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Jain R, Dhillon NS, Kanchustambham VL, Lodowski DT, Farquhar ER, Kiselar J, Chance MR. Evaluating Mass Spectrometry-Based Hydroxyl Radical Protein Footprinting of a Benchtop Flash Oxidation System against a Synchrotron X-ray Beamline. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:476-486. [PMID: 38335063 DOI: 10.1021/jasms.3c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Hydroxyl radical protein footprinting (HRPF) using synchrotron X-ray radiation (XFP) and mass spectrometry is a well-validated structural biology method that provides critical insights into macromolecular structural dynamics, such as determining binding sites, measuring affinity, and mapping epitopes. Numerous alternative sources for generating the hydroxyl radicals (•OH) needed for HRPF, such as laser photolysis and plasma irradiation, complement synchrotron-based HRPF, and a recently developed commercially available instrument based on flash lamp photolysis, the FOX system, enables access to laboratory benchtop HRPF. Here, we evaluate performing HRPF experiments in-house with a benchtop FOX instrument compared to synchrotron-based X-ray footprinting at the NSLS-II XFP beamline. Using lactate oxidase (LOx) as a model system, we carried out •OH labeling experiments using both instruments, followed by nanoLC-MS/MS bottom-up peptide mass mapping. Experiments were performed under high glucose concentrations to mimic the highly scavenging conditions present in biological buffers and human clinical samples, where less •OH are available for reaction with the biomolecule(s) of interest. The performance of the FOX and XFP HRPF methods was compared, and we found that tuning the •OH dosage enabled optimal labeling coverage for both setups under physiologically relevant highly scavenging conditions. Our study demonstrates the complementarity of FOX and XFP labeling approaches, demonstrating that benchtop instruments such as the FOX photolysis system can increase both the throughput and the accessibility of the HRPF technique.
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Affiliation(s)
- Rohit Jain
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nanak S Dhillon
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Vijaya Lakshmi Kanchustambham
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - David T Lodowski
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Erik R Farquhar
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Janna Kiselar
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Mark R Chance
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Center for Proteomics and Bioinformatics, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
- Department of Nutrition, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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2
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Structural Investigation of Therapeutic Antibodies Using Hydroxyl Radical Protein Footprinting Methods. Antibodies (Basel) 2022; 11:antib11040071. [PMID: 36412837 PMCID: PMC9680451 DOI: 10.3390/antib11040071] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Commercial monoclonal antibodies are growing and important components of modern therapies against a multitude of human diseases. Well-known high-resolution structural methods such as protein crystallography are often used to characterize antibody structures and to determine paratope and/or epitope binding regions in order to refine antibody design. However, many standard structural techniques require specialized sample preparation that may perturb antibody structure or require high concentrations or other conditions that are far from the conditions conducive to the accurate determination of antigen binding or kinetics. We describe here in this minireview the relatively new method of hydroxyl radical protein footprinting, a solution-state method that can provide structural and kinetic information on antibodies or antibody-antigen interactions useful for therapeutic antibody design. We provide a brief history of hydroxyl radical footprinting, examples of current implementations, and recent advances in throughput and accessibility.
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3
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Zabilska A, Clark AH, Ferri D, Nachtegaal M, Kröcher O, Safonova OV. Beware of beam damage under reaction conditions: X-ray induced photochemical reduction of supported VO x catalysts during in situ XAS experiments. Phys Chem Chem Phys 2022; 24:21916-21926. [PMID: 36069029 PMCID: PMC9641748 DOI: 10.1039/d2cp02721f] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 08/20/2022] [Indexed: 11/04/2023]
Abstract
In situ X-ray absorption spectroscopy (XAS) is a powerful technique for the investigation of heterogeneous catalysts and electrocatalysts. The obtained XAS spectra are usually interpreted from the point of view of the investigated chemical processes, thereby sometimes omitting the fact that intense X-ray irradiation may induce additional transformations in metal speciation and, thus, in the corresponding XAS spectra. In this work, we report on X-ray induced photochemical reduction of vanadium in supported vanadia (VOx) catalysts under reaction conditions, detected at a synchrotron beamline. While this process was not observed in an inert atmosphere and in the presence of water vapor, it occurred at room temperature in the presence of a reducing agent (ethanol or hydrogen) alone or mixed with oxygen. Temperature programmed experiments have shown that X-ray induced reduction of VOx species appeared very clear at 30-100 °C but was not detected at higher temperatures, where the thermocatalytic ethanol oxidative hydrogenation (ODH) takes place. Similar to other studies on X-ray induced effects, we suggest approaches, which can help to mitigate vanadium photoreduction, including defocusing of the X-ray beam and attenuation of the X-ray beam intensity by filters. To recognize beam damage under in situ/operando conditions, we suggest performing X-ray beam switching (on and off) tests at different beam intensities under in situ conditions.
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Affiliation(s)
- Anna Zabilska
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Adam H Clark
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
| | - Davide Ferri
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
| | | | - Oliver Kröcher
- Paul Scherrer Institute, 5232 Villigen, Switzerland.
- École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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4
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Rosi M, Russell B, Kristensen LG, Farquhar ER, Jain R, Abel D, Sullivan M, Costello SM, Dominguez-Martin MA, Chen Y, Marqusee S, Petzold CJ, Kerfeld CA, DePonte DP, Farahmand F, Gupta S, Ralston CY. An automated liquid jet for fluorescence dosimetry and microsecond radiolytic labeling of proteins. Commun Biol 2022; 5:866. [PMID: 36008591 PMCID: PMC9411504 DOI: 10.1038/s42003-022-03775-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 07/27/2022] [Indexed: 12/02/2022] Open
Abstract
X-ray radiolytic labeling uses broadband X-rays for in situ hydroxyl radical labeling to map protein interactions and conformation. High flux density beams are essential to overcome radical scavengers. However, conventional sample delivery environments, such as capillary flow, limit the use of a fully unattenuated focused broadband beam. An alternative is to use a liquid jet, and we have previously demonstrated that use of this form of sample delivery can increase labeling by tenfold at an unfocused X-ray source. Here we report the first use of a liquid jet for automated inline quantitative fluorescence dosage characterization and sample exposure at a high flux density microfocused synchrotron beamline. Our approach enables exposure times in single-digit microseconds while retaining a high level of side-chain labeling. This development significantly boosts the method’s overall effectiveness and efficiency, generates high-quality data, and opens up the arena for high throughput and ultrafast time-resolved in situ hydroxyl radical labeling. A high-speed liquid jet delivery system improves the X-ray footprinting and mass spectrometry method to label proteins for structural studies.
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Affiliation(s)
- Matthew Rosi
- Sonoma State University, Rohnert Park, Sonoma, CA, 94928, US
| | - Brandon Russell
- Sonoma State University, Rohnert Park, Sonoma, CA, 94928, US
| | - Line G Kristensen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Erik R Farquhar
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Rohit Jain
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Donald Abel
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Michael Sullivan
- Center for Synchrotron Biosciences, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, US
| | - Shawn M Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Maria Agustina Dominguez-Martin
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, US.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Susan Marqusee
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,Department of Chemistry, University of California, Berkeley, CA, USA.,California Institute for Quantitative Biosciences, University of California, Berkeley, CA, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, US.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US
| | | | - Farid Farahmand
- Sonoma State University, Rohnert Park, Sonoma, CA, 94928, US
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US.
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, US.
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5
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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.
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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.
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6
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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]
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7
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Polák M, Yassaghi G, Kavan D, Filandr F, Fiala J, Kukačka Z, Halada P, Loginov DS, Novák P. Utilization of Fast Photochemical Oxidation of Proteins and Both Bottom-up and Top-down Mass Spectrometry for Structural Characterization of a Transcription Factor-dsDNA Complex. Anal Chem 2022; 94:3203-3210. [PMID: 35134296 DOI: 10.1021/acs.analchem.1c04746] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A combination of covalent labeling techniques and mass spectrometry (MS) is currently a progressive approach for deriving insights related to the mapping of protein surfaces or protein-ligand interactions. In this study, we mapped an interaction interface between the DNA binding domain (DBD) of FOXO4 protein and the DNA binding element (DAF16) using fast photochemical oxidation of proteins (FPOP). Residues involved in protein-DNA interaction were identified using the bottom-up approach. To confirm the findings and avoid a misinterpretation of the obtained data, caused by possible multiple radical oxidations leading to the protein surface alteration and oxidation of deeply buried amino acid residues, a top-down approach was employed for the first time in FPOP analysis. An isolation of singly oxidized ions enabled their gas-phase separation from multiply oxidized species followed by CID and ECD fragmentation. Application of both fragmentation techniques allowed generation of complementary fragment sets, out of which the regions shielded in the presence of DNA were deduced. The findings obtained by bottom-up and top-down approaches were highly consistent. Finally, FPOP results were compared with those of the HDX study of the FOXO4-DBD·DAF16 complex. No contradictions were found between the methods. Moreover, their combination provides complementary information related to the structure and dynamics of the protein-DNA complex. Data are available via ProteomeXchange with identifier PXD027624.
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Affiliation(s)
- Marek Polák
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - Ghazaleh Yassaghi
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - František Filandr
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - Jan Fiala
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Faculty of Science, Charles University, Prague, 12843, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Petr Halada
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
| | - Dmitry S Loginov
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic.,Orekhovich Institute of Biomedical Chemistry, Moscow, 119191, Russia
| | - Petr Novák
- Institute of Microbiology, The Czech Academy of Sciences, Prague, 14220, Czech Republic
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8
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Reid DJ, Rohrbough JG, Kostelic MM, Marty MT. Investigating Antimicrobial Peptide-Membrane Interactions Using Fast Photochemical Oxidation of Peptides in Nanodiscs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:62-67. [PMID: 34866389 PMCID: PMC8732327 DOI: 10.1021/jasms.1c00252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Antimicrobial peptides (AMPs) are an important part of the innate immune system and demonstrate promising applications in the fight against antibiotic-resistant infections due to their unique mechanism of targeting bacterial membranes. However, it is challenging to study the interactions of these peptides within lipid bilayers, making it difficult to understand their mechanisms of toxicity and selectivity. Here, we used fast photochemical oxidation of peptides, an irreversible footprinting technique that labels solvent accessible residues, and native charge detection-mass spectrometry to study AMP-lipid interactions with different lipid bilayer nanodiscs. We observed differences in the oxidation of two peptides, indolicidin and LL-37, in three distinct lipid environments, which reveal their affinity for lipid bilayers. Our findings suggest that indolicidin interacts with lipid head groups via a simple charge-driven mechanism, but LL-37 is more specific for Escherichia coli nanodiscs. These results provide complementary information on the potential modes of action and lipid selectivity of AMPs.
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Affiliation(s)
- Deseree J. Reid
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - James G. Rohrbough
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Marius M. Kostelic
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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9
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Pan X, Vachet RW. MEMBRANE PROTEIN STRUCTURES AND INTERACTIONS FROM COVALENT LABELING COUPLED WITH MASS SPECTROMETRY. MASS SPECTROMETRY REVIEWS 2022; 41:51-69. [PMID: 33145813 PMCID: PMC8093322 DOI: 10.1002/mas.21667] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 05/31/2023]
Abstract
Membrane proteins are incredibly important biomolecules because they mediate interactions between a cell's external and internal environment. Obtaining information about membrane protein structure and interactions is thus important for understanding these essential biomolecules. Compared with the analyses of water-soluble proteins, the structural analysis of membrane proteins is more challenging owing to their unique chemical properties and the presence of lipid components that are necessary to solubilize them. The combination of covalent labeling (CL) and mass spectrometry (MS) has recently been applied with great success to study membrane protein structure and interactions. These studies have demonstrated the many advantages that CL-MS methods have over other traditional biophysical techniques. In this review, we discuss both amino acid-specific and non-specific labeling approaches and the special considerations needed to address the unique challenges associated with interrogating membrane proteins. This review highlights the aspects of this approach that require special care to be applied correctly and provides a comprehensive review of the membrane protein systems that have been studied by CL-MS. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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10
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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.
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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
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11
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Fenton-Chemistry-Based Oxidative Modification of Proteins Reflects Their Conformation. Int J Mol Sci 2021; 22:ijms22189927. [PMID: 34576105 PMCID: PMC8469487 DOI: 10.3390/ijms22189927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 11/25/2022] Open
Abstract
In order to understand protein structure to a sufficient extent for, e.g., drug discovery, no single technique can provide satisfactory information on both the lowest-energy conformation and on dynamic changes over time (the ‘four-dimensional’ protein structure). Instead, a combination of complementary techniques is required. Mass spectrometry methods have shown promise in addressing protein dynamics, but often rely on the use of high-end commercial or custom instruments. Here, we apply well-established chemistry to conformation-sensitive oxidative protein labelling on a timescale of a few seconds, followed by analysis through a routine protein analysis workflow. For a set of model proteins, we show that site selectivity of labelling can indeed be rationalised in terms of known structural information, and that conformational changes induced by ligand binding are reflected in the modification pattern. In addition to conventional bottom-up analysis, further insights are obtained from intact mass measurement and native mass spectrometry. We believe that this method will provide a valuable and robust addition to the ‘toolbox’ of mass spectrometry researchers studying higher-order protein structure.
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12
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Britt HM, Cragnolini T, Thalassinos K. Integration of Mass Spectrometry Data for Structural Biology. Chem Rev 2021; 122:7952-7986. [PMID: 34506113 DOI: 10.1021/acs.chemrev.1c00356] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mass spectrometry (MS) is increasingly being used to probe the structure and dynamics of proteins and the complexes they form with other macromolecules. There are now several specialized MS methods, each with unique sample preparation, data acquisition, and data processing protocols. Collectively, these methods are referred to as structural MS and include cross-linking, hydrogen-deuterium exchange, hydroxyl radical footprinting, native, ion mobility, and top-down MS. Each of these provides a unique type of structural information, ranging from composition and stoichiometry through to residue level proximity and solvent accessibility. Structural MS has proved particularly beneficial in studying protein classes for which analysis by classic structural biology techniques proves challenging such as glycosylated or intrinsically disordered proteins. To capture the structural details for a particular system, especially larger multiprotein complexes, more than one structural MS method with other structural and biophysical techniques is often required. Key to integrating these diverse data are computational strategies and software solutions to facilitate this process. We provide a background to the structural MS methods and briefly summarize other structural methods and how these are combined with MS. We then describe current state of the art approaches for the integration of structural MS data for structural biology. We quantify how often these methods are used together and provide examples where such combinations have been fruitful. To illustrate the power of integrative approaches, we discuss progress in solving the structures of the proteasome and the nuclear pore complex. We also discuss how information from structural MS, particularly pertaining to protein dynamics, is not currently utilized in integrative workflows and how such information can provide a more accurate picture of the systems studied. We conclude by discussing new developments in the MS and computational fields that will further enable in-cell structural studies.
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Affiliation(s)
- Hannah M Britt
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom
| | - Tristan Cragnolini
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
| | - Konstantinos Thalassinos
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, United Kingdom.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom
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13
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亀田 雅, 近藤 祥. [Metabolites for frailty biomarkers]. Nihon Ronen Igakkai Zasshi 2021; 58:333-340. [PMID: 34483155 DOI: 10.3143/geriatrics.58.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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McKenzie-Coe A, Shortt R, Jones LM. THE MAKING OF A FOOTPRINT IN PROTEIN FOOTPRINTING: A REVIEW IN HONOR OF MICHAEL L. GROSS. MASS SPECTROMETRY REVIEWS 2021; 40:177-200. [PMID: 32400038 PMCID: PMC7849054 DOI: 10.1002/mas.21632] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Within the past decade protein footprinting in conjunction with mass spectrometry has become a powerful and versatile means to unravel the higher order structure of proteins. Footprinting-based approaches has demonstrated the capacity to inform on interaction sites and dynamic regions that participate in conformational changes. These findings when set in a biological perspective inform on protein folding/unfolding, protein-protein interactions, and protein-ligand interactions. In this review, we will look at the contribution of Dr. Michael L. Gross to protein footprinting approaches such as hydrogen deuterium exchange mass spectrometry and hydroxyl radical protein footprinting. This review details the development of novel footprinting methods as well as their applications to study higher order protein structure. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, 21201
| | - Raquel Shortt
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, 21201
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland Baltimore, Baltimore, Maryland, 21201
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15
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Li J, Liu C, Chen H, Zare RN. Accelerated Oxidation of Organic Sulfides by Microdroplet Chemistry. J Org Chem 2021; 86:5011-5015. [PMID: 33656874 DOI: 10.1021/acs.joc.0c02942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the rapid oxidation of organic sulfides to sulfoxides by means of microdroplet chemistry at room temperature using a spray solution containing an organic sulfide dissolved in water/methanol, dilute (11%-14%) sodium hypochlorite (NaClO), and 5% chloroauric acid (HAuCl4). Ultrasonic nebulization, easy ambient sonic-spray ionization, or electrosonic spray ionization serves as the microdroplet source. High-resolution mass spectrometry was used as an online detector, and nuclear magnetic resonance was used as an offline detector. We found that the sulfoxide yields vary between 66 and 95%, the highest rate of product formation is 195 mg/min for benzyl phenyl sulfoxide, and the time required is a few minutes, which is much less than that required for the conventional means of achieving this chemical transformation. We also applied this microdroplet method to protein fingerprinting. We found that protein sequences containing methionine can be quickly oxidized, providing useful information for protein structure determinations.
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Affiliation(s)
- Jia Li
- Department of Chemistry, Fudan University, Shanghai 200438, China
| | - Chengyuan Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei 230029, China
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Richard N Zare
- Department of Chemistry, Fudan University, Shanghai 200438, China.,Department of Chemistry, Stanford University, Stanford, California 94305, United States
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16
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Shi RL, Xiao G, Dillon TM, McAuley A, Ricci MS, Bondarenko PV. Identification of critical chemical modifications by size exclusion chromatography of stressed antibody-target complexes with competitive binding. MAbs 2021; 13:1887612. [PMID: 33616001 PMCID: PMC7899689 DOI: 10.1080/19420862.2021.1887612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Chemical modifications (attributes) in the binding regions of stressed therapeutic proteins may affect binding to target and efficacy of therapeutic proteins. The method presented here describes the criticality assessment of therapeutic antibody modifications by size-exclusion chromatography (SEC) of competitive binding between a stressed antibody and its target, human epidermal growth factor receptor-2 (HER2), followed by SEC fractionation and peptide mapping characterization of bound and unbound antibodies. When stressed antibody and its target were mixed at a stoichiometric molar ratio of 1:2, only antibody-receptor complex eluted from SEC, indicating that binding was not decreased to break the complex. When a smaller amount of the receptor was provided (1:1), the antibody species with modifications reducing binding eluted as unbound from SEC, while the antibody-receptor complex eluted as the bound fraction. Peptide mapping revealed ratios of modifications between unbound and bound fractions. Statistical analysis after triplicate measurements (n = 3) indicated that heavy chain (HC) D102 isomerization and light chain (LC) N30 deamidation were four-fold higher in unbound fraction with high statistical significance. Although HC N55 deamidation and M107 oxidation were also abundant, they were not statistically different between unbound and bound. Our findings agree with previously published potency measurements of collected CEX fractions and the crystal structure of antibody and HER2. Overall, competitive SEC of stressed antibody-receptor mixture followed by peptide mapping is a useful tool in revealing critical residues and modifications involved in the antibody-target binding, even if they elute as a complex from SEC when mixed at 1:2 stoichiometric ratio.
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Affiliation(s)
- Rachel Liuqing Shi
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Gang Xiao
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Thomas M Dillon
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Arnold McAuley
- Drug Product Technologies, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Margaret S Ricci
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA.,Drug Product Technologies, Process Development, Amgen Inc , Thousand Oaks, CA, USA
| | - Pavel V Bondarenko
- Attribute Sciences, Process Development, Amgen Inc , Thousand Oaks, CA, USA
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17
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Abstract
X-ray crystallography enables detailed structural studies of proteins to understand and modulate their function. Conducting crystallographic experiments at cryogenic temperatures has practical benefits but potentially limits the identification of functionally important alternative protein conformations that can be revealed only at room temperature (RT). This review discusses practical aspects of preparing, acquiring, and analyzing X-ray crystallography data at RT to demystify preconceived impracticalities that freeze progress of routine RT data collection at synchrotron sources. Examples are presented as conceptual and experimental templates to enable the design of RT-inspired studies; they illustrate the diversity and utility of gaining novel insights into protein conformational landscapes. An integrative view of protein conformational dynamics enables opportunities to advance basic and biomedical research.
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18
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Whole Blood Metabolomics in Aging Research. Int J Mol Sci 2020; 22:ijms22010175. [PMID: 33375345 PMCID: PMC7796096 DOI: 10.3390/ijms22010175] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/25/2020] [Accepted: 12/25/2020] [Indexed: 02/08/2023] Open
Abstract
Diversity is observed in the wave of global aging because it is a complex biological process exhibiting individual variability. To assess aging physiologically, markers for biological aging are required in addition to the calendar age. From a metabolic perspective, the aging hypothesis includes the mitochondrial hypothesis and the calorie restriction (CR) hypothesis. In experimental models, several compounds or metabolites exert similar lifespan-extending effects, like CR. However, little is known about whether these metabolic modulations are applicable to human longevity, as human aging is greatly affected by a variety of factors, including lifestyle, genetic or epigenetic factors, exposure to stress, diet, and social environment. A comprehensive analysis of the human blood metabolome captures complex changes with individual differences. Moreover, a non-targeted analysis of the whole blood metabolome discloses unexpected aspects of human biology. By using such approaches, markers for aging or aging-relevant conditions were identified. This information should prove valuable for future diagnosis or clinical interventions in diseases relevant to aging.
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19
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Liu XR, Rempel DL, Gross ML. Protein higher-order-structure determination by fast photochemical oxidation of proteins and mass spectrometry analysis. Nat Protoc 2020; 15:3942-3970. [PMID: 33169002 PMCID: PMC10476649 DOI: 10.1038/s41596-020-0396-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/03/2020] [Indexed: 11/09/2022]
Abstract
The higher-order structure (HOS) of proteins plays a critical role in their function; therefore, it is important to our understanding of their function that we have as much information as possible about their three-dimensional structure and how it changes with time. Mass spectrometry (MS) has become an important tool for determining protein HOS owing to its high throughput, mid-to-high spatial resolution, low sample amount requirement and broad compatibility with various protein systems. Modern MS-based protein HOS analysis relies, in part, on footprinting, where a reagent reacts 'to mark' the solvent-accessible surface of the protein, and MS-enabled proteomic analysis locates the modifications to afford a footprint. Fast photochemical oxidation of proteins (FPOP), first introduced in 2005, has become a powerful approach for protein footprinting. Laser-induced hydrogen peroxide photolysis generates hydroxyl radicals that react with solvent-accessible side chains (14 out of 20 amino acid side chains) to fulfill the footprinting. The reaction takes place at sub-milliseconds, faster than most of labeling-induced protein conformational changes, thus enabling a 'snapshot' of protein HOS in solution. As a result, FPOP has been employed in solving several important problems, including mapping epitopes, following protein aggregation, locating small molecule binding, measuring ligand-binding affinity, monitoring protein folding and unfolding and determining hidden conformational changes invisible to other methods. Broader adoption will be promoted by dissemination of the technical details for assembling the FPOP platform and for dealing with the complexities of analyzing FPOP data. In this protocol, we describe the FPOP platform, the conditions for successful footprinting and its examination by mass measurements of the intact protein, the post-labeling sample handling and digestion, the liquid chromatography-tandem MS analysis of the digested sample and the data analysis with Protein Metrics Suite. This protocol is intended not only as a guide for investigators trying to establish an FPOP platform in their own lab but also for those willing to incorporate FPOP as an additional tool in addressing their questions of interest.
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Affiliation(s)
- Xiaoran Roger Liu
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA.
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20
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Du PC, Tu ZC, Wang H, Hu YM, Zhang JJ, Zhong BZ. Investigation of the effect of oxidation on the structure of β-lactoglobulin by high resolution mass spectrometry. Food Chem 2020; 339:127939. [PMID: 33152852 DOI: 10.1016/j.foodchem.2020.127939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/24/2020] [Accepted: 08/23/2020] [Indexed: 12/19/2022]
Abstract
In this work, high-resolution mass spectrometry was used to identify the oxidation sites and forms of β-lactoglobulin (β-Lg) induced by hydrogen peroxide with 1.5% concentration, and the influence of oxidation sites on the structure of β-Lg was discussed from the molecular level. Twelve kinds of oxidation products and 36 oxidation sites were identified, including sulfoxidation in sulfur-containing amino acid residue, hydroxylation in aromatic group residue, deamination in amino-containing amino acid etc. The destruction of hydrogen bonds and disulfide bonds in β-Lg caused by oxidation is the main factor causing its structural changes, which were manifested in the decrease of β-sheet component and increase of β-turns and random coil contents, intrinsic fluorescence intensity and surface hydrophobicity. In addition, several peptides as potential oxidative markers were found to be capable of monitoring the degree of oxidation of β-Lg. In short, this work provided insights into structural changes of β-Lg by oxidation.
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Affiliation(s)
- Peng-Cheng Du
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Zong-Cai Tu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China; National R&D Center of Freshwater Fish Processing, Jiangxi Normal University, Nanchang 330022, China; Engineering Research Center of Freshwater Fish High-value Utilization of Jiangxi Province, Jiangxi Normal University, Nanchang 330022, China.
| | - Hui Wang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China.
| | - Yue-Ming Hu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Jing-Jing Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
| | - Bi-Zhen Zhong
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330047, China
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21
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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.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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22
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Cheng M, Asuru A, Kiselar J, Mathai G, Chance MR, Gross ML. Fast Protein Footprinting by X-ray Mediated Radical Trifluoromethylation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1019-1024. [PMID: 32255631 PMCID: PMC7486011 DOI: 10.1021/jasms.0c00085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Synchrotron radiolysis generates hydroxyl radicals (•OH) that are successful footprinting reagents. Here, we describe a new reagent for the synchrotron platform, the trifluoromethyl radical (•CF3). The radical is produced by •OH displacement of •CF3 from sodium triflinate (Langlois reagent). Upon X-ray beam exposure, the reagent labels proteins extensively without any additional chemicals on a millisecond or shorter time scale. The •CF3 is comparably reactive to •OH and produces footprinting information that complements that of •OH alone. This reagent in combination with •OH should enable novel chemistry for protein footprinting on the synchrotron platform.
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Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Awuri Asuru
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Janna Kiselar
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - George Mathai
- Department of Chemistry, Sacred Heart College, Thevara, Kochi, Kerala 682013, India
| | - Mark R. Chance
- Center for Proteomics & Bioinformatics, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106, United States
- Corresponding Authors: MLG: Tel: (314)935-4814. Fax: (314)935-7484. , MRC: Phone: (216) 368-4406. Fax: (216) 368-3812.
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
- Corresponding Authors: MLG: Tel: (314)935-4814. Fax: (314)935-7484. , MRC: Phone: (216) 368-4406. Fax: (216) 368-3812.
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23
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Frailty markers comprise blood metabolites involved in antioxidation, cognition, and mobility. Proc Natl Acad Sci U S A 2020; 117:9483-9489. [PMID: 32295884 PMCID: PMC7196897 DOI: 10.1073/pnas.1920795117] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Frailty resulting from age-related deterioration of multiple organ systems displays complex features, including cognitive dysfunction, hypomobility, and impaired daily activity. However, metabolic aspects of frailty remain unclear. We performed untargeted, comprehensive metabolomics of whole blood from 19 frail and nonfrail elderly patients. We identified 22 markers, including 15 for frailty, 6 for cognition, and 12 for hypomobility, most of which are abundant in blood. Frailty markers include 5 of 6 for cognition and 6 of 12 for hypomobility. These overlapping markers include decreased levels of metabolites related to antioxidation, nitrogen, and amino acid metabolism. Ergothioneine, an antioxidant involved in neuronal diseases, declines in frailty. Thus, we reveal essential metabolites linked to the pathogenesis of frailty, including vulnerability to oxidative stress. As human society ages globally, age-related disorders are becoming increasingly common. Due to decreasing physiological reserves and increasing organ system dysfunction associated with age, frailty affects many elderly people, compromising their ability to cope with acute stressors. Frail elderly people commonly manifest complex clinical symptoms, including cognitive dysfunction, hypomobility, and impaired daily activity, the metabolic basis of which remains poorly understood. We applied untargeted, comprehensive LC-MS metabolomic analysis to human blood from 19 frail and nonfrail elderly patients who were clinically evaluated using the Edmonton Frail Scale, the MoCA-J for cognition, and the TUG for mobility. Among 131 metabolites assayed, we identified 22 markers for frailty, cognition, and hypomobility, most of which were abundant in blood. Frailty markers included 5 of 6 markers specifically related to cognition and 6 of 12 markers associated with hypomobility. These overlapping sets of markers included metabolites related to antioxidation, muscle or nitrogen metabolism, and amino acids, most of which are decreased in frail elderly people. Five frailty-related metabolites that decreased—1,5-anhydroglucitol, acetyl-carnosine, ophthalmic acid, leucine, and isoleucine—have been previously reported as markers of aging, providing a metabolic link between human aging and frailty. Our findings clearly indicate that metabolite profiles efficiently distinguish frailty from nonfrailty. Importantly, the antioxidant ergothioneine, which decreases in frailty, is neuroprotective. Oxidative stress resulting from diminished antioxidant levels could be a key vulnerability for the pathogenesis of frailty, exacerbating illnesses related to human aging.
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24
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Cheng M, Guo C, Gross ML. The Application of Fluorine-Containing Reagents in Structural Proteomics. Angew Chem Int Ed Engl 2020; 59:5880-5889. [PMID: 31588625 PMCID: PMC7485648 DOI: 10.1002/anie.201907662] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 01/01/2023]
Abstract
Structural proteomics refers to large-scale mapping of protein structures in order to understand the relationship between protein sequence, structure, and function. Chemical labeling, in combination with mass-spectrometry (MS) analysis, have emerged as powerful tools to enable a broad range of biological applications in structural proteomics. The key to success is a biocompatible reagent that modifies a protein without affecting its high-order structure. Fluorine, well-known to exert profound effects on the physical and chemical properties of reagents, should have an impact on structural proteomics. In this Minireview, we describe several fluorine-containing reagents that can be applied in structural proteomics. We organize their applications around four MS-based techniques: a) affinity labeling, b) activity-based protein profiling (ABPP), c) protein footprinting, and d) protein cross-linking. Our aim is to provide an overview of the research, development, and application of fluorine-containing reagents in protein structural studies.
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Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University in St Louis, St Louis, MO 63130
| | - Chunyang Guo
- Department of Chemistry, Washington University in St Louis, St Louis, MO 63130
| | - Michael L Gross
- Department of Chemistry, Washington University in St Louis, St Louis, MO 63130
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25
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Bender J, Schmidt C. Mass spectrometry of membrane protein complexes. Biol Chem 2020; 400:813-829. [PMID: 30956223 DOI: 10.1515/hsz-2018-0443] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/25/2019] [Indexed: 12/24/2022]
Abstract
Membrane proteins are key players in the cell. Due to their hydrophobic nature they require solubilising agents such as detergents or membrane mimetics during purification and, consequently, are challenging targets in structural biology. In addition, their natural lipid environment is crucial for their structure and function further hampering their analysis. Alternative approaches are therefore required when the analysis by conventional techniques proves difficult. In this review, we highlight the broad application of mass spectrometry (MS) for the characterisation of membrane proteins and their interactions with lipids. We show that MS unambiguously identifies the protein and lipid components of membrane protein complexes, unravels their three-dimensional arrangements and further provides clues of protein-lipid interactions.
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Affiliation(s)
- Julian Bender
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Institute for Biochemistry and Biotechnology, Kurt-Mothes-Str. 3a, D-06120 Halle, Germany
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26
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de Souza N, Picotti P. Mass spectrometry analysis of the structural proteome. Curr Opin Struct Biol 2020; 60:57-65. [DOI: 10.1016/j.sbi.2019.10.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/16/2019] [Indexed: 01/01/2023]
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28
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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: 14] [Impact Index Per Article: 2.8] [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.
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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
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29
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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.
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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
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30
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Bellamy-Carter J, Oldham NJ. PepFoot: A Software Package for Semiautomated Processing of Protein Footprinting Data. J Proteome Res 2019; 18:2925-2930. [DOI: 10.1021/acs.jproteome.9b00238] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeddidiah Bellamy-Carter
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
| | - Neil J. Oldham
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, United Kingdom
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31
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Munro JB, Lee KK. Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein. Curr HIV Res 2019; 16:5-12. [PMID: 29268688 DOI: 10.2174/1570162x16666171222110025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 11/22/2022]
Abstract
BACKGROUND Recent advances in structural characterization of the HIV envelope glycoprotein (Env) have provided a high-resolution glimpse of the architecture of this target for neutralizing antibodies and the machinery responsible for mediating receptor binding and membrane fusion. These structures primarily capture the detailed organization of the receptor-naive, prefusion conformation of Env, but under native solution conditions Env is highly dynamic, sampling multiple conformational states as well as exhibiting local protein flexibility. METHODS Special emphasis is placed on the use of biophysical methods, including single-molecule fluorescence microscopy and hydrogen/deuterium-exchange mass spectrometry. RESULTS Using novel biophysical approaches, striking isolate-specific differences in Env's dynamic profile have been revealed that appear to underlie phenotypic differences of the viral isolates such as neutralization sensitivity and CD4 receptor reactivity. CONCLUSION Structural studies are complemented by novel biophysical investigations that enable visualization of the dynamics of HIV-1 Env under native conditions. These approaches will also enable us to gain new insights into the mechanisms of action of antibodies and drugs.
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Affiliation(s)
- James B Munro
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States
| | - Kelly K Lee
- Department of Medicinal Chemistry and Biological Physics Structure and Design Program, University of Washington, Seattle, WA, United States
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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.
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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
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Maleknia SD, Downard KM. Protein Footprinting with Radical Probe Mass Spectrometry- Two Decades of Achievement. Protein Pept Lett 2019; 26:4-15. [PMID: 30484400 DOI: 10.2174/0929866526666181128124241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/31/2018] [Accepted: 09/11/2018] [Indexed: 01/19/2023]
Abstract
BACKGROUND Radical Probe Mass Spectrometry (RP-MS) describes a pioneering methodology in structural biology that enables the study of protein structures, their interactions, and dynamics on fast timescales (down to sub-milliseconds). Hydroxyl radicals (•OH) generated directly from water within aqueous solutions induce the oxidation of reactive, solvent accessible amino acid side chains that are then analyzed by mass spectrometry. Introduced in 1998 at the American Society for Mass Spectrometry annual conference, RP-MS was first published on in 1999. OBJECTIVE This review article describes developments and applications of the RP-MS methodology over the past two decades. METHODS The RP-MS method has been variously referred to as synchrotron X-ray radiolysis footprinting, Hydroxyl Radical Protein Footprinting (HRPF), X-ray Footprinting with Mass Spectrometry (XF-MS), Fast Photochemical Oxidation of Proteins (FPOP), oxidative labelling, covalent oxidative labelling, and even the Stability of Proteins from Rates of Oxidation (SPROX). RESULTS The article describes the utility of hydroxyl radicals as a protein structural probe, the advantages of RP-MS in comparison to other MS-based approaches, its proof of concept using ion mobility mass spectrometry, its application to protein structure, folding, complex and aggregation studies, its extension to study the onset of protein damage, its implementation using a high throughput sample loading approach, and the development of protein docking algorithms to aid with data analysis and visualization. CONCLUSION RP-MS represents a powerful new structural approach that can aid in our understanding of the structure and functions of proteins, and the impact of sustained oxidation on proteins in disease pathogenesis.
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Affiliation(s)
- Simin D Maleknia
- School of Mathematical and Physical Sciences, University of Technology Sydney, Sydney, NSW, Australia
| | - Kevin M Downard
- Infectious Disease Responses Laboratory, University of New South Wales-Medicine, Sydney, NSW, Australia
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Garcia NK, Deperalta G, Wecksler AT. Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry. Protein Pept Lett 2019; 26:35-43. [PMID: 30484396 DOI: 10.2174/0929866526666181128141953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/01/2018] [Accepted: 10/29/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. CONCLUSION Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.
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Affiliation(s)
- Natalie K Garcia
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| | - Galahad Deperalta
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
| | - Aaron T Wecksler
- Department of Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA 94080, United States
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35
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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.
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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
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Shi L, Gross ML. Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry. Protein Pept Lett 2019; 26:27-34. [PMID: 30484399 DOI: 10.2174/0929866526666181128124554] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/30/2018] [Accepted: 09/27/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Determination of the composition and some structural features of macromolecules can be achieved by using structural proteomics approaches coupled with mass spectrometry (MS). One approach is hydroxyl radical protein footprinting whereby amino-acid side chains are modified with reactive reagents to modify irreversibly a protein side chain. The outcomes, when deciphered with mass-spectrometry-based proteomics, can increase our knowledge of structure, assembly, and conformational dynamics of macromolecules in solution. Generating the hydroxyl radicals by laser irradiation, Hambly and Gross developed the approach of Fast Photochemical Oxidation of Proteins (FPOP), which labels proteins on the sub millisecond time scale and provides, with MS analysis, deeper understanding of protein structure and protein-ligand and protein- protein interactions. This review highlights the fundamentals of FPOP and provides descriptions of hydroxyl-radical and other radical and carbene generation, of the hydroxyl labeling of proteins, and of determination of protein modification sites. We also summarize some recent applications of FPOP coupled with MS in protein footprinting. CONCLUSION We survey results that show the capability of FPOP for qualitatively measuring protein solvent accessibility on the residue level. To make these approaches more valuable, we describe recent method developments that increase FPOP's quantitative capacity and increase the spatial protein sequence coverage. To improve FPOP further, several new labeling reagents including carbenes and other radicals have been developed. These growing improvements will allow oxidative- footprinting methods coupled with MS to play an increasingly significant role in determining the structure and dynamics of macromolecules and their assemblies.
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Affiliation(s)
- Liuqing Shi
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
| | - Michael L Gross
- Department of Chemistry, Washington University, St. Louis, MO 63130, United States
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Bohon J. Development of Synchrotron Footprinting at NSLS and NSLS-II. Protein Pept Lett 2019; 26:55-60. [PMID: 30484397 DOI: 10.2174/0929866526666181128125125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 10/30/2018] [Accepted: 11/06/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND First developed in the 1990's at the National Synchrotron Light Source, xray synchrotron footprinting is an ideal technique for the analysis of solution-state structure and dynamics of macromolecules. Hydroxyl radicals generated in aqueous samples by intense x-ray beams serve as fine probes of solvent accessibility, rapidly and irreversibly reacting with solvent exposed residues to provide a "snapshot" of the sample state at the time of exposure. Over the last few decades, improvements in instrumentation to expand the technology have continuously pushed the boundaries of biological systems that can be studied using the technique. CONCLUSION Dedicated synchrotron beamlines provide important resources for examining fundamental biological mechanisms of folding, ligand binding, catalysis, transcription, translation, and macromolecular assembly. The legacy of synchrotron footprinting at NSLS has led to significant improvement in our understanding of many biological systems, from identifying key structural components in enzymes and transporters to in vivo studies of ribosome assembly. This work continues at the XFP (17-BM) beamline at NSLS-II and facilities at ALS, which are currently accepting proposals for use.
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Affiliation(s)
- Jen Bohon
- Center for Synchrotron Biosciences, Department of Nutrition, Case Western Reserve University, Cleveland, OH, United States
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38
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Zhang MM, Rempel DL, Gross ML. A Fast Photochemical Oxidation of Proteins (FPOP) platform for free-radical reactions: the carbonate radical anion with peptides and proteins. Free Radic Biol Med 2019; 131:126-132. [PMID: 30502457 PMCID: PMC6331213 DOI: 10.1016/j.freeradbiomed.2018.11.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/09/2018] [Accepted: 11/26/2018] [Indexed: 01/05/2023]
Abstract
Fast Photochemical Oxidation of Protein (FPOP), based on a pulsed KrF laser (248 nm) for free-radical generation, is a biophysical method that utilizes hydroxyl radicals to footprint proteins in solution. FPOP has been recognized for structural proteomics investigations, including epitope mapping, protein-aggregation characterization, protein-folding monitoring, and binding-affinity determination. The distinct merits of the platform are: i) the use of a scavenger to control radical lifetime and allow fast ("snapshot") footprinting of solvent-accessible residues in a protein; ii) the employment of a flow system to enable single-shot irradiation of small plugs of the targeted sample; iii) the use of methionine and catalase after radical oxidation chemistry to prevent post-oxidation with residual oxidizing species; and iv) the utilization of mature mass spectrometry-based proteomic methods to afford detailed analysis. In addition to •OH, other reactive reagents (e.g., carbenes, iodide, sulfate radical anion, and trifluoromethyl radical) can be implemented on this platform to increase the versatility and scope. In this study, we further elaborate the use of FPOP platform to generate secondary radicals and establish a workflow to answer fundamental questions regarding the intrinsic selectivity and reactivity of radicals that are important in biology. Carbonate radical anion is the example we chose owing to its oxidative character and important putative pathogenic roles in inflammation. This systematic study with model proteins/peptides gives consistent results with a previous study that evaluated reactivity with free amino acids and shows that methionine and tryptophan are the most reactive residues with CO3-•. Other aromatic amino acids (i.e., tyrosine, histidine and phenylalanine) exhibit moderate reactivity, whereas, aliphatic amino acids are inert, unlike with •OH. The outcome demonstrates this approach to be appropriate for studying the fast reactions of radicals with proteins.
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Affiliation(s)
- Mengru Mira Zhang
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Don L Rempel
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA.
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39
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Downard KM, Maleknia SD. Mass spectrometry in structural proteomics: The case for radical probe protein footprinting. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.11.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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40
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Limpikirati P, Liu T, Vachet RW. Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions. Methods 2018; 144:79-93. [PMID: 29630925 PMCID: PMC6051898 DOI: 10.1016/j.ymeth.2018.04.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 12/13/2022] Open
Abstract
Using mass spectrometry (MS) to obtain information about a higher order structure of protein requires that a protein's structural properties are encoded into the mass of that protein. Covalent labeling (CL) with reagents that can irreversibly modify solvent accessible amino acid side chains is an effective way to encode structural information into the mass of a protein, as this information can be read-out in a straightforward manner using standard MS-based proteomics techniques. The differential reactivity of proteins under two or more conditions can be used to distinguish protein topologies, conformations, and/or binding sites. CL-MS methods have been effectively used for the structural analysis of proteins and protein complexes, particularly for systems that are difficult to study by other more traditional biochemical techniques. This review provides an overview of the non-specific CL approaches that have been combined with MS with a particular emphasis on the reagents that are commonly used, including hydroxyl radicals, carbenes, and diethylpyrocarbonate. We describe the reagent and protein factors that affect the reactivity of amino acid side chains. We also include details about experimental design and workflow, data analysis, recent applications, and some future prospects of CL-MS methods.
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Affiliation(s)
| | - Tianying Liu
- Department of Chemistry, University of Massachusetts Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, MA 01003, United States.
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Aprahamian ML, Chea EE, Jones LM, Lindert S. Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data. Anal Chem 2018; 90:7721-7729. [PMID: 29874044 DOI: 10.1021/acs.analchem.8b01624] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In recent years mass spectrometry-based covalent labeling techniques such as hydroxyl radical footprinting (HRF) have emerged as valuable structural biology techniques, yielding information on protein tertiary structure. These data, however, are not sufficient to predict protein structure unambiguously, as they provide information only on the relative solvent exposure of certain residues. Despite some recent advances, no software currently exists that can utilize covalent labeling mass spectrometry data to predict protein tertiary structure. We have developed the first such tool, which incorporates mass spectrometry derived protection factors from HRF labeling as a new centroid score term for the Rosetta scoring function to improve the prediction of protein tertiary structures. We tested our method on a set of four soluble benchmark proteins with known crystal structures and either published HRF experimental results or internally acquired data. Using the HRF labeling data, we rescored large decoy sets of structures predicted with Rosetta for each of the four benchmark proteins. As a result, the model quality improved for all benchmark proteins as compared to when scored with Rosetta alone. For two of the four proteins we were even able to identify atomic resolution models with the addition of HRF data.
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Affiliation(s)
- Melanie L Aprahamian
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
| | - Emily E Chea
- 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
| | - Steffen Lindert
- Department of Chemistry and Biochemistry , Ohio State University , Columbus , Ohio 43210 , United States
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42
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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.
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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
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43
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MS-based conformation analysis of recombinant proteins in design, optimization and development of biopharmaceuticals. Methods 2018; 144:134-151. [PMID: 29678586 DOI: 10.1016/j.ymeth.2018.04.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/10/2018] [Accepted: 04/12/2018] [Indexed: 01/18/2023] Open
Abstract
Mass spectrometry (MS)-based methods for analyzing protein higher order structures have gained increasing application in the field of biopharmaceutical development. The predominant methods used in this area include native MS, hydrogen deuterium exchange-MS, covalent labeling, cross-linking and limited proteolysis. These MS-based methods will be briefly described in this article, followed by a discussion on how these methods contribute at different stages of discovery and development of protein therapeutics.
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44
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Li KS, Shi L, Gross ML. Mass Spectrometry-Based Fast Photochemical Oxidation of Proteins (FPOP) for Higher Order Structure Characterization. Acc Chem Res 2018; 51:736-744. [PMID: 29450991 DOI: 10.1021/acs.accounts.7b00593] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Assessment of protein structure and interaction is crucial for understanding protein structure/function relationships. Compared to high-resolution structural tools, including X-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, and traditional low-resolution methods, such as circular dichroism, UV-vis, and florescence spectroscopy, mass spectrometry (MS)-based protein footprinting affords medium-to-high resolution (i.e., regional and residue-specific insights) by taking advantage of proteomics methods focused on the primary structure. The methodology relies on "painting" the reactive and solvent-exposed amino acid residues with chemical tags and using the pattern of modifications as footprints from analysis by bottom-up MS-based proteomics to deduce protein higher order structures. The outcome can refer to proteins in solution or even in cells and is complementary to those of X-ray crystallography and NMR. It is particularly useful in mapping protein-ligand interfaces and conformational changes resulting from ligand binding, mutation, and aggregation. Fast photochemical oxidation of proteins (FPOP), in its original conception, is a type of hydroxyl-radical-based protein footprinting that utilizes a pulsed KrF laser (248 nm) to trigger hydrolysis of hydrogen peroxide to produce solution hydroxyl radicals, which subsequently modify the protein in situ. The platform is expanding to adopt other reactive species including carbenes. The reactivity of the probe depends on the intrinsic reactivity of the radical with the residue side chain and the solvent accessibility of the residue as a function of the tertiary/quaternary structures. By introducing an appropriate scavenger to compete with hydroxyl radical self-quenching, the lifetime of the primary radicals is remarkably shortened to approximately microsecond. Thus, the sampling time scale of FPOP is much faster than hydrogen-deuterium exchange and other covalent labeling methods relying on nonradical reactions. The short footprinting time scale of FPOP offers two major advantages for protein structure elucidation: (1) it allows the protein to be interrogated in its native or near-native state with minimum structural perturbation; (2) it exhibits high sensitivity toward alterations in protein higher order structures because its sampling time is short with respect to protein conformational changes and dynamic motion. In addition, the covalent and irreversible oxidation by the hydroxyl radical provides more flexibility in the downstream proteomics workflow and MS analysis, permitting high spatial resolution with residue-specific information. Since its invention in 2005 by Hambly and Gross, FPOP has developed from proof-of-concept to a valuable biophysical tool for interrogating protein structure. In this Account, we summarize the principles and experimental design of FPOP that enable its fast labeling and describe the current and unique capabilities of the technique in protein higher order structure elucidation. Application examples include characterization of amyloid β self-assembly, protein-ligand interactions with a special emphasis on epitope mapping for protein therapeutics (e.g., antibody, Fab, and adnectin), protein folding detailed to residue-specific folding kinetics, and protein flexibility/dynamics. Additionally, the utility of FPOP-based oxidative footprinting should grow with our continuing developments of novel reagents (e.g., sulfate radical anion, carbene diradical, and trifluoromethyl radical). These reactive reagents are compatible with the current FPOP platform and offer different reactivity and selectivity toward various types of amino acid residues, providing complementary insights into protein higher order structures for soluble proteins and ultimately for membrane-bound proteins.
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Affiliation(s)
- Ke Sherry Li
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Liuqing Shi
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
| | - Michael L. Gross
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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45
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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46
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Chea EE, Jones LM. Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting. Analyst 2018; 143:798-807. [DOI: 10.1039/c7an01323j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins in live cells.
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Affiliation(s)
- Emily E. Chea
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
| | - Lisa M. Jones
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
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47
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Cheng M, Zhang B, Cui W, Gross ML. Laser-Initiated Radical Trifluoromethylation of Peptides and Proteins: Application to Mass-Spectrometry-Based Protein Footprinting. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201706697] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ming Cheng
- Department of Chemistry; Washington University in St. Louis; One Brookings Drive Saint Louis MO 63130 USA
| | - Bojie Zhang
- Department of Chemistry; Washington University in St. Louis; One Brookings Drive Saint Louis MO 63130 USA
| | - Weidong Cui
- Department of Chemistry; Washington University in St. Louis; One Brookings Drive Saint Louis MO 63130 USA
| | - Michael L. Gross
- Department of Chemistry; Washington University in St. Louis; One Brookings Drive Saint Louis MO 63130 USA
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48
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Cheng M, Zhang B, Cui W, Gross ML. Laser-Initiated Radical Trifluoromethylation of Peptides and Proteins: Application to Mass-Spectrometry-Based Protein Footprinting. Angew Chem Int Ed Engl 2017; 56:14007-14010. [PMID: 28901679 DOI: 10.1002/anie.201706697] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/14/2017] [Indexed: 11/10/2022]
Abstract
Described is a novel, laser-initiated radical trifluoromethylation for protein footprinting and its broad residue coverage. . CF3 reacts with 18 of the 20 common amino acids, including Gly, Ala, Ser, Thr, Asp, and Glu, which are relatively silent with regard to . OH. This new approach to footprinting is a bridge between trifluoromethylation in materials and medicinal chemistry and structural biology and biotechnology. Its application to a membrane protein and to myoglobin show that the approach is sensitive to protein conformational change and solvent accessibility.
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Affiliation(s)
- Ming Cheng
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Bojie Zhang
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Weidong Cui
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, One Brookings Drive, Saint Louis, MO, 63130, USA
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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.
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50
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Zhu Y, Serra A, Guo T, Park JE, Zhong Q, Sze SK. Application of Nanosecond Laser Photolysis Protein Footprinting to Study EGFR Activation by EGF in Cells. J Proteome Res 2017; 16:2282-2293. [DOI: 10.1021/acs.jproteome.7b00154] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Yi Zhu
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Aida Serra
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Tiannan Guo
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Jung Eun Park
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Qing Zhong
- Department
of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
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