1
|
Polák M, Černý J, Novák P. Isotopic Depletion Increases the Spatial Resolution of FPOP Top-Down Mass Spectrometry Analysis. Anal Chem 2024; 96:1478-1487. [PMID: 38226459 PMCID: PMC10831798 DOI: 10.1021/acs.analchem.3c03759] [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] [Received: 08/22/2023] [Revised: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/17/2024]
Abstract
Protein radical labeling, like fast photochemical oxidation of proteins (FPOP), coupled to a top-down mass spectrometry (MS) analysis offers an alternative analytical method for probing protein structure or protein interaction with other biomolecules, for instance, proteins and DNA. However, with the increasing mass of studied analytes, the MS/MS spectra become complex and exhibit a low signal-to-noise ratio. Nevertheless, these difficulties may be overcome by protein isotope depletion. Thus, we aimed to use protein isotope depletion to analyze FPOP-oxidized samples by top-down MS analysis. For this purpose, we prepared isotopically natural (IN) and depleted (ID) forms of the FOXO4 DNA binding domain (FOXO4-DBD) and studied the protein-DNA interaction interface with double-stranded DNA, the insulin response element (IRE), after exposing the complex to hydroxyl radicals. As shown by comparing tandem mass spectra of natural and depleted proteins, the ID form increased the signal-to-noise ratio of useful fragment ions, thereby enhancing the sequence coverage by more than 19%. This improvement in the detection of fragment ions enabled us to detect 22 more oxidized residues in the ID samples than in the IN sample. Moreover, less common modifications were detected in the ID sample, including the formation of ketones and lysine carbonylation. Given the higher quality of ID top-down MSMS data set, these results provide more detailed information on the complex formation between transcription factors and DNA-response elements. Therefore, our study highlights the benefits of isotopic depletion for quantitative top-down proteomics. Data are available via ProteomeXchange with the identifier PXD044447.
Collapse
Affiliation(s)
- Marek Polák
- Institute
of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12843 Prague, Czech Republic
| | - Jiří Černý
- Laboratory
of Structural Bioinformatics of Proteins, Institute of Biotechnology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
| | - Petr Novák
- Institute
of Microbiology of the Czech Academy of Sciences, 14220 Prague, Czech Republic
- Department
of Biochemistry, Faculty of Science, Charles
University, 12843 Prague, Czech Republic
| |
Collapse
|
2
|
Dyck YFK, Rehm D, Winkler K, Sandig V, Jabs W, Parr MK. Comparison of middle- and bottom-up mass spectrometry in forced degradation studies of bevacizumab and infliximab. J Pharm Biomed Anal 2023; 235:115596. [PMID: 37540995 DOI: 10.1016/j.jpba.2023.115596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/06/2023]
Abstract
Monoclonal antibodies (mAbs) used as therapeutics need comprehensive characterization for appropriate quality assurance. For analysis, cost-effective methods are of high importance, especially when it comes to biosimilar development which is based on extended physicochemical characterization. The use of forced degradation to study the occurrence of modifications for analysis is well established in drug development and may be used for the evaluation of critical quality attributes (CQAs). For mAb analysis different procedures of liquid chromatography hyphenated with mass spectrometry (LC-MS) analyses are commonly applied. In this study the middle-up approach is compared to the more expensive bottom-up analysis in a forced oxidation biosimilar comparability study. Bevacizumab and infliximab as well as biosimilar candidates for the two mAbs were forcefully oxidized by H2O2 for 24, 48 and 72 h. For bottom-up, the reduced and alkylated trypsin or Lys-C digested samples were analysed by LC-MS with quadrupole time-of-flight mass analyser (LC-QTOF-MS) to detect susceptible residues. By middle-up analysis several species of every subunit (Fc/2, light chain and Fd') were detected which differed in the number of oxidations. For the most abundant species, results from middle-up were in line with results from bottom-up analysis, confirming the strength of middle-up analysis. However, for less abundant species of some subunits, results differed between the two approaches. In both mAbs, the Fc was extensively oxidized. In infliximab, additional extensive oxidation was found in the Fab. Assignment to specific amino acid residues was finally possible using the results from bottom-up analyses. Interestingly, the C-terminal cysteine of the light chain was partially found triply oxidized in both mAbs. The comparison of susceptibility to oxidation showed high similarity between the reference products and their biosimilar candidates. It is suggested that the findings of middle-up experiments should be complemented by bottom-up analysis to confirm the assignments of the localization of modifications. Once the consistency of results has been established, middle-up analyses are sufficient in extended forced degradation biosimilar studies.
Collapse
Affiliation(s)
- Yan Felix Karl Dyck
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany; Department of Life Sciences & Technology, Berlin University of Applied Science, Seestraße 64, 13347 Berlin, Germany
| | - Daniel Rehm
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany; ProBioGen AG, Herbert-Bayer-Straße 8, 13086 Berlin, Germany
| | | | - Volker Sandig
- ProBioGen AG, Herbert-Bayer-Straße 8, 13086 Berlin, Germany
| | - Wolfgang Jabs
- Department of Life Sciences & Technology, Berlin University of Applied Science, Seestraße 64, 13347 Berlin, Germany
| | - Maria Kristina Parr
- Department of Pharmaceutical & Medicinal Chemistry, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Straße 2+4, 14195 Berlin, Germany.
| |
Collapse
|
3
|
Mohrhardt B, Barrios B, Kibler R, King W, Doskey PV, Minakata D. Elucidation of the Photochemical Fate of Methionine in the Presence of Surrogate and Standard Dissolved Organic Matter under Sunlight Irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:14363-14372. [PMID: 37715305 DOI: 10.1021/acs.est.3c04176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/17/2023]
Abstract
The abiotic fate of dissolved free amino acids considerably contributes to the cycling of dissolved sulfur and nitrogen in natural aquatic environments. However, the roles of the functional groups of chromophoric dissolved organic matter (CDOM) and the fate of free amino acids under sunlight irradiation in fresh waters are not fully understood. This study aims to elucidate the fate of photolabile methionine in the presence of three CDOM surrogate compounds, i.e., 1,4-naphthoquinone, 2-naphthaldehyde, and umbelliferone, and two standard CDOM by coupling experimental measurement, quantum chemical computations, and kinetic modeling. Results indicate that excited triplet-state CDOM and hydroxyl radicals are able to cleave the C-S bond in methionine, resulting in the formation of smaller amino acids and volatile sulfur-containing compounds. Singlet oxygen forms methionine sulfoxide and methionine sulfone. The distribution of phototransformation products offers an improved understanding of the fate of nitrogen- and sulfur-containing compounds and their uptake by microorganisms in natural aquatic environments.
Collapse
Affiliation(s)
- Benjamin Mohrhardt
- Department of Civil, Environmental and Geospatial Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Benjamin Barrios
- Department of Civil, Environmental and Geospatial Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Ryan Kibler
- Department of Civil, Environmental and Geospatial Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Wynter King
- Department of Civil, Environmental and Geospatial Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Paul V Doskey
- College of Forest Resources and Environmental Science, Michigan Technological, 1400 Townsend Drive, Houghton, Michigan 49931, United States University
| | - Daisuke Minakata
- Department of Civil, Environmental and Geospatial Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| |
Collapse
|
4
|
Han Z, Omata N, Matsuda T, Hishida S, Takiguchi S, Komori R, Suzuki R, Chen LC. Tuning oxidative modification by a strong electric field using nanoESI of highly conductive solutions near the minimum flow rate. Chem Sci 2023; 14:4506-4515. [PMID: 37152264 PMCID: PMC10155921 DOI: 10.1039/d2sc07113d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Oxidative modification is usually used in mass spectrometry (MS) for labeling and structural analysis. Here we report a highly tunable oxidation that can be performed in line with the nanoESI-MS analysis at the same ESI emitter without the use of oxidative reagents such as ozone and H2O2, and UV activation. The method is based on the high-pressure nanoESI of a highly conductive (conductivity >3.8 S m-1) aqueous solution near the minimum flow rate. The ion source is operated under super-atmospheric pressure (0.5 MPa gauge pressure) to avoid the contribution of electric discharge. The analyte at the tip of the Taylor cone or in the emitter droplet can be locally oxidized in an on-demand manner by varying the nanoflow rate. With an offline nanoESI, the degree of oxidation, i.e., the average number of incorporated oxygen atoms, can be finely tuned by voltage modulation using spray current as the feedback signal. Oxidations of easily oxidized residues present in peptides/proteins and the double bonds of the unsaturated phosphatidylcholine occur at low flow rate operation (<5 nL min-1) when the electric field at the tip of the Taylor cone and the initially produced charged droplet reaches approximately 1.3 V nm-1. The oxidized ion signal responds instantaneously to changes in flow rate, indicating that the oxidation is highly localized. Using isotope labeling, it was found that the incorporated oxygen primarily originates from the gas phase, suggesting a direct oxidation pathway for the analyte enriched on the liquid surface via the reactive oxygen atoms formed by the strong electric field.
Collapse
Affiliation(s)
- Zhongbao Han
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Nozomu Omata
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Takeshi Matsuda
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Shoki Hishida
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Shuuhei Takiguchi
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Ryoki Komori
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Riku Suzuki
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| | - Lee Chuin Chen
- Faculty of Engineering, University of Yamanashi 4-3-11, Takeda Kofu Yamanashi 400-8511 Japan +81-55-220-8072
| |
Collapse
|
5
|
Tiefenthaler L, Scheier P, Erdmann E, Aguirre NF, Díaz-Tendero S, Luxford TFM, Kočišek J. Non-ergodic fragmentation upon collision-induced activation of cysteine-water cluster cations. Phys Chem Chem Phys 2023; 25:5361-5371. [PMID: 36647750 PMCID: PMC9930733 DOI: 10.1039/d2cp04172c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cysteine-water cluster cations Cys(H2O)3,6+ and Cys(H2O)3,6H+ are assembled in He droplets and probed by tandem mass spectrometry with collision-induced activation. Benchmark experimental data for this biologically important system are complemented with theory to elucidate the details of the collision-induced activation process. Experimental energy thresholds for successive release of water are compared to water dissociation energies from DFT calculations showing that clusters do not only fragment exclusively by sequential emission of single water molecules but also by the release of small water clusters. Release of clustered water is observed also in the ADMP (atom centered density matrix propagation) molecular dynamics model of small Cys(H2O)3+ and Cys(H2O)3H+ clusters. For large clusters Cys(H2O)6+ and Cys(H2O)6H+ the less computationally demanding statistical Microcanonical Metropolis Monte-Carlo method (M3C) is used to model the experimental fragmentation patterns. We are able to detail the energy redistribution in clusters upon collision activation. In the present case, about two thirds of the collision energy redistribute via an ergodic process, while the remaining one third is transferred into a non-ergodic channel leading to ejection of a single water molecule from the cluster. In contrast to molecular fragmentation, which can be well described by statistical models, modelling of collision-induced activation of weakly bound clusters requires inclusion of non-ergodic processes.
Collapse
Affiliation(s)
- Lukas Tiefenthaler
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Paul Scheier
- Institute for Ion Physics and Applied Physics, University of Innsbruck, Austria.
| | - Ewa Erdmann
- Faculty of Applied Physics and Mathematics, Gdansk University of Technology, Narutowicza 11/12, 80-233 Gdansk, Poland.,Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | | | - Sergio Díaz-Tendero
- Departamento de Química, Universidad Autónoma de Madrid, 28049, Madrid, Spain. .,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in ChemicalSciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Thomas F. M. Luxford
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of SciencesDolejškova 318223 PragueCzechia
| | - Jaroslav Kočišek
- J. Heyrovský Institute of Physical Chemistry v.v.i., The Czech Academy of Sciences, Dolejškova 3, 18223 Prague, Czechia.
| |
Collapse
|
6
|
Jain R, Dhillon NS, Farquhar ER, Wang B, Li X, Kiselar J, Chance MR. Multiplex Chemical Labeling of Amino Acids for Protein Footprinting Structure Assessment. Anal Chem 2022; 94:9819-9825. [PMID: 35763792 PMCID: PMC9983563 DOI: 10.1021/acs.analchem.2c01640] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein footprinting with mass spectrometry is an established structural biology technique for mapping solvent accessibility and assessing molecular-level interactions of proteins. In hydroxyl radical protein footprinting (HRPF), hydroxyl (OH) radicals generated by water radiolysis or other methods covalently label protein side chains. Because of the wide dynamic range of OH reactivity, not all side chains are easily detected in a single experiment. Novel reagent development and the use of radical chain reactions for labeling, including trifluoromethyl radicals, is a potential approach to normalize the labeling across a diverse set of residues. HRPF in the presence of a trifluoromethylation reagent under the right conditions could provide a "one-pot" reaction for multiplex labeling of protein side chains. Toward this goal, we have systematically evaluated amino acid labeling with the recently investigated Langlois' reagent (LR) activated by X-ray-mediated water radiolysis, followed by three different mass spectrometry methods. We compared the reactivity of CF3 and OH radical labeling for all 20 protein side chains in a competition-free environment. We found that all 20 amino acids exhibited CF3 or OH labeling in LR. Our investigations provide the evidence and knowledge set to perfect hydroxyl radical-activated trifluoromethyl chemistry as "one-pot" reaction for multiplex labeling of protein side chains to achieve higher resolution in HRPF.
Collapse
Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Nanak S. Dhillon
- Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Erik R. Farquhar
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Benlian Wang
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Xiaolin Li
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Mark R. Chance
- Center for Synchrotron Biosciences, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Center for Proteomics and Bioinformatics, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA,Corresponding Author: Mark R. Chance - Center for Synchrotron Biosciences; Center for Proteomics and Bioinformatics; Department of Nutrition, Case Western Reserve University, School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA.
| |
Collapse
|
7
|
Khaje NA, Eletsky A, Biehn SE, Mobley CK, Rogals MJ, Kim Y, Mishra SK, Doerksen RJ, Lindert S, Prestegard JH, Sharp JS. Validated determination of NRG1 Ig-like domain structure by mass spectrometry coupled with computational modeling. Commun Biol 2022; 5:452. [PMID: 35551273 PMCID: PMC9098640 DOI: 10.1038/s42003-022-03411-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 04/25/2022] [Indexed: 01/03/2023] Open
Abstract
High resolution hydroxyl radical protein footprinting (HR-HRPF) is a mass spectrometry-based method that measures the solvent exposure of multiple amino acids in a single experiment, offering constraints for experimentally informed computational modeling. HR-HRPF-based modeling has previously been used to accurately model the structure of proteins of known structure, but the technique has never been used to determine the structure of a protein of unknown structure. Here, we present the use of HR-HRPF-based modeling to determine the structure of the Ig-like domain of NRG1, a protein with no close homolog of known structure. Independent determination of the protein structure by both HR-HRPF-based modeling and heteronuclear NMR was carried out, with results compared only after both processes were complete. The HR-HRPF-based model was highly similar to the lowest energy NMR model, with a backbone RMSD of 1.6 Å. To our knowledge, this is the first use of HR-HRPF-based modeling to determine a previously uncharacterized protein structure. A mass spectrometry-based method guides computational modeling for de novo protein structure prediction.
Collapse
Affiliation(s)
- Niloofar Abolhasani Khaje
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Analytical Operations Department, Gilead Sciences, Foster City, CA, USA
| | - Alexander Eletsky
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sarah E Biehn
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - Charles K Mobley
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Protein Discovery Department, Impossible Foods, Redwood City, CA, USA
| | - Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yoonkyoo Kim
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Sushil K Mishra
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA
| | - Robert J Doerksen
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA.,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA
| | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS, USA. .,Glycoscience Center of Research Excellence, University of Mississippi, University, MS, USA. .,Department of Chemistry and Biochemistry, University of Mississippi, University, MS, USA.
| |
Collapse
|
8
|
Advances in Mass Spectrometry-based Epitope Mapping of Protein Therapeutics. J Pharm Biomed Anal 2022; 215:114754. [DOI: 10.1016/j.jpba.2022.114754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/21/2022]
|
9
|
McKenzie-Coe A, Montes NS, Jones LM. Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins. Chem Rev 2021; 122:7532-7561. [PMID: 34633178 DOI: 10.1021/acs.chemrev.1c00432] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.
Collapse
Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicholas S Montes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| |
Collapse
|
10
|
Lisboa J, Pereira C, Rifflet A, Ayala J, Terceti MS, Barca AV, Rodrigues I, Pereira PJB, Osorio CR, García-Del Portillo F, Gomperts Boneca I, do Vale A, Dos Santos NMS. A Secreted NlpC/P60 Endopeptidase from Photobacterium damselae subsp. piscicida Cleaves the Peptidoglycan of Potentially Competing Bacteria. mSphere 2021; 6:e00736-20. [PMID: 33536321 PMCID: PMC7860986 DOI: 10.1128/msphere.00736-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/08/2021] [Indexed: 11/20/2022] Open
Abstract
Peptidoglycan (PG) is a major component of the bacterial cell wall, forming a mesh-like structure enwrapping the bacteria that is essential for maintaining structural integrity and providing support for anchoring other components of the cell envelope. PG biogenesis is highly dynamic and requires multiple enzymes, including several hydrolases that cleave glycosidic or amide bonds in the PG. This work describes the structural and functional characterization of an NlpC/P60-containing peptidase from Photobacterium damselae subsp. piscicida (Phdp), a Gram-negative bacterium that causes high mortality of warm-water marine fish with great impact for the aquaculture industry. PnpA ( PhotobacteriumNlpC-like protein A) has a four-domain structure with a hydrophobic and narrow access to the catalytic center and specificity for the γ-d-glutamyl-meso-diaminopimelic acid bond. However, PnpA does not cleave the PG of Phdp or PG of several Gram-negative and Gram-positive bacterial species. Interestingly, it is secreted by the Phdp type II secretion system and degrades the PG of Vibrio anguillarum and Vibrio vulnificus This suggests that PnpA is used by Phdp to gain an advantage over bacteria that compete for the same resources or to obtain nutrients in nutrient-scarce environments. Comparison of the muropeptide composition of PG susceptible and resistant to the catalytic activity of PnpA showed that the global content of muropeptides is similar, suggesting that susceptibility to PnpA is determined by the three-dimensional organization of the muropeptides in the PG.IMPORTANCE Peptidoglycan (PG) is a major component of the bacterial cell wall formed by long chains of two alternating sugars interconnected by short peptides, generating a mesh-like structure that enwraps the bacterial cell. Although PG provides structural integrity and support for anchoring other components of the cell envelope, it is constantly being remodeled through the action of specific enzymes that cleave or join its components. Here, it is shown that Photobacterium damselae subsp. piscicida, a bacterium that causes high mortality in warm-water marine fish, produces PnpA, an enzyme that is secreted into the environment and is able to cleave the PG of potentially competing bacteria, either to gain a competitive advantage and/or to obtain nutrients. The specificity of PnpA for the PG of some bacteria and its inability to cleave others may be explained by differences in the structure of the PG mesh and not by different muropeptide composition.
Collapse
Affiliation(s)
- Johnny Lisboa
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Cassilda Pereira
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Aline Rifflet
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Juan Ayala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mateus S Terceti
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alba V Barca
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Inês Rodrigues
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Pedro José Barbosa Pereira
- Biomolecular Structure Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Macromolecular Structure Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Carlos R Osorio
- Departamento de Microbioloxía e Parasitoloxía, Instituto de Acuicultura, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Francisco García-Del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Ivo Gomperts Boneca
- Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, Paris, France
- INSERM Groupe Avenir, Paris, France
- CNRS, UMR "Integrated and Molecular Microbiology," Paris, France
| | - Ana do Vale
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| | - Nuno M S Dos Santos
- Fish Immunology and Vaccinology Group, Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto, Portugal
- Fish Immunology and Vaccinology Group, Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal
| |
Collapse
|
11
|
Misra SK, Sharp JS. Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes. J Vis Exp 2020. [PMID: 32955502 DOI: 10.3791/61580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area of proteins. This technique relies on the reaction of amino acid side chains with hydroxyl radicals freely diffusing in solution. FPOP generates these radicals in situ by laser photolysis of hydrogen peroxide, creating a burst of hydroxyl radicals that is depleted on the order of a microsecond. When these hydroxyl radicals react with a solvent-accessible amino acid side chain, the reaction products exhibit a mass shift that can be measured and quantified by mass spectrometry. Since the rate of reaction of an amino acid depends in part on the average solvent accessible surface of that amino acid, measured changes in the amount of oxidation of a given region of a protein can be directly correlated to changes in the solvent accessibility of that region between different conformations (e.g., ligand-bound versus ligand-free, monomer vs. aggregate, etc.) FPOP has been applied in a number of problems in biology, including protein-protein interactions, protein conformational changes, and protein-ligand binding. As the available concentration of hydroxyl radicals varies based on many experimental conditions in the FPOP experiment, it is important to monitor the effective radical dose to which the protein analyte is exposed. This monitoring is efficiently achieved by incorporating an inline dosimeter to measure the signal from the FPOP reaction, with laser fluence adjusted in real-time to achieve the desired amount of oxidation. With this compensation, changes in protein topography reflecting conformational changes, ligand-binding surfaces, and/or protein-protein interaction interfaces can be determined in heterogeneous samples using relatively low sample amounts.
Collapse
Affiliation(s)
- Sandeep K Misra
- Department of Biomolecular Sciences, University of Mississippi
| | - Joshua S Sharp
- Department of Biomolecular Sciences, University of Mississippi; Department of Chemistry and Biochemistry, University of Mississippi; GenNext Technologies, Inc.;
| |
Collapse
|
12
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
13
|
Khaje NA, Sharp JS. Rapid Quantification of Peptide Oxidation Isomers From Complex Mixtures. Anal Chem 2020; 92:3834-3843. [PMID: 32039584 DOI: 10.1021/acs.analchem.9b05268] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Hydroxyl radical protein footprinting (HRPF) is a powerful technique for probing changes in protein topography, based on quantifying the amount of oxidation of different regions of a protein. While quantification of HRPF oxidation at the peptide level is relatively common and straightforward, quantification at the residue level is challenging because of the influence of oxidation on MS/MS fragmentation and the large number of complex and only partially chromatographically resolved isomeric peptide oxidation products. HRPF quantification of isomeric peptide oxidation products (where the peptide sequence is the same but isomeric oxidation products are formed at different sites) at the residue level by electron transfer dissociation tandem mass spectrometry (ETD MS/MS) has been demonstrated in both model peptides and HRPF products, but the method is hampered by the partial separation of oxidation isomers by reversed phase chromatography. This requires custom MS/MS methods to equally sample all isomeric oxidation products across their elution window, greatly increasing method development time and reducing the oxidation products quantified in a single LC-MS/MS run. Here, we present a zwitterionic hydrophilic interaction capillary chromatography (ZIC-HILIC) method to ideally coelute all isomeric peptide oxidation products while separating different peptides. This allows us to relatively quantify peptide oxidation isomers using an ETD MS/MS spectrum acquired at any point across the single peptide oxidation isomer peak, greatly simplifying data acquisition and data analysis.
Collapse
Affiliation(s)
- Niloofar Abolhasani Khaje
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
| | - Joshua S Sharp
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States.,Depertmant of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
| |
Collapse
|
14
|
Semelak JA, Battistini F, Radi R, Trujillo M, Zeida A, Estrin DA. Multiscale Modeling of Thiol Overoxidation in Peroxiredoxins by Hydrogen Peroxide. J Chem Inf Model 2019; 60:843-853. [PMID: 31718175 DOI: 10.1021/acs.jcim.9b00817] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, we employ a multiscale quantum-classical mechanics (QM/MM) scheme to investigate the chemical reactivity of sulfenic acids toward hydrogen peroxide, both in aqueous solution and in the protein environment of the peroxiredoxin alkyl hydroperoxide reductase E from Mycobacterium tuberculosis (MtAhpE). The reaction of oxidation of cysteine with hydrogen peroxides, catalyzed by peroxiredoxins, is usually accelerated several orders of magnitude in comparison with the analogous reaction in solution. The resulting cysteine sulfenic acid is then reduced in other steps of the catalytic cycle, recovering the original thiol. However, under some conditions, the sulfenic acid can react with another equivalent of oxidant to form a sulfinic acid. This process is called overoxidation and has been associated with redox signaling. Herein, we employed a multiscale scheme based on density function theory calculations coupled to the classical AMBER force field, developed in our group, to establish the molecular basis of thiol overoxidation by hydrogen peroxide. Our results suggest that residues that play key catalytic roles in the oxidation of MtAhpE are not relevant in the overoxidation process. Indeed, the calculations propose that the process is unfavored by this particular enzyme microenvironment.
Collapse
Affiliation(s)
- J A Semelak
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
| | - F Battistini
- Institute for Research in Biomedicine (IRB Barcelona) , The Barcelona Institute of Science and Technology , 08028 Barcelona , Spain
| | - R Radi
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - M Trujillo
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - A Zeida
- Departamento de Bioquímica and Centro de Investigaciones Biomédicas (CEINBIO) , Facultad de Medicina , Av. Gral. Flores 2125 , CP 11800 Montevideo , Uruguay
| | - D A Estrin
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET , Facultad de Ciencias Exactas y Naturales , Ciudad Universitaria, Pab. 2 , CP 1428 , Buenos Aires , Argentina
| |
Collapse
|
15
|
Li G, Ma F, Cao Q, Zheng Z, DeLaney K, Liu R, Li L. Nanosecond photochemically promoted click chemistry for enhanced neuropeptide visualization and rapid protein labeling. Nat Commun 2019; 10:4697. [PMID: 31619683 PMCID: PMC6795811 DOI: 10.1038/s41467-019-12548-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 09/17/2019] [Indexed: 12/28/2022] Open
Abstract
Comprehensive protein identification and concomitant structural probing of proteins are of great biological significance. However, this is challenging to accomplish simultaneously in one confined space. Here, we develop a nanosecond photochemical reaction (nsPCR)-based click chemistry, capable of structural probing of proteins and enhancing their identifications through on-demand removal of surrounding matrices within nanoseconds. The nsPCR is initiated using a photoactive compound, 2-nitrobenzaldehyde (NBA), and is examined by matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS). Benefiting from the on-demand matrix-removal effect, this nsPCR strategy enables enhanced neuropeptide identification and visualization from complex tissue samples such as mouse brain tissue. The design shows great promise for structural probing of proteins up to 155 kDa due to the exclusive accessibility of nsPCR to primary amine groups, as demonstrated by its general applicability using a series of proteins with various lysine residues from multiple sample sources, with accumulated labeling efficiencies greater than 90%. Mass spectrometry-based quantitative proteomics aim to identify and quantify proteins from complex biological samples. Here, the authors developed a method for simultaneous high-throughput protein labelling and on-demand matrix removal within nanoseconds.
Collapse
Affiliation(s)
- Gongyu Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Fengfei Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Qinjingwen Cao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Zhen Zheng
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Kellen DeLaney
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Rui Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA. .,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| |
Collapse
|
16
|
Liu XR, Zhang MM, Zhang B, Rempel DL, Gross ML. Hydroxyl-Radical Reaction Pathways for the Fast Photochemical Oxidation of Proteins Platform As Revealed by 18O Isotopic Labeling. Anal Chem 2019; 91:9238-9245. [PMID: 31241913 PMCID: PMC6635036 DOI: 10.1021/acs.analchem.9b02134] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fast photochemical oxidation of protein (FPOP) has become an important mass spectrometry-based protein footprinting approach. Although the hydroxyl radical (•OH) generated by photolysis of hydrogen peroxide (H2O2) is most commonly used, the pathways for its reaction with amino-acid side chains remain unclear. Here, we report a systematic study of •OH oxidative modification of 13 amino acid residues by using 18O isotopic labeling. The results differentiate three classes of residues on the basis of their oxygen uptake preference toward different oxygen sources. Histidine, arginine, tyrosine, and phenylalanine residues preferentially take oxygen from H2O2. Methionine residues competitively take oxygen from H2O2 and dissolved oxygen (O2), whereas the remaining residues take oxygen exclusively from O2. Results reported in this work deepen the understanding of •OH labeling pathway on a FPOP platform, opening new possibilities for tailoring FPOP conditions in addressing many biological questions in a profound way.
Collapse
Affiliation(s)
- Xiaoran Roger Liu
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri, 63130, United
States
| | - Mengru Mira Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri, 63130, United
States
| | - Bojie Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri, 63130, United
States
| | - Don L. Rempel
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri, 63130, United
States
| | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri, 63130, United
States
| |
Collapse
|
17
|
Chen Y, Doud E, Stone T, Xin L, Hong W, Li Y. Rapid global characterization of immunoglobulin G1 following oxidative stress. MAbs 2019; 11:1089-1100. [PMID: 31156028 PMCID: PMC6748588 DOI: 10.1080/19420862.2019.1625676] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Although peroxide and leachable metal-induced chemical modifications are among the most important quality attributes in bioprocess development, there is no mainstream characterization method covering all common modifications theoretically possible on therapeutic proteins that also gives consistent results quickly. Here, we describe a method for rapid and consistent global characterization of leachable metals- or peroxide-stressed immunoglobulin (Ig) G1 monoclonal antibodies (mAbs). Using two independent protease digestions, data-independent acquisition and data-dependent acquisition liquid chromatography high-resolution mass spectrometry, we monitored 55 potential chemical modifications on trastuzumab, a humanized IgG1 mAb. Processing templates including all observed peptides were developed on Skyline to consistently monitor all modifications throughout the stress conditions for both enzymatic digestions. The Global Characterization Data Processing Site, a universal automated data processing application, was created to batch process data, plot modification trends for peptides, generate sortable and downloadable modification tables, and produce Jmol code for three-dimensional structural models of the analyzed protein. In total, 53 sites on the mAb were found to be modified. Oxidation rates generally increased with the peroxide concentration, while leachable metals alone resulted in lower rates of modifications but more oxidative degradants. Multiple chemical modifications were found on IgG1 surfaces known to interact with FcɣRIII, complement protein C1q, and FcRn, potentially affecting activity. The combination of Skyline templates and the Global Characterization Data Processing Site results in a universally applicable assay allowing users to batch process numerous modifications. Applying this new method to stability studies will promote a broader and deeper understanding of stress modifications on therapeutic proteins.
Collapse
Affiliation(s)
- Yao Chen
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Emma Doud
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Todd Stone
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Lun Xin
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Wei Hong
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| | - Yunsong Li
- a Process Development, Catalent Pharma Solutions, Inc , Bloomington , IN , USA
| |
Collapse
|
18
|
van den Bedem H, Wilson MA. Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. JOURNAL OF SYNCHROTRON RADIATION 2019; 26:958-966. [PMID: 31274417 PMCID: PMC6613112 DOI: 10.1107/s160057751900568x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/25/2019] [Indexed: 05/04/2023]
Abstract
Cysteine is a rare but functionally important amino acid that is often subject to covalent modification. Cysteine oxidation plays an important role in many human disease processes, and basal levels of cysteine oxidation are required for proper cellular function. Because reactive cysteine residues are typically ionized to the thiolate anion (Cys-S-), their formation of a covalent bond alters the electrostatic and steric environment of the active site. X-ray-induced photo-oxidation to sulfenic acids (Cys-SOH) can recapitulate some aspects of the changes that occur under physiological conditions. Here we propose how site-specific cysteine photo-oxidation can be used to interrogate ensuing changes in protein structure and dynamics at atomic resolution. Although this powerful approach can connect cysteine covalent modification to global protein conformational changes and function, careful biochemical validation must accompany all such studies to exclude misleading artifacts. New types of X-ray crystallography experiments and powerful computational methods are creating new opportunities to connect conformational dynamics to catalysis for the large class of systems that use covalently modified cysteine residues for catalysis or regulation.
Collapse
Affiliation(s)
- Henry van den Bedem
- Bioscience Division, SLAC National Accelerator Laboratory, Stanford University, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA
| | - Mark A Wilson
- Department of Biochemistry and the Redox Biology Center, University of Nebraska, Lincoln, NE 68588, USA
| |
Collapse
|
19
|
Minkoff BB, Bruckbauer ST, Sabat G, Cox MM, Sussman MR. Covalent Modification of Amino Acids and Peptides Induced by Ionizing Radiation from an Electron Beam Linear Accelerator Used in Radiotherapy. Radiat Res 2019; 191:447-459. [PMID: 30849023 PMCID: PMC6506356 DOI: 10.1667/rr15288.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To identify modifications to amino acids that are directly induced by ionizing radiation, free amino acids and 3-residue peptides were irradiated using a linear accelerator (Linac) radiotherapy device. Mass spectrometry was performed to detail the relative sensitivity to radiation as well as identify covalent, radiation-dependent adducts. The order of reactivity of the 20 common amino acids was generally in agreement with published literature except for His (most reactive of the 20) and Cys (less reactive). Novel and previously identified modifications on the free amino acids were detected. Amino acids were far less reactive when flanked by glycine residues in a tripeptide. Order of reactivity, with GVG most and GEG least, was substantially altered, as were patterns of modification. Radiation reactivity of amino acids is clearly and strongly affected by conversion of the α-amino and α-carboxyl groups to peptide bonds, and the presence of neighboring amino acid residues.
Collapse
Affiliation(s)
- Benjamin B. Minkoff
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Steven T. Bruckbauer
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Grzegorz Sabat
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Michael R. Sussman
- Biotechnology Center, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
20
|
Young D, Pedre B, Ezeriņa D, De Smet B, Lewandowska A, Tossounian MA, Bodra N, Huang J, Astolfi Rosado L, Van Breusegem F, Messens J. Protein Promiscuity in H 2O 2 Signaling. Antioxid Redox Signal 2019; 30:1285-1324. [PMID: 29635930 DOI: 10.1089/ars.2017.7013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
SIGNIFICANCE Decrypting the cellular response to oxidative stress relies on a comprehensive understanding of the redox signaling pathways stimulated under oxidizing conditions. Redox signaling events can be divided into upstream sensing of oxidants, midstream redox signaling of protein function, and downstream transcriptional redox regulation. Recent Advances: A more and more accepted theory of hydrogen peroxide (H2O2) signaling is that of a thiol peroxidase redox relay, whereby protein thiols with low reactivity toward H2O2 are instead oxidized through an oxidative relay with thiol peroxidases. CRITICAL ISSUES These ultrareactive thiol peroxidases are the upstream redox sensors, which form the first cellular port of call for H2O2. Not all redox-regulated interactions between thiol peroxidases and cellular proteins involve a transfer of oxidative equivalents, and the nature of redox signaling is further complicated through promiscuous functions of redox-regulated "moonlighting" proteins, of which the precise cellular role under oxidative stress can frequently be obscured by "polygamous" interactions. An ultimate goal of redox signaling is to initiate a rapid response, and in contrast to prokaryotic oxidant-responsive transcription factors, mammalian systems have developed redox signaling pathways, which intersect both with kinase-dependent activation of transcription factors, as well as direct oxidative regulation of transcription factors through peroxiredoxin (Prx) redox relays. FUTURE DIRECTIONS We highlight that both transcriptional regulation and cell fate can be modulated either through oxidative regulation of kinase pathways, or through distinct redox-dependent associations involving either Prxs or redox-responsive moonlighting proteins with functional promiscuity. These protein associations form systems of crossregulatory networks with multiple nodes of potential oxidative regulation for H2O2-mediated signaling.
Collapse
Affiliation(s)
- David Young
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Brandan Pedre
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Daria Ezeriņa
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Barbara De Smet
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Aleksandra Lewandowska
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria-Armineh Tossounian
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nandita Bodra
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jingjing Huang
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Leonardo Astolfi Rosado
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| | - Frank Van Breusegem
- 2 Brussels Center for Redox Biology, Brussels, Belgium.,4 Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,5 Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Joris Messens
- 1 Center for Structural Biology, VIB, Brussels, Belgium.,2 Brussels Center for Redox Biology, Brussels, Belgium.,3 Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium
| |
Collapse
|
21
|
Frank P, Sarangi R, Hedman B, Hodgson KO. Synchrotron X-radiolysis of l-cysteine at the sulfur K-edge: Sulfurous products, experimental surprises, and dioxygen as an oxidoreductant. J Chem Phys 2019; 150:105101. [PMID: 30876351 PMCID: PMC7791807 DOI: 10.1063/1.5079419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/12/2019] [Indexed: 11/14/2022] Open
Abstract
In situ inventory of sulfurous products from the sulfur K-edge synchrotron X-radiolysis of l-cysteine in solid-phase and anaerobic (pH 5) and air-saturated (pH 5, 7, and 9) solutions without and with 40% glycerol is reported. Sequential K-edge X-ray Absorption Spectroscopic (XAS) spectra were acquired. l-cysteine degraded systematically in the X-ray beam. Radiolytic products were inventoried by fits using the XAS spectra of sulfur model compounds. Solid l-cysteine declined to 92% fraction after a single K-edge XAS scan. After six scans, 60% remained, accompanied by 14% cystine, 16% thioether, 5.4% elemental sulfur, and smaller fractions of more highly oxidized products. In air-saturated pH 5 solution, 73% of l-cysteine remained after ten scans, with 2% cystine and 19% elemental sulfur. Oxidation increased with 40% glycerol, yielding 67%, 5%, and 23% fractions, respectively, after ten scans. Higher pH solutions exhibited less radiolytic chemistry. All the reactivity followed first-order kinetics. The anaerobic experiment displayed two reaction phases, with sharp changes in kinetics and radiolytic chemistry. Unexpectedly, the radiolytic oxidation of l-cysteine was increased in anaerobic solution. After ten scans, only 60% of the l-cysteine remained, along with 17% cystine, 22% elemental sulfur, and traces of more highly oxidized products. A new aerobic reaction cycle is hypothesized, wherein dissolved dioxygen captures radiolytic H• or eaq -, enters HO2 •/O2 •-, reductively quenches cysteine thiyl radicals, and cycles back to O2. This cycle is suggested to suppress the radiolytic production of cystine in aerobic solution.
Collapse
Affiliation(s)
- Patrick Frank
- Author to whom correspondence should be addressed: . Tel.: 650-723-2479
| | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, California 94025, USA
| | | |
Collapse
|
22
|
Leser M, Chapman JR, Khine M, Pegan J, Law M, Makkaoui ME, Ueberheide BM, Brenowitz M. Chemical Generation of Hydroxyl Radical for Oxidative 'Footprinting'. Protein Pept Lett 2019; 26:61-69. [PMID: 30543161 DOI: 10.2174/0929866526666181212164812] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/21/2018] [Accepted: 10/30/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative 'footprinting' of macromolecules. OBJECTIVE In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the application of nucleic acid and protein footprinting. METHOD Pyrite Shrink-Wrap Laminate is fabricated by depositing pyrite (Fe-S2, aka 'fool's gold') nanocrystals onto thermolabile plastic (Shrinky Dink). The laminate can be thermoformed into a microtiter plate format into which samples are deposited for oxidation. RESULTS We demonstrate the utility of the Pyrite Shrink-Wrap Laminate for the chemical generation of hydroxyl radicals by mapping the surface of the T-cell co-stimulatory protein Programmed Death - 1 (PD-1) and the interface of the complex with its ligand PD-L1. CONCLUSION We have developed and validated an affordable and reliable benchtop method of hydroxyl radical generation that will broaden the application of protein oxidative footprinting. Due to the minimal equipment required to implement this method, it should be easily adaptable by many laboratories with access to mass spectrometry.
Collapse
Affiliation(s)
- Micheal Leser
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Jessica R Chapman
- Proteomics Laboratory, Department of Biochemistry, New York University School of Medicine, New York, NY, United States
| | - Michelle Khine
- Department of Biomedical Engineering, University of California, Irvine, CA, United States.,Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States
| | - Jonathan Pegan
- Department of Biomedical Engineering, University of California, Irvine, CA, United States
| | - Matt Law
- Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States.,Department of Chemistry, University of California, Irvine, CA, United States
| | - Mohammed El Makkaoui
- Department of Chemical Engineering & Materials Science, University of California, Irvine, CA, United States.,Department of Chemistry, University of California, Irvine, CA, United States
| | - Beatrix M Ueberheide
- Proteomics Laboratory, Department of Biochemistry, New York University School of Medicine, New York, NY, United States.,Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States
| | - Michael Brenowitz
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, United States
| |
Collapse
|
23
|
Sharp JS, Misra SK, Persoff JJ, Egan RW, Weinberger SR. Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry. Anal Chem 2018; 90:12625-12630. [PMID: 30290117 PMCID: PMC7811273 DOI: 10.1021/acs.analchem.8b02787] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) is a powerful method for measuring protein topography, allowing researchers to monitor events that alter the solvent accessible surface of a protein (e.g., ligand binding, aggregation, conformational changes, etc.) by measuring changes in the apparent rate of reaction of portions of the protein to hydroxyl radicals diffusing in solution. Fast Photochemical Oxidation of Proteins (FPOP) offers an ultrafast benchtop method for radical generation for HRPF, photolyzing hydrogen peroxide using a UV laser to generate high concentrations of hydroxyl radicals that are consumed on roughly a microsecond time scale. The broad reactivity of hydroxyl radicals means that almost anything added to the solution (e.g., ligands, buffers, excipients, etc.) will scavenge hydroxyl radicals, altering their half-life and changing the effective radical concentration experienced by the protein. Similarly, minute changes in peroxide concentration, laser fluence, and buffer composition can alter the effective radical concentration, making reproduction of data challenging. Here, we present a simple method for radical dosimetry that can be carried out as part of the FPOP workflow, allowing for measurement of effective radical concentration in real time. Additionally, by modulating the amount of radical generated, we demonstrate that effective hydroxyl radical yields in FPOP HRPF experiments carried out in buffers with widely differing levels of hydroxyl radical scavenging capacity can be compensated on the fly, yielding statistically indistinguishable results for the same conformer. This method represents a major step in transforming FPOP into a robust and reproducible technology capable of probing protein structure in a wide variety of contexts.
Collapse
Affiliation(s)
- Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677
- GenNext Technologies, Inc., Montara, CA 94037
| | - Sandeep K. Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677
| | | | | | | |
Collapse
|
24
|
Kiselar J, Chance MR. High-Resolution Hydroxyl Radical Protein Footprinting: Biophysics Tool for Drug Discovery. Annu Rev Biophys 2018. [DOI: 10.1146/annurev-biophys-070317-033123] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution. Lastly, advances in understanding of the chemistry of the approach have led to the determination of absolute protein topologies from HRF data. Overall, the technology can provide precise and accurate measures of side-chain solvent accessibility in a wide range of interesting and useful contexts for the study of protein structure and dynamics in both academia and industry.
Collapse
Affiliation(s)
- Janna Kiselar
- Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
| | - Mark R. Chance
- Center for Proteomics and Bioinformatics, and Department of Nutrition, Case Western Reserve University, Cleveland, Ohio 44106, USA
| |
Collapse
|
25
|
Tossounian MA, Van Molle I, Wahni K, Jacques S, Gevaert K, Van Breusegem F, Vertommen D, Young D, Rosado LA, Messens J. Disulfide bond formation protects Arabidopsis thaliana glutathione transferase tau 23 from oxidative damage. Biochim Biophys Acta Gen Subj 2017; 1862:775-789. [PMID: 29031766 DOI: 10.1016/j.bbagen.2017.10.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/04/2017] [Accepted: 10/10/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Glutathione transferases play an important role as detoxifying enzymes. In A. thaliana, elevated levels of reactive oxygen species (ROS), provoked during biotic and abiotic stress, influence the activity of GSTU23. The aim of this study is to determine the impact of oxidative stress on the function and structure of GSTU23. METHODS The impact of oxidation on the function of GSTU23 was studied using a glutathione transferase biochemical assay and mass spectrometry. With kinetics, circular dichroism and thermodynamics, we compared reduced with oxidized GSTU23. X-ray crystal structures of GSTU23 visualize the impact of oxidation on methionines and cysteines. RESULTS In the presence of 100μM H2O2, oxidation of the methionine side-chain to a sulfoxide is the prominent post-translational modification, which can be reduced by C. diphtheriae MsrA and MsrB. However, increasing the level to 200μM H2O2 results in a reversible intramolecular disulfide between Cys65-Cys110, which is substrate for glutaredoxin. Under these oxidizing conditions, GSTU23 undergoes a structural change and forms a more favourable enzyme-substrate complex to overcome kcat decrease. CONCLUSIONS AND SIGNIFICANCE At lower H2O2 levels (100μM), GSTU23 forms methionine sulfoxides. Specifically, oxidation of Met14, located near the catalytic Ser13, could interfere with both GSH binding and catalytic activation. At higher H2O2 levels (200μM), the Cys65-Cys110 disulfide bond protects other cysteines and also methionines from overoxidation. This study shows the impact of oxidative stress on GSTU23 regulated by methionine sulfoxide reductases and glutaredoxin, and the mechanisms involved in maintaining its catalytic functionality under oxidizing conditions.
Collapse
Affiliation(s)
- Maria-Armineh Tossounian
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Inge Van Molle
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Khadija Wahni
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Silke Jacques
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Kris Gevaert
- Department of Biochemistry, Ghent University, B-9000 Ghent, Belgium; VIB Center for Medical Biotechnology, B-9000 Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052 Ghent, Belgium
| | - Didier Vertommen
- de Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - David Young
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Leonardo Astolfi Rosado
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium
| | - Joris Messens
- VIB-VUB Center for Structural Biology, B-1050 Brussels, Belgium; Brussels Center for Redox Biology, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussels, Belgium.
| |
Collapse
|
26
|
Quantitative Protein Topography Measurements by High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection. Sci Rep 2017; 7:4552. [PMID: 28674401 PMCID: PMC5495787 DOI: 10.1038/s41598-017-04689-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/18/2017] [Indexed: 11/23/2022] Open
Abstract
We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids. The accuracy of the resulting <SASA> measurements was tested by using well-characterized protein models. Moreover, we demonstrated the ability to use <SASA> measurements from HR-HRPF to differentiate molecular models of high accuracy (<3 Å backbone RMSD) from models of lower accuracy (>4 Å backbone RMSD). The ability of <SASA> data from HR-HRPF to differentiate molecular model quality was found to be comparable to that of <SASA> data obtained from X-ray crystal structures, indicating the accuracy and utility of HR-HRPF for evaluating the accuracy of computational models.
Collapse
|
27
|
Scuderi D, Bergès J, de Oliveira P, Houée-Levin C. Methionine one-electron oxidation: Coherent contributions from radiolysis, IRMPD spectroscopy, DFT calculations and electrochemistry. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
28
|
Barata-Vallejo S, Ferreri C, Zhang T, Permentier H, Bischoff R, Bobrowski K, Chatgilialoglu C. Radiation chemical studies of Gly-Met-Gly in aqueous solution. Free Radic Res 2016; 50:S24-S39. [PMID: 27592721 DOI: 10.1080/10715762.2016.1231402] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Important biological consequences are related to the reaction of HO• radicals with methionine (Met). Several fundamental aspects remain to be defined when Met is an amino acid residue incorporated in the interior of peptides and proteins. The present study focuses on Gly-Met-Gly, the simplest peptide where Met is not a terminal residue. The reactions of HO• with Gly-Met-Gly and its N-acetyl derivative were studied by pulse radiolysis technique. The transient absorption spectra were resolved into contributions from specific components of radical intermediates. Moreover, a detailed product analysis is provided for the first time for Met-containing peptides in radiolytic studies to support the mechanistic proposal. By parallel radiolytical and electrochemical reactions and consequent product identification, the formation of sulfoxide attributed to the direct HO• radical attack on the sulfide functionality of the Met residue could be excluded, with the in situ generated hydrogen peroxide responsible for this oxidation. LC-MS and high resolution MS/MS were powerful analytical tools to envisage the structures of five products, thus allowing to complete the mechanistic picture of the overall Met-containing peptide reactivity.
Collapse
Affiliation(s)
| | - Carla Ferreri
- a ISOF , Consiglio Nazionale delle Ricerche , Bologna , Italy
| | - Tao Zhang
- b Department of Pharmacy , University of Groningen , Groningen , The Netherlands
| | - Hjalmar Permentier
- b Department of Pharmacy , University of Groningen , Groningen , The Netherlands
| | - Rainer Bischoff
- b Department of Pharmacy , University of Groningen , Groningen , The Netherlands
| | | | - Chryssostomos Chatgilialoglu
- a ISOF , Consiglio Nazionale delle Ricerche , Bologna , Italy.,d Institute of Nanoscience and Nanotechnology , NCSR Demokritos , Athens , Greece
| |
Collapse
|
29
|
Yamada Y, Koori D, Oshikawa Y, Koikawa M. Stereospecific interaction of optically active sulfur-bridged dinuclear Co(III)–Pt(II) complex with pseudo-enantiomeric Co(III)–M(II) (M: Pd or Pt) complex involving unequivalent π electronic system. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
30
|
Meng X, Li X, Wang X, Gao J, Yang H, Chen H. Potential allergenicity response to structural modification of irradiated bovine α-lactalbumin. Food Funct 2016; 7:3102-10. [DOI: 10.1039/c6fo00400h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bovine α-lactalbumin (α-La) is a major food allergen found in milk and is characterized by high conformational stability because of its four disulfide bridges and being calcium bound.
Collapse
Affiliation(s)
- Xuanyi Meng
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- P.R. China
- School of Food Science & Technology
| | - Xin Li
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- P.R. China
- School of Food Science & Technology
| | - Xinkang Wang
- School of Food Science & Technology
- Nanchang University
- Nanchang 330031
- P.R. China
| | - Jinyan Gao
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- P.R. China
- School of Food Science & Technology
| | - Hao Yang
- School of Food Science & Technology
- Nanchang University
- Nanchang 330031
- P.R. China
| | - Hongbing Chen
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- P.R. China
- Jiangxi-OAI Joint Research Institute
| |
Collapse
|
31
|
Zabel R, Weber G. Comparative study of the oxidation behavior of sulfur-containing amino acids and glutathione by electrochemistry-mass spectrometry in the presence and absence of cisplatin. Anal Bioanal Chem 2015; 408:1237-47. [DOI: 10.1007/s00216-015-9233-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/20/2015] [Accepted: 11/30/2015] [Indexed: 12/15/2022]
|
32
|
Rodacka A. The effect of radiation-induced reactive oxygen species (ROS) on the structural and functional properties of yeast alcohol dehydrogenase (YADH). Int J Radiat Biol 2015; 92:11-23. [DOI: 10.3109/09553002.2015.1106022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
33
|
Rivera-Santiago RF, Sriswasdi S, Harper SL, Speicher DW. Probing structures of large protein complexes using zero-length cross-linking. Methods 2015; 89:99-111. [PMID: 25937394 PMCID: PMC4628899 DOI: 10.1016/j.ymeth.2015.04.031] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 04/10/2015] [Accepted: 04/24/2015] [Indexed: 02/02/2023] Open
Abstract
Structural mass spectrometry (MS) is a field with growing applicability for addressing complex biophysical questions regarding proteins and protein complexes. One of the major structural MS approaches involves the use of chemical cross-linking coupled with MS analysis (CX-MS) to identify proximal sites within macromolecules. Identified cross-linked sites can be used to probe novel protein-protein interactions or the derived distance constraints can be used to verify and refine molecular models. This review focuses on recent advances of "zero-length" cross-linking. Zero-length cross-linking reagents do not add any atoms to the cross-linked species due to the lack of a spacer arm. This provides a major advantage in the form of providing more precise distance constraints as the cross-linkable groups must be within salt bridge distances in order to react. However, identification of cross-linked peptides using these reagents presents unique challenges. We discuss recent efforts by our group to minimize these challenges by using multiple cycles of LC-MS/MS analysis and software specifically developed and optimized for identification of zero-length cross-linked peptides. Representative data utilizing our current protocol are presented and discussed.
Collapse
Affiliation(s)
- Roland F Rivera-Santiago
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Sira Sriswasdi
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Department of Biological Sciences, Graduate School of Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Sandra L Harper
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States
| | - David W Speicher
- The Center for Systems and Computational Biology and Molecular and Cellular Oncogenesis Program, The Wistar Institute, Philadelphia, PA 19104, United States; Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, United States.
| |
Collapse
|
34
|
Quantitative mapping of protein structure by hydroxyl radical footprinting-mediated structural mass spectrometry: a protection factor analysis. Biophys J 2015; 108:107-15. [PMID: 25564857 DOI: 10.1016/j.bpj.2014.11.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 11/23/2022] Open
Abstract
Measurements from hydroxyl radical footprinting (HRF) provide rich information about the solvent accessibility of amino acid side chains of a protein. Traditional HRF data analyses focus on comparing the difference in the modification/footprinting rate of a specific site to infer structural changes across two protein states, e.g., between a free and ligand-bound state. However, the rate information itself is not fully used for the purpose of comparing different protein sites within a protein on an absolute scale. To provide such a cross-site comparison, we present a new, to our knowledge, data analysis algorithm to convert the measured footprinting rate constant to a protection factor (PF) by taking into account the known intrinsic reactivity of amino acid side chain. To examine the extent to which PFs can be used for structural interpretation, this PF analysis is applied to three model systems where radiolytic footprinting data are reported in the literature. By visualizing structures colored with the PF values for individual peptides, a rational view of the structural features of various protein sites regarding their solvent accessibility is revealed, where high-PF regions are buried and low-PF regions are more exposed to the solvent. Furthermore, a detailed analysis correlating solvent accessibility and local structural contacts for gelsolin shows a statistically significant agreement between PF values and various structure measures, demonstrating that the PFs derived from this PF analysis readily explain fundamental HRF rate measurements. We also tested this PF analysis on alternative, chemical-based HRF data, showing improved correlations of structural properties of a model protein barstar compared to examining HRF rate data alone. Together, this PF analysis not only permits a novel, to our knowledge, approach of mapping protein structures by using footprinting data, but also elevates the use of HRF measurements from a qualitative, cross-state comparison to a quantitative, cross-site assessment of protein structures in the context of individual conformational states of interest.
Collapse
|
35
|
Kaur P, Tomechko S, Kiselar J, Shi W, Deperalta G, Wecksler AT, Gokulrangan G, Ling V, Chance MR. Characterizing monoclonal antibody structure by carbodiimide/GEE footprinting. MAbs 2015; 6:1486-99. [PMID: 25484052 DOI: 10.4161/19420862.2014.975096] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Amino acid-specific covalent labeling is well suited to probe protein structure and macromolecular interactions, especially for macromolecules and their complexes that are difficult to examine by alternative means, due to size, complexity, or instability. Here we present a detailed account of carbodiimide-based covalent labeling (with GEE tagging) applied to a glycosylated monoclonal antibody therapeutic, which represents an important class of biologic drugs. Characterization of such proteins and their antigen complexes is essential to development of new biologic-based medicines. In this study, the experiments were optimized to preserve the structural integrity of the protein, and experimental conditions were varied and replicated to establish the reproducibility and precision of the technique. Homology-based models were generated and used to compare the solvent accessibility of the labeled residues, which include D, E, and the C-terminus, against the experimental surface accessibility data in order to understand the accuracy of the approach in providing an unbiased assessment of structure. Data from the protein were also compared to reactivity measures of several model peptides to explain sequence or structure-based variations in reactivity. The results highlight several advantages of this approach. These include: the ease of use at the bench top, the linearity of the dose response plots at high levels of labeling (indicating that the label does not significantly perturb the structure of the protein), the high reproducibility of replicate experiments (<2 % variation in modification extent), the similar reactivity of the 3 target probe residues (as suggested by analysis of model peptides), and the overall positive and significant correlation of reactivity and solvent accessible surface area (the latter values predicted by the homology modeling). Attenuation of reactivity, in otherwise solvent accessible probes, is documented as arising from the effects of positive charge or bond formation between adjacent amine and carboxyl groups, the latter accompanied by observed water loss. The results are also compared with data from hydroxyl radical-mediated oxidative footprinting on the same protein, showing that complementary information is gained from the 2 approaches, although the number of target residues in carbodiimide/GEE labeling is fewer. Overall, this approach is an accurate and precise method for assessing protein structure of biologic drugs.
Collapse
Key Words
- ACN, acetonitrile
- CD, circular dichroism
- CL, covalent labeling
- DR, dose response
- EDC, 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide
- EIC, extracts the ion chromatogram
- FPOP, fast photochemical oxidation of proteins
- GEE
- GEE, glycine ethyl ester
- HC, heavy chain
- HDX, hydrogen-deuterium exchange
- HRF, hydroxyl radical footprinting
- IT, ion trap
- IgG, immunoglobulin gamma
- LC, light chain
- LysC, Lysyl endopeptidase
- MS, mass spectrometry
- NMR, nuclear magnetic resonance
- RC, rate constant
- SASA, solvent accessible surface area
- SEC, size-exclusion chromatography
- VEGF, vascular endothelial growth factor
- covalent labeling
- footprinting
- mAb, monoclonal antibody
- protein structure
- structural proteomics
Collapse
Affiliation(s)
- Parminder Kaur
- a Center for Proteomics and Bioinformatics ; Case Western Reserve University ; Cleveland , OH USA
| | | | | | | | | | | | | | | | | |
Collapse
|
36
|
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
| |
Collapse
|
37
|
Kamariah N, Manimekalai MSS, Nartey W, Eisenhaber F, Eisenhaber B, Grüber G. Crystallographic and solution studies of NAD(+)- and NADH-bound alkylhydroperoxide reductase subunit F (AhpF) from Escherichia coli provide insight into sequential enzymatic steps. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1139-52. [PMID: 26092085 DOI: 10.1016/j.bbabio.2015.06.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/03/2015] [Accepted: 06/11/2015] [Indexed: 10/23/2022]
Abstract
Redox homeostasis is significant for the survival of pro- and eukaryotic cells and is crucial for defense against reactive oxygen species like superoxide and hydrogen peroxide. In Escherichia coli, the reduction of peroxides occurs via the redox active disulfide center of the alkyl hydroperoxide reductase C subunit (AhpC), whose reduced state becomes restored by AhpF. The 57kDa EcAhpF contains an N-terminal domain (NTD), which catalyzes the electron transfer from NADH via an FAD of the C-terminal domain into EcAhpC. The NTD is connected to the C-terminal domain via a linker. Here, the first crystal structure of E. coli AhpF bound with NADH and NAD(+) has been determined at 2.5Å and 2.4Å resolution, respectively. The NADH-bound form of EcAhpF reveals that the NADH-binding domain is required to alter its conformation to bring a bound NADH to the re-face of the isoalloxazine ring of the flavin, and thereby render the NADH-domain dithiol center accessible to the NTD disulfide center for electron transfer. The NAD(+)-bound form of EcAhpF shows conformational differences for the nicotinamide end moieties and its interacting residue M467, which is proposed to represent an intermediate product-release conformation. In addition, the structural alterations in EcAhpF due to NADH- and NAD(+)-binding in solution are shown by small angle X-ray scattering studies. The EcAhpF is revealed to adopt many intermediate conformations in solution to facilitate the electron transfer from the substrate NADH to the C-terminal domain, and subsequently to the NTD of EcAhpF for the final step of AhpC reduction.
Collapse
Affiliation(s)
- Neelagandan Kamariah
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | | | - Wilson Nartey
- Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; School of Computer Engineering, Nanyang Technological University (NTU), 50 Nanyang Drive, Singapore 637553, Republic of Singapore; Department of Biological Sciences, National University of Singapore, 8 Medical Drive, Singapore 117597, Republic of Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore
| | - Gerhard Grüber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Republic of Singapore; Nanyang Technological University, School of Biological Sciences, 60 Nanyang Drive, Singapore 637551, Republic of Singapore.
| |
Collapse
|
38
|
Yamada Y, Nagasaki T. Stereospecific π–π stacking interactions between pseudo-enantiomeric sulfur-bridged dinuclear Co(III)–Pd(II) and Co(III)–Pt(II) complexes of optically active penicillaminates. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.01.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
39
|
Furdui CM, Poole LB. Chemical approaches to detect and analyze protein sulfenic acids. MASS SPECTROMETRY REVIEWS 2014; 33:126-46. [PMID: 24105931 PMCID: PMC3946320 DOI: 10.1002/mas.21384] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 04/03/2013] [Accepted: 04/04/2013] [Indexed: 05/08/2023]
Abstract
Orchestration of many processes relying on intracellular signal transduction is recognized to require the generation of hydrogen peroxide as a second messenger, yet relatively few molecular details of how this oxidant acts to regulate protein function are currently understood. This review describes emerging chemical tools and approaches that can be applied to study protein oxidation in biological systems, with a particular emphasis on a key player in protein redox regulation, cysteine sulfenic acid. While sulfenic acids (within purified proteins or simple mixtures) are detectable by physical approaches like X-ray crystallography, nuclear magnetic resonance and mass spectrometry, the propensity of these moieties to undergo further modification in complex biological systems has necessitated the development of chemical probes, reporter groups and analytical approaches to allow for their selective detection and quantification. Provided is an overview of techniques that are currently available for the study of sulfenic acids, and some of the biologically meaningful data that have been collected using such approaches.
Collapse
Affiliation(s)
- Cristina M. Furdui
- Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, North Carolina 27157
- Correspondence to: Leslie B. Poole, Department of Biochemistry, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157; ; telephone: 336-716-6711
| |
Collapse
|
40
|
Silva AMN, Vitorino R, Domingues MRM, Spickett CM, Domingues P. Post-translational modifications and mass spectrometry detection. Free Radic Biol Med 2013; 65:925-941. [PMID: 24002012 DOI: 10.1016/j.freeradbiomed.2013.08.184] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 08/22/2013] [Accepted: 08/24/2013] [Indexed: 12/14/2022]
Abstract
In this review, we provide a comprehensive bibliographic overview of the role of mass spectrometry and the recent technical developments in the detection of post-translational modifications (PTMs). We briefly describe the principles of mass spectrometry for detecting PTMs and the protein and peptide enrichment strategies for PTM analysis, including phosphorylation, acetylation and oxidation. This review presents a bibliographic overview of the scientific achievements and the recent technical development in the detection of PTMs is provided. In order to ascertain the state of the art in mass spectrometry and proteomics methodologies for the study of PTMs, we analyzed all the PTM data introduced in the Universal Protein Resource (UniProt) and the literature published in the last three years. The evolution of curated data in UniProt for proteins annotated as being post-translationally modified is also analyzed. Additionally, we have undertaken a careful analysis of the research articles published in the years 2010 to 2012 reporting the detection of PTMs in biological samples by mass spectrometry.
Collapse
Affiliation(s)
- André M N Silva
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui Vitorino
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - M Rosário M Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham B4 7 ET, United Kingdom
| | - Pedro Domingues
- Mass Spectrometry Centre, QOPNA, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| |
Collapse
|
41
|
Gau BC, Chen J, Gross ML. Fast photochemical oxidation of proteins for comparing solvent-accessibility changes accompanying protein folding: data processing and application to barstar. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1834:1230-8. [PMID: 23485913 PMCID: PMC3663899 DOI: 10.1016/j.bbapap.2013.02.023] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 11/21/2022]
Abstract
Mass spectrometry-based protein footprinting reveals regional and even amino-acid structural changes and fills the gap for many proteins and protein interactions that cannot be studied by X-ray crystallography or NMR spectroscopy. Hydroxyl radical-mediated labeling has proven to be particularly informative in this pursuit because many solvent-accessible residues can be labeled by OH in a protein or protein complex, thus providing more coverage than does specific amino-acid modifications. Finding all the OH-labeling sites requires LC/MS/MS analysis of a proteolyzed sample, but data processing is daunting without the help of automated software. We describe here a systematic means for achieving a comprehensive residue-resolved analysis of footprinting data in an efficient manner, utilizing software common to proteomics core laboratories. To demonstrate the method and the utility of OH-mediated labeling, we show that FPOP easily distinguishes the buried and exposed residues of barstar in its folded and unfolded states. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.
Collapse
Affiliation(s)
- Brian C Gau
- Donald Danforth Plant Science Center, Washington University, St. Louis, MO 63132, USA
| | | | | |
Collapse
|
42
|
Abstract
Targeted agents are increasingly used for treating cancer and other diseases, but patients may need to be carefully selected to maximize the potential for therapeutic benefit. One way to select patients is to bind an imaging radionuclide to a targeting agent of interest, so that its uptake in specific sites of disease can be visualized by positron-emission tomography (PET) or single-photon emission computed tomography.18F is the most commonly used radionuclide for PET imaging. Its half-life of approximately 2 h is suited for same-day imaging of many compounds that clear quickly from the body to allow visualization of uptake in the intended target. A significant impediment to its use, however, is the challenging coupling of 18F to a carbon atom of the targeting agent. Because fluorine binds to aluminum, we developed a procedure where the Al18F complex could be captured by a chelate, thereby greatly simplifying the way that imaging agents can be fluorinated for PET imaging. This article reviews our experience with this technology.
Collapse
|
43
|
High-resolution MS for structural characterization of protein therapeutics: advances and future directions. Bioanalysis 2013; 5:1299-313. [DOI: 10.4155/bio.13.80] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
High-resolution MS (HRMS) is a central analytical technique for the study of biomolecules and is widely used in the biopharmaceutical industry. This paper reviews recent advances in commonly used HRMS instrumentation and experimental strategies for HRMS-based structural characterization of protein therapeutics. An overview of protein higher order structural characterization using HRMS-based technologies is presented, including the use of hydrogen/deuterium exchange and hydroxyl radical footprinting methods for probing protein conformational dynamics and interactions in solution. Future directions in application of HRMS for characterizing protein therapeutics are also described.
Collapse
|
44
|
Vaz AF, Souza MP, Vieira LD, Aguiar JS, Silva TG, Medeiros PL, Melo AM, Silva-Lucca RA, Santana LA, Oliva ML, Perez KR, Cuccovia IM, Coelho LC, Correia MT. High doses of gamma radiation suppress allergic effect induced by food lectin. Radiat Phys Chem Oxf Engl 1993 2013. [DOI: 10.1016/j.radphyschem.2012.12.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
45
|
Houée-Levin C, Bobrowski K. The use of the methods of radiolysis to explore the mechanisms of free radical modifications in proteins. J Proteomics 2013; 92:51-62. [PMID: 23454334 DOI: 10.1016/j.jprot.2013.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 02/01/2013] [Accepted: 02/02/2013] [Indexed: 10/27/2022]
Abstract
The method of radiolysis is based upon the interaction of ionising radiation with the solvent (water). One can form the same free radicals as in conditions of oxidative stress ((•)OH, O2(•)(-), NO2(•)…). Moreover, the quantity of reactive oxygen (ROS) or nitrogen (RNS) species formed in the irradiated medium can be calculated knowing the dose and the radiation chemical yield, G, thus this method is quantitative. The use of the method of radiolysis has provided a wealth of data, especially about the kinetics of the oxidation by various free radicals and their mechanisms, the identification of transients formed, their lifetimes and the possibility to repair them by the so-called antioxidants. In this review we have collected the most recent data about protein oxidation that might be useful to a proteomic approach. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
Collapse
Affiliation(s)
- Chantal Houée-Levin
- Laboratoire de Chimie Physique, UMR 8000, Université Paris Sud, (France), also at CNRS, France
| | | |
Collapse
|
46
|
Luo C, Hu C, Gao J, Li X, Wu Z, Yang A, Chen H. A potential practical approach to reduce Ara h 6 allergenicity by gamma irradiation. Food Chem 2013. [DOI: 10.1016/j.foodchem.2012.09.091] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
47
|
Conformational dynamics of activation for the pentameric complex of dimeric G protein-coupled receptor and heterotrimeric G protein. Structure 2012; 20:826-40. [PMID: 22579250 DOI: 10.1016/j.str.2012.03.017] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 03/05/2012] [Accepted: 03/05/2012] [Indexed: 01/08/2023]
Abstract
Photoactivation of rhodopsin (Rho), a G protein-coupled receptor, causes conformational changes that provide a specific binding site for the rod G protein, G(t). In this work we employed structural mass spectrometry techniques to elucidate the structural changes accompanying transition of ground state Rho to photoactivated Rho (Rho(∗)) and in the pentameric complex between dimeric Rho(∗) and heterotrimeric G(t). Observed differences in hydroxyl radical labeling and deuterium uptake between Rho(∗) and the (Rho(∗))(2)-G(t) complex suggest that photoactivation causes structural relaxation of Rho following its initial tightening upon G(t) coupling. In contrast, nucleotide-free G(t) in the complex is significantly more accessible to deuterium uptake allowing it to accept GTP and mediating complex dissociation. Thus, we provide direct evidence that in the critical step of signal amplification, Rho(∗) and G(t) exhibit dissimilar conformational changes when they are coupled in the (Rho(∗))(2)-G(t) complex.
Collapse
|
48
|
Salsbury FR, Poole LB, Fetrow JS. Electrostatics of cysteine residues in proteins: parameterization and validation of a simple model. Proteins 2012; 80:2583-91. [PMID: 22777874 DOI: 10.1002/prot.24142] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 06/04/2012] [Accepted: 06/27/2012] [Indexed: 12/17/2022]
Abstract
One of the most popular and simple models for the calculation of pK(a) s from a protein structure is the semi-macroscopic electrostatic model MEAD. This model requires empirical parameters for each residue to calculate pK(a) s. Analysis of current, widely used empirical parameters for cysteine residues showed that they did not reproduce expected cysteine pK(a) s; thus, we set out to identify parameters consistent with the CHARMM27 force field that capture both the behavior of typical cysteines in proteins and the behavior of cysteines which have perturbed pK(a) s. The new parameters were validated in three ways: (1) calculation across a large set of typical cysteines in proteins (where the calculations are expected to reproduce expected ensemble behavior); (2) calculation across a set of perturbed cysteines in proteins (where the calculations are expected to reproduce the shifted ensemble behavior); and (3) comparison to experimentally determined pK(a) values (where the calculation should reproduce the pK(a) within experimental error). Both the general behavior of cysteines in proteins and the perturbed pK(a) in some proteins can be predicted reasonably well using the newly determined empirical parameters within the MEAD model for protein electrostatics. This study provides the first general analysis of the electrostatics of cysteines in proteins, with specific attention paid to capturing both the behavior of typical cysteines in a protein and the behavior of cysteines whose pK(a) should be shifted, and validation of force field parameters for cysteine residues.
Collapse
Affiliation(s)
- Freddie R Salsbury
- Department of Physics, Wake Forest University, Winston-Salem, NC 27109, USA
| | | | | |
Collapse
|
49
|
Vaz AF, Souza MP, Carneiro-da-Cunha MG, Medeiros PL, Melo AM, Aguiar JS, Silva TG, Silva-Lucca RA, Oliva ML, Correia MT. Molecular fragmentation of wheat-germ agglutinin induced by food irradiation reduces its allergenicity in sensitised mice. Food Chem 2012. [DOI: 10.1016/j.foodchem.2011.11.097] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
50
|
Lewney S, Smith LJ. Characterization of an alternative low energy fold for bovine α-lactalbumin formed by disulfide bond shuffling. Proteins 2011; 80:913-9. [PMID: 22189830 DOI: 10.1002/prot.23247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/02/2011] [Accepted: 11/04/2011] [Indexed: 11/11/2022]
Abstract
Bovine α-lactalbumin (αLA) forms a misfolded disulfide bond shuffled isomer, X-αLA. This X-αLA isomer contains two native disulfide bridges (Cys 6-Cys 120 and Cys 28-Cys 111) and two non-native disulfide bridges (Cys 61-Cys 73 and Cys 77-Cys 91). MD simulations have been used to characterize the X-αLA isomer and its formation via disulfide bond shuffling and to compare it with the native fold of αLA. In the simulations of the X-αLA isomer the structure of the α-domain of native αLA is largely retained in agreement with experimental data. However, there are significant rearrangements in the β-domain, including the loss of the native β-sheet and calcium binding site. Interestingly, the energies of X-αLA and native αLA in simulations in the absence of calcium are closely similar. Thus, the X-αLA isomer represents a different low energy fold for the protein. Calcium binding to native αLA is shown to help preserve the structure of the β-domain of the protein limiting possibilities for disulfide bond shuffling. Hence, binding calcium plays an important role in both maintaining the native structure of αLA and providing a mechanism for distinguishing between folded and misfolded species.
Collapse
Affiliation(s)
- Sarah Lewney
- Department of Chemistry, University of Oxford, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom
| | | |
Collapse
|