This is most effectively accomplished using short (e.g., 2 h) proteolytic digestions with enzymes such as immobilized chymotrypsin or Glu-C rather than using methods (e.g., microwave or ultrasonic irradiation) that accelerate proteolysis in other ways. Using short digestion times, we show that the percentage of solvent accessible residues that can be modified by DEPC increases from 44% to 67% for cytochrome c, 35% to 81% for myoglobin, and 76% to 95% for β-2-microglobulin. In effect, these increased numbers of modified residues improve the protein structural resolution available from this covalent labeling method. Compared with typical overnight digestion conditions, the short digestion times decrease the average distance between modified residues from 11 to 7 Å for myoglobin, 13 to 10 Å for cytochrome c, and 9 to 8 Å for β-2-microglobulin.
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Affiliation(s)
| | - Richard W. Vachet
- Corresponding Author: Department of Chemistry, LGRT 104, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003,
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47
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Watson C, Sharp JS. Conformational analysis of therapeutic proteins by hydroxyl radical protein footprinting. AAPS JOURNAL 2012; 14:206-17. [PMID: 22382679 DOI: 10.1208/s12248-012-9336-7] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 02/15/2012] [Indexed: 12/21/2022]
Abstract
Unlike small molecule drugs, therapeutic protein pharmaceuticals must not only have the correct amino acid sequence and modifications, but also the correct conformation to ensure safety and efficacy. Here, we describe a method for comparison of therapeutic protein conformations by hydroxyl radical protein footprinting using liquid chromatography-mass spectrometry (LC-MS) as an analytical platform. Hydroxyl radical protein footprinting allows for rapid analysis of the conformation of therapeutic proteins based on the apparent rate of oxidation of various amino acids by hydroxyl radicals generated in situ. Conformations of Neupogen®, a patented granulocyte colony-stimulating factor (GCSF), were compared to several expired samples of recombinant GCSF, as well as heat-treated Neupogen®. Conformations of different samples of the therapeutic proteins interferon α-2A and erythropoietin were also compared. Differences in the hydroxyl radical footprint were measured between Neupogen® and the expired or mishandled GCSF samples, and confirmed by circular dichroism spectroscopy. Samples that had identical circular dichroism spectra were also found to be indistinguishable by hydroxyl radical footprinting. The method is applicable to a wide variety of therapeutic proteins and formulations through the use of separations techniques to clean up the protein samples after radical oxidation. The reaction products are stable, allowing for flexibility in sample handling, as well as archiving and reanalysis of samples. Initial screening can be performed on small amounts of therapeutic protein with minimal training in LC-MS, but samples with structural differences from the reference can be more carefully analyzed by LC-MS/MS to attain higher spatial resolution, which can aid in engineering and troubleshooting.
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Affiliation(s)
- Caroline Watson
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, Georgia 30602, USA
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48
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Leitner A, Reischl R, Walzthoeni T, Herzog F, Bohn S, Förster F, Aebersold R. Expanding the chemical cross-linking toolbox by the use of multiple proteases and enrichment by size exclusion chromatography. Mol Cell Proteomics 2012; 11:M111.014126. [PMID: 22286754 PMCID: PMC3316732 DOI: 10.1074/mcp.m111.014126] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chemical cross-linking in combination with mass spectrometric analysis offers the potential to obtain low-resolution structural information from proteins and protein complexes. Identification of peptides connected by a cross-link provides direct evidence for the physical interaction of amino acid side chains, information that can be used for computational modeling purposes. Despite impressive advances that were made in recent years, the number of experimentally observed cross-links still falls below the number of possible contacts of cross-linkable side chains within the span of the cross-linker. Here, we propose two complementary experimental strategies to expand cross-linking data sets. First, enrichment of cross-linked peptides by size exclusion chromatography selects cross-linked peptides based on their higher molecular mass, thereby depleting the majority of unmodified peptides present in proteolytic digests of cross-linked samples. Second, we demonstrate that the use of proteases in addition to trypsin, such as Asp-N, can additionally boost the number of observable cross-linking sites. The benefits of both SEC enrichment and multiprotease digests are demonstrated on a set of model proteins and the improved workflow is applied to the characterization of the 20S proteasome from rabbit and Schizosaccharomyces pombe.
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Affiliation(s)
- Alexander Leitner
- Institute of Molecular Systems Biology, Eidgenössische Technische Hochschule Zurich, Wolfgang-Pauli-Strasse 16, 8093 Zurich, Switzerland
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Pacholarz KJ, Garlish RA, Taylor RJ, Barran PE. Mass spectrometry based tools to investigate protein–ligand interactions for drug discovery. Chem Soc Rev 2012; 41:4335-55. [DOI: 10.1039/c2cs35035a] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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50
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Kharlamova A, DeMuth JC, McLuckey SA. Vapor treatment of electrospray droplets: evidence for the folding of initially denatured proteins on the sub-millisecond time-scale. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:88-101. [PMID: 22016004 DOI: 10.1007/s13361-011-0258-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 09/16/2011] [Accepted: 09/18/2011] [Indexed: 05/31/2023]
Abstract
The exposure of electrospray droplets generated from either highly acidic or highly basic solutions to basic or acidic vapors, respectively, admitted into the counter-current drying gas, has been shown to lead to significant changes in the observed charge state distributions of proteins. In both cases, distributions of charge states changed from relatively high charge states, indicative of largely denatured proteins, to lower charge state distributions that are more consistent with native protein conformations. Ubiquitin, cytochrome c, myoglobin, and carbonic anhydrase were used as model systems. In some cases, bimodal distributions were observed that are not noted under any solution pH conditions. The extent to which changes in charge state distributions occur depends upon the initial solution pH and the pK(a) or pK(b) of the acidic or basic reagent, respectively. The evolution of charged droplets in the sampling region of the mass spectrometer inlet aperture, where the vapor exposure takes place, occurs within roughly 1 ms. The observed changes in the spectra, therefore, are a function of the magnitude of the pH change as well as the rates at which the proteins can respond to this change. The exposure of electrospray droplets in this fashion may provide means for accessing transient folding states for further characterization by mass spectrometry.
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Affiliation(s)
- Anastasia Kharlamova
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907-2084, USA
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