1
|
Chapman J, Paukner M, Leser M, Teng KW, Koide S, Holder M, Armache KJ, Becker C, Ueberheide B, Brenowitz M. Systematic Fe(II)-EDTA Method of Dose-Dependent Hydroxyl Radical Generation for Protein Oxidative Footprinting. Anal Chem 2023; 95:18316-18325. [PMID: 38049117 PMCID: PMC10734636 DOI: 10.1021/acs.analchem.3c02319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 12/06/2023]
Abstract
Correlating the structure and dynamics of proteins with biological function is critical to understanding normal and dysfunctional cellular mechanisms. We describe a quantitative method of hydroxyl radical generation via Fe(II)-ethylenediaminetetraacetic acid (EDTA)-catalyzed Fenton chemistry that provides ready access to protein oxidative footprinting using equipment commonly found in research and process control laboratories. Robust and reproducible dose-dependent oxidation of protein samples is observed and quantitated by mass spectrometry with as fine a single residue resolution. An oxidation analysis of lysozyme provides a readily accessible benchmark for our method. The efficacy of our oxidation method is demonstrated by mapping the interface of a RAS-monobody complex, the surface of the NIST mAb, and the interface between PRC2 complex components. These studies are executed using standard laboratory tools and a few pennies of reagents; the mass spectrometry analysis can be streamlined to map the protein structure with single amino acid residue resolution.
Collapse
Affiliation(s)
- Jessica
R. Chapman
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
| | - Max Paukner
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Micheal Leser
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
| | - Kai Wen Teng
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
| | - Shohei Koide
- Perlmutter
Cancer Center, NYU Langone Health, New York, New York 10016, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Marlene Holder
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Karim-Jean Armache
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
- Skirball
Institute of Biomolecular Medicine, NYU
School of Medicine, New York, New York 10013, United States
| | - Chris Becker
- Protein
Metrics Inc., Cupertino, California 95014, United States
| | - Beatrix Ueberheide
- The
Proteomics Laboratory, New York University
(NYU) School of Medicine, New York, New York 10013, United States
- Department
of Biochemistry and Molecular Pharmacology, NYU School of Medicine, 430 East 29th Street, Suite 860, New York, New York 10013, United States
| | - Michael Brenowitz
- Department
of Biochemistry, Albert Einstein College
of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
- Department
of Molecular Pharmacology, Albert Einstein
College of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
2
|
Castel J, Delaux S, Hernandez-Alba O, Cianférani S. Recent advances in structural mass spectrometry methods in the context of biosimilarity assessment: from sequence heterogeneities to higher order structures. J Pharm Biomed Anal 2023; 236:115696. [PMID: 37713983 DOI: 10.1016/j.jpba.2023.115696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/17/2023]
Abstract
Biotherapeutics and their biosimilar versions have been flourishing in the biopharmaceutical market for several years. Structural and functional characterization is needed to achieve analytical biosimilarity through the assessment of critical quality attributes as required by regulatory authorities. The role of analytical strategies, particularly mass spectrometry-based methods, is pivotal to gathering valuable information for the in-depth characterization of biotherapeutics and biosimilarity assessment. Structural mass spectrometry methods (native MS, HDX-MS, top-down MS, etc.) provide information ranging from primary sequence assessment to higher order structure evaluation. This review focuses on recent developments and applications in structural mass spectrometry for biotherapeutic and biosimilar characterization.
Collapse
Affiliation(s)
- Jérôme Castel
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Delaux
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Oscar Hernandez-Alba
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse Bio-Organique, IPHC UMR 7178, Université de Strasbourg, CNRS, Strasbourg 67087, France; Infrastructure Nationale de Protéomique ProFI, FR2048 CNRS CEA, Strasbourg 67087, France.
| |
Collapse
|
3
|
Cheng Z, Misra SK, Shami A, Sharp JS. Structural Analysis of Phosphorylation Proteoforms in a Dynamic Heterogeneous System Using Flash Oxidation Coupled In-Line with Ion Exchange Chromatography. Anal Chem 2022; 94:18017-18024. [PMID: 36512753 PMCID: PMC9912381 DOI: 10.1021/acs.analchem.2c04365] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein posttranslational modifications (PTMs) are key modulators of protein structure and function that often change in a dynamic fashion in response to cellular stimuli. Dynamic PTMs are very challenging to structurally characterize using modern techniques, including covalent labeling methods, due to the presence of multiple proteoforms and conformers together in solution. We have coupled an ion exchange high-performance liquid chromatography separation with a flash oxidation system [ion exchange chromatography liquid chromatography-flash oxidation (IEX LC-FOX)] to successfully elucidate structural changes among three phosphoproteoforms of ovalbumin (OVA) during dephosphorylation with alkaline phosphatase. Real-time dosimetry indicates no difference in the effective radical dose between peaks or across the peak, demonstrating both the lack of scavenging of the NaCl gradient and the lack of a concentration effect on radical dose between peaks of different intensities. The use of IEX LC-FOX allows us to structurally probe into each phosphoproteoform as it elutes from the column, capturing structural data before the dynamics of the system to reintroduce heterogeneity. We found significant differences in the residue-level oxidation between the hydroxyl radical footprint of nonphosphorylated, monophosphorylated, and diphosphorylated OVA. Not only were our data consistent with the previously reported stabilization of OVA structure by phosphorylation, but local structural changes were also consistent with the measured order of dephosphorylation of Ser344 being removed first. These results demonstrate the utility of IEX LC-FOX for measuring the structural effects of PTMs, even in dynamic systems.
Collapse
Affiliation(s)
- Zhi Cheng
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677, United States
| | - Sandeep K. Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677, United States
| | - Anter Shami
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677, United States
| | - Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677, United States
- Department of Chemistry and Biochemistry, University of Mississippi, Oxford, MS 38677, United States
| |
Collapse
|
4
|
Cornwell O, Ault JR. Fast photochemical oxidation of proteins coupled with mass spectrometry. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140829. [PMID: 35933084 DOI: 10.1016/j.bbapap.2022.140829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/17/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP) is a hydroxyl radical footprinting approach whereby radicals, produced by UV laser photolysis of hydrogen peroxide, induce oxidation of amino acid side-chains. Mass Spectrometry (MS) is employed to locate and quantify the resulting irreversible, covalent oxidations to use as a surrogate for side-chain solvent accessibility. Modulation of oxidation levels under different conditions allows for the characterisation of protein conformation, dynamics and binding epitopes. FPOP has been applied to structurally diverse and biopharmaceutically relevant systems from small, monomeric aggregation-prone proteins to proteome-wide analysis of whole organisms. This review evaluates the current state of FPOP, the progress needed to address data analysis bottlenecks, particularly for residue-level analysis, and highlights significant developments of the FPOP platform that have enabled its versatility and complementarity to other structural biology techniques.
Collapse
Affiliation(s)
- Owen Cornwell
- Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow SK9 4AX, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
5
|
Lupu LM, Wiegand P, Holdschick D, Mihoc D, Maeser S, Rawer S, Völklein F, Malek E, Barka F, Knauer S, Uth C, Hennermann J, Kleinekofort W, Hahn A, Barka G, Przybylski M. Identification and Affinity Determination of Protein-Antibody and Protein-Aptamer Epitopes by Biosensor-Mass Spectrometry Combination. Int J Mol Sci 2021; 22:12832. [PMID: 34884636 PMCID: PMC8657952 DOI: 10.3390/ijms222312832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022] Open
Abstract
Analytical methods for molecular characterization of diagnostic or therapeutic targets have recently gained high interest. This review summarizes the combination of mass spectrometry and surface plasmon resonance (SPR) biosensor analysis for identification and affinity determination of protein interactions with antibodies and DNA-aptamers. The binding constant (KD) of a protein-antibody complex is first determined by immobilizing an antibody or DNA-aptamer on an SPR chip. A proteolytic peptide mixture is then applied to the chip, and following removal of unbound material by washing, the epitope(s) peptide(s) are eluted and identified by MALDI-MS. The SPR-MS combination was applied to a wide range of affinity pairs. Distinct epitope peptides were identified for the cardiac biomarker myoglobin (MG) both from monoclonal and polyclonal antibodies, and binding constants determined for equine and human MG provided molecular assessment of cross immunoreactivities. Mass spectrometric epitope identifications were obtained for linear, as well as for assembled ("conformational") antibody epitopes, e.g., for the polypeptide chemokine Interleukin-8. Immobilization using protein G substantially improved surface fixation and antibody stabilities for epitope identification and affinity determination. Moreover, epitopes were successfully determined for polyclonal antibodies from biological material, such as from patient antisera upon enzyme replacement therapy of lysosomal diseases. The SPR-MS combination was also successfully applied to identify linear and assembled epitopes for DNA-aptamer interaction complexes of the tumor diagnostic protein C-Met. In summary, the SPR-MS combination has been established as a powerful molecular tool for identification of protein interaction epitopes.
Collapse
Affiliation(s)
- Loredana-Mirela Lupu
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Pascal Wiegand
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Daria Holdschick
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Delia Mihoc
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stefan Maeser
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Stephan Rawer
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
| | - Friedemann Völklein
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Ebrahim Malek
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Frederik Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Sascha Knauer
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Christina Uth
- Sulfotools GmbH, Bahnhofsplatz 1, 65428 Rüsselsheim am Main, Germany; (S.K.); (C.U.)
| | - Julia Hennermann
- Department of Pediatrics, Universitätsmedizin Mainz, 55130 Mainz, Germany;
| | - Wolfgang Kleinekofort
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| | - Andreas Hahn
- Department of Child Neurology, Justus-Liebig-University Giessen, Feulgenstraße 10-12, 35389 Giessen, Germany;
| | - Günes Barka
- Sunchrom GmbH, Industriestr. 18, 61381 Friedrichsdorf, Germany; (F.B.); (G.B.)
| | - Michael Przybylski
- Centre for Analytical Biochemistry and Biomedical Mass Spectrometry (AffyMSLifeChem), and Steinbeis Transfer Centre for Biopolymer Analysis and Biomedical Mass Spectrometry, Marktstrasse 29, 65428 Rüsselsheim am Main, Germany; (L.-M.L.); (P.W.); (D.H.); (D.M.); (S.M.); (S.R.); (E.M.); (W.K.)
- Department of Engineering & Institute for Microtechnologies (IMTECH), RheinMain University, 65428 Rüsselsheim am Main, Germany;
| |
Collapse
|
6
|
McKenzie-Coe A, Montes NS, Jones LM. Hydroxyl Radical Protein Footprinting: A Mass Spectrometry-Based Structural Method for Studying the Higher Order Structure of Proteins. Chem Rev 2021; 122:7532-7561. [PMID: 34633178 DOI: 10.1021/acs.chemrev.1c00432] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) coupled to mass spectrometry has been successfully used to investigate a plethora of protein-related questions. The method, which utilizes hydroxyl radicals to oxidatively modify solvent-accessible amino acids, can inform on protein interaction sites and regions of conformational change. Hydroxyl radical-based footprinting was originally developed to study nucleic acids, but coupling the method with mass spectrometry has enabled the study of proteins. The method has undergone several advancements since its inception that have increased its utility for more varied applications such as protein folding and the study of biotherapeutics. In addition, recent innovations have led to the study of increasingly complex systems including cell lysates and intact cells. Technological advances have also increased throughput and allowed for better control of experimental conditions. In this review, we provide a brief history of the field of HRPF and detail recent innovations and applications in the field.
Collapse
Affiliation(s)
- Alan McKenzie-Coe
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Nicholas S Montes
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| |
Collapse
|
7
|
Cornwell O, Ault JR, Bond NJ, Radford SE, Ashcroft AE. Investigation of D76N β 2-Microglobulin Using Protein Footprinting and Structural Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1583-1592. [PMID: 33586970 PMCID: PMC9282677 DOI: 10.1021/jasms.0c00438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
NMR studies and X-ray crystallography have shown that the structures of the 99-residue amyloidogenic protein β2-microglobulin (β2m) and its more aggregation-prone variant, D76N, are indistinguishable, and hence, the reason for the striking difference in their aggregation propensities remains elusive. Here, we have employed two protein footprinting methods, hydrogen-deuterium exchange (HDX) and fast photochemical oxidation of proteins (FPOP), in conjunction with ion mobility-mass spectrometry, to probe the differences in conformational dynamics of the two proteins. Using HDX-MS, a clear difference in HDX protection is observed between these two proteins in the E-F loop (residues 70-77) which contains the D76N substitution, with a significantly higher deuterium uptake being observed in the variant protein. Conversely, following FPOP-MS only minimal differences in the level of oxidation between the two proteins are observed in the E-F loop region, suggesting only modest side-chain movements in that area. Together the HDX-MS and FPOP-MS data suggest that a tangible perturbation to the hydrogen-bonding network in the E-F loop has taken place in the D76N variant and furthermore illustrate the benefit of using multiple complementary footprinting methods to address subtle, but possibly biologically important, differences between highly similar proteins.
Collapse
Affiliation(s)
- Owen Cornwell
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - James R. Ault
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Nicholas J. Bond
- Biopharmaceuticals
R & D, AstraZeneca, Granta Park, Cambridge CB21 6GP, U.K.
| | - Sheena E. Radford
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Alison E. Ashcroft
- Astbury
Centre for Structural Molecular Biology & School of Molecular
and Cellular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| |
Collapse
|
8
|
Cheng Z, Mobley C, Misra SK, Gadepalli RS, Hammond RI, Brown LS, Rimoldi JM, Sharp JS. Self-Organized Amphiphiles Are Poor Hydroxyl Radical Scavengers in Fast Photochemical Oxidation of Proteins Experiments. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1155-1161. [PMID: 33881849 PMCID: PMC8790760 DOI: 10.1021/jasms.0c00457] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Analysis of membrane protein topography using fast photochemical oxidation of proteins (FPOP) has been reported in recent years but is still underrepresented in literature. Based on the hydroxyl radical reactivity of lipids and other amphiphiles, it is believed that the membrane environment acts as a hydroxyl radical scavenger decreasing effective hydroxyl radical doses and resulting in less observed oxidation of proteins. We found no significant change in bulk solvent radical scavenging activity upon the addition of disrupted cellular membranes up to 25600 cells/μL using an inline radical dosimeter. We confirmed the nonscavenging nature of the membrane in bulk solution with the FPOP results of a soluble model protein in the presence of cell membranes, which showed no significant difference in oxidation with or without membranes. The use of detergents revealed that, while soluble detergent below the critical micelle concentration is a potent hydroxyl radical scavenger, additional detergent has little to no hydroxyl radical scavenging effect once the critical micelle concentration is reached. Examination of both an extracellular peptide of the integral membrane protein bacteriorhodopsin as well as a novel hydroxyl radical dosimeter tethered to a Triton X-series amphiphile indicate that proximity to the membrane surface greatly decreases reaction with hydroxyl radicals, even though the oxidation target is equally solvent accessible. These results suggest that the observed reduced oxidation of solvent-accessible surfaces of integral membrane proteins is due to the high local concentration of radical scavengers in the membrane or membrane mimetics competing for the local concentration of hydroxyl radicals.
Collapse
Affiliation(s)
- Zhi Cheng
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Charles Mobley
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Sandeep K. Misra
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Rama S. Gadepalli
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Rachel I. Hammond
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Leonid S. Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - John M. Rimoldi
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
| | - Joshua S. Sharp
- Department of Biomolecular Sciences, University of Mississippi, University, MS 38677
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677
- GenNext Technologies, Inc. Half Moon Bay, CA 94019
- Correspondence to
| |
Collapse
|
9
|
Beveridge R, Calabrese AN. Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins. Front Chem 2021; 9:603639. [PMID: 33791275 PMCID: PMC8006314 DOI: 10.3389/fchem.2021.603639] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 01/19/2021] [Indexed: 12/21/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) and regions of intrinsic disorder (IDRs) are abundant in proteomes and are essential for many biological processes. Thus, they are often implicated in disease mechanisms, including neurodegeneration and cancer. The flexible nature of IDPs and IDRs provides many advantages, including (but not limited to) overcoming steric restrictions in binding, facilitating posttranslational modifications, and achieving high binding specificity with low affinity. IDPs adopt a heterogeneous structural ensemble, in contrast to typical folded proteins, making it challenging to interrogate their structure using conventional tools. Structural mass spectrometry (MS) methods are playing an increasingly important role in characterizing the structure and function of IDPs and IDRs, enabled by advances in the design of instrumentation and the development of new workflows, including in native MS, ion mobility MS, top-down MS, hydrogen-deuterium exchange MS, crosslinking MS, and covalent labeling. Here, we describe the advantages of these methods that make them ideal to study IDPs and highlight recent applications where these tools have underpinned new insights into IDP structure and function that would be difficult to elucidate using other methods.
Collapse
Affiliation(s)
- Rebecca Beveridge
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio N. Calabrese
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
10
|
Misra SK, Sharp JS. Enabling Real-Time Compensation in Fast Photochemical Oxidations of Proteins for the Determination of Protein Topography Changes. J Vis Exp 2020. [PMID: 32955502 DOI: 10.3791/61580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Fast photochemical oxidation of proteins (FPOP) is a mass spectrometry-based structural biology technique that probes the solvent-accessible surface area of proteins. This technique relies on the reaction of amino acid side chains with hydroxyl radicals freely diffusing in solution. FPOP generates these radicals in situ by laser photolysis of hydrogen peroxide, creating a burst of hydroxyl radicals that is depleted on the order of a microsecond. When these hydroxyl radicals react with a solvent-accessible amino acid side chain, the reaction products exhibit a mass shift that can be measured and quantified by mass spectrometry. Since the rate of reaction of an amino acid depends in part on the average solvent accessible surface of that amino acid, measured changes in the amount of oxidation of a given region of a protein can be directly correlated to changes in the solvent accessibility of that region between different conformations (e.g., ligand-bound versus ligand-free, monomer vs. aggregate, etc.) FPOP has been applied in a number of problems in biology, including protein-protein interactions, protein conformational changes, and protein-ligand binding. As the available concentration of hydroxyl radicals varies based on many experimental conditions in the FPOP experiment, it is important to monitor the effective radical dose to which the protein analyte is exposed. This monitoring is efficiently achieved by incorporating an inline dosimeter to measure the signal from the FPOP reaction, with laser fluence adjusted in real-time to achieve the desired amount of oxidation. With this compensation, changes in protein topography reflecting conformational changes, ligand-binding surfaces, and/or protein-protein interaction interfaces can be determined in heterogeneous samples using relatively low sample amounts.
Collapse
Affiliation(s)
- Sandeep K Misra
- Department of Biomolecular Sciences, University of Mississippi
| | - Joshua S Sharp
- Department of Biomolecular Sciences, University of Mississippi; Department of Chemistry and Biochemistry, University of Mississippi; GenNext Technologies, Inc.;
| |
Collapse
|
11
|
Cornwell O, Bond NJ, Radford SE, Ashcroft AE. Long-Range Conformational Changes in Monoclonal Antibodies Revealed Using FPOP-LC-MS/MS. Anal Chem 2019; 91:15163-15170. [DOI: 10.1021/acs.analchem.9b03958] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Owen Cornwell
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Nicholas J. Bond
- Analytical Sciences, BioPharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca, Granta Park, Cambridge, CB21 6GH, U.K
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, U.K
| |
Collapse
|
12
|
Johnson DT, Di Stefano LH, Jones LM. Fast photochemical oxidation of proteins (FPOP): A powerful mass spectrometry-based structural proteomics tool. J Biol Chem 2019; 294:11969-11979. [PMID: 31262727 DOI: 10.1074/jbc.rev119.006218] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fast photochemical oxidation of proteins (FPOP) is a MS-based method that has proved useful in studies of protein structures, interactions, conformations, and protein folding. The success of this method relies on the irreversible labeling of solvent-exposed amino acid side chains by hydroxyl radicals. FPOP generates these radicals through laser-induced photolysis of hydrogen peroxide. The data obtained provide residue-level resolution of protein structures and interactions on the microsecond timescale, enabling investigations of fast processes such as protein folding and weak protein-protein interactions. An extensive comparison between FPOP and other footprinting techniques gives insight on their complementarity as well as the robustness of FPOP to provide unique structural information once unattainable. The versatility of this method is evidenced by both the heterogeneity of samples that can be analyzed by FPOP and the myriad of applications for which the method has been successfully used: from proteins of varying size to intact cells. This review discusses the wide applications of this technique and highlights its high potential. Applications including, but not limited to, protein folding, membrane proteins, structure elucidation, and epitope mapping are showcased. Furthermore, the use of FPOP has been extended to probing proteins in cells and in vivo These promising developments are also presented herein.
Collapse
Affiliation(s)
- Danté T Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Luciano H Di Stefano
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201
| | - Lisa M Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201.
| |
Collapse
|
13
|
Ziemianowicz DS, Sarpe V, Schriemer DC. Quantitative Analysis of Protein Covalent Labeling Mass Spectrometry Data in the Mass Spec Studio. Anal Chem 2019; 91:8492-8499. [PMID: 31198032 DOI: 10.1021/acs.analchem.9b01625] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Covalent labeling with mass spectrometry (CL-MS) provides a direct measure of the chemical and structural features of proteins with the potential for resolution at the amino-acid level. Unfortunately, most applications of CL-MS are limited to narrowly defined differential analyses, where small numbers of residues are compared between two or more protein states. Extending the utility of high-resolution CL-MS for structure-based applications requires more robust computational routines and the development of methodology capable of reporting of labeling yield accurately. Here, we provide a substantial improvement in the analysis of CL-MS data with the development of an extended plug-in built within the Mass Spec Studio development framework (MSS-CLEAN). All elements of data analysis-from database search to site-resolved and normalized labeling output-are accommodated, as illustrated through the nonselective labeling of the human kinesin Eg5 with photoconverted 3,3'-azibutan-1-ol. In developing the new features within the CL-MS plug-in, we identified additional complexities associated with the application of CL reagents, arising primarily from digestion-induced bias in yield measurements and ambiguities in site localization. A strategy is presented involving the use of redundant site labeling data from overlapping peptides, the imputation of missing data, and a normalization routine to determine relative protection factors. These elements together provide for a robust structural interpretation of CL-MS/MS data while minimizing the over-reporting of labeling site resolution. Finally, to minimize bias, we recommend that digestion strategies for the generation of useful overlapping peptides involve the application of complementary enzymes that drive digestion to completion.
Collapse
|
14
|
Abstract
![]()
Protein
footprinting coupled with mass spectrometry is being increasingly
used for the study of protein interactions and conformations. The
hydroxyl radical footprinting method, fast photochemical oxidation
of proteins (FPOP), utilizes hydroxyl radicals to oxidatively modify
solvent accessible amino acids. Here, we describe the further development
of FPOP for protein structural analysis in vivo (IV-FPOP) with Caenorhabditis elegans. C. elegans, part
of the nematode family, are used as model systems for many human diseases.
The ability to perform structural studies in these worms would provide
insight into the role of structure in disease pathogenesis. Many parameters
were optimized for labeling within the worms including the microfluidic
flow system and hydrogen peroxide concentration. IV-FPOP was able
to modify several hundred proteins in various organs within the worms.
The method successfully probed solvent accessibility similarily to
in vitro FPOP, demonstrating its potential for use as a structural
technique in a multiorgan system. The coupling of the method with
mass spectrometry allows for amino-acid-residue-level structural information,
a higher resolution than currently available in vivo methods.
Collapse
Affiliation(s)
- Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| |
Collapse
|
15
|
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.
Collapse
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
| |
Collapse
|
16
|
Sheng Y, Capri J, Waring A, Valentine JS, Whitelegge J. Exposure of Solvent-Inaccessible Regions in the Amyloidogenic Protein Human SOD1 Determined by Hydroxyl Radical Footprinting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:218-226. [PMID: 30328005 PMCID: PMC6347482 DOI: 10.1007/s13361-018-2075-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/18/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
Solvent-accessibility change plays a critical role in protein misfolding and aggregation, the culprit for several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Mass spectrometry-based hydroxyl radical (·OH) protein footprinting has evolved as a powerful and fast tool in elucidating protein solvent accessibility. In this work, we used fast photochemical oxidation of protein (FPOP) hydroxyl radical (·OH) footprinting to investigate solvent accessibility in human copper-zinc superoxide dismutase (SOD1), misfolded or aggregated forms of which underlie a portion of ALS cases. ·OH-mediated modifications to 56 residues were detected with locations largely as predicted based on X-ray crystallography data, while the interior of SOD1 β-barrel is hydrophobic and solvent-inaccessible and thus protected from modification. There were, however, two notable exceptions-two closely located residues inside the β-barrel, predicted to have minimal or no solvent accessibility, that were found modified by FPOP (Phe20 and Ile112). Molecular dynamics (MD) simulations were consistent with differential access of peroxide versus quencher to SOD1's interior complicating surface accessibility considerations. Modification of these two residues could potentially be explained either by local motions of the β-barrel that increased peroxide/solvent accessibility to the interior or by oxidative events within the interior that might include long-distance radical transfer to buried sites. Overall, comparison of modification patterns for the metal-free apoprotein versus zinc-bound forms demonstrated that binding of zinc protected the electrostatic loop and organized the copper-binding site. Our study highlights SOD1 hydrophobic groups that may contribute to early events in aggregation and discusses caveats to surface accessibility conclusions. Graphical Abstract.
Collapse
Affiliation(s)
- Yuewei Sheng
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Joseph Capri
- The Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA, USA
| | - Alan Waring
- Department of Medicine, University of California, Los Angeles, CA, USA
| | | | - Julian Whitelegge
- The Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA, USA.
- The Brain Research Institute, University of California, Los Angeles, CA, USA.
| |
Collapse
|
17
|
Kaur U, Johnson DT, Chea EE, Deredge DJ, Espino JA, Jones LM. Evolution of Structural Biology through the Lens of Mass Spectrometry. Anal Chem 2019; 91:142-155. [PMID: 30457831 DOI: 10.1021/acs.analchem.1028b05014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| |
Collapse
|
18
|
Kaur U, Johnson DT, Chea EE, Deredge DJ, Espino JA, Jones LM. Evolution of Structural Biology through the Lens of Mass Spectrometry. Anal Chem 2018; 91:142-155. [PMID: 30457831 DOI: 10.1021/acs.analchem.8b05014] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| |
Collapse
|
19
|
Riaz M, Misra SK, Sharp JS. Towards high-throughput fast photochemical oxidation of proteins: Quantifying exposure in high fluence microtiter plate photolysis. Anal Biochem 2018; 561-562:32-36. [PMID: 30240591 PMCID: PMC6186496 DOI: 10.1016/j.ab.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/06/2018] [Accepted: 09/17/2018] [Indexed: 01/15/2023]
Abstract
Protein structural analysis by mass spectrometry has gained significant popularity in recent years, including high-resolution protein topographical mapping by fast photochemical oxidation of proteins (FPOP). The ability to provide protein topographical information at moderate spatial resolution makes FPOP an attractive technology for the protein pharmaceutical discovery and development processes. However, current technology limits the throughput and requires significant manual sample manipulation. Similarly, as FPOP is being used on larger samples, sample flow through the capillary becomes challenging. No systematic comparison of the performance of static flash photolysis with traditional flow FPOP has been reported. Here, we evaluate a 96-well microtiter-based laser flash photolysis method for the topographical probing of proteins, which subsequently could be used to analyze higher order structure of the protein in a high-throughput fashion with minimal manual sample manipulation. We used multiple metrics to compare microtiter FPOP performance with that of traditional flow FPOP: adenine-based hydroxyl radical dosimetry, oxidation efficiency of a model peptide, and hydroxyl radical protein footprint of myoglobin. In all cases, microtiter plate FPOP performed comparably with traditional flow FPOP, requiring a small fraction of the time for exposure. This greatly reduced sample exposure time, coupled with automated sample handling in 96-well microtiter plates, makes microtiter-based FPOP an important step in achieving the throughput required to adapt hydroxyl radical protein footprinting for screening purposes.
Collapse
Affiliation(s)
- Mohammad Riaz
- Department of BioMolecular Sciences, University of Mississippi, University, MS, 38677, USA
| | - Sandeep K Misra
- Department of BioMolecular Sciences, University of Mississippi, University, MS, 38677, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, University of Mississippi, University, MS, 38677, USA.
| |
Collapse
|
20
|
Kaur U, Meng H, Lui F, Ma R, Ogburn RN, Johnson JHR, Fitzgerald MC, Jones LM. Proteome-Wide Structural Biology: An Emerging Field for the Structural Analysis of Proteins on the Proteomic Scale. J Proteome Res 2018; 17:3614-3627. [PMID: 30222357 DOI: 10.1021/acs.jproteome.8b00341] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, a suite of new mass-spectrometry-based proteomics methods has been developed that now enables the conformational properties of proteins and protein-ligand complexes to be studied in complex biological mixtures, from cell lysates to intact cells. Highlighted here are seven of the techniques in this new toolbox. These techniques include chemical cross-linking (XL-MS), hydroxyl radical footprinting (HRF), Drug Affinity Responsive Target Stability (DARTS), Limited Proteolysis (LiP), Pulse Proteolysis (PP), Stability of Proteins from Rates of Oxidation (SPROX), and Thermal Proteome Profiling (TPP). The above techniques all rely on conventional bottom-up proteomics strategies for peptide sequencing and protein identification. However, they have required the development of unconventional proteomic data analysis strategies. Discussed here are the current technical challenges associated with these different data analysis strategies as well as the relative analytical capabilities of the different techniques. The new biophysical capabilities that the above techniques bring to bear on proteomic research are also highlighted in the context of several different application areas in which these techniques have been used, including the study of protein ligand binding interactions (e.g., protein target discovery studies and protein interaction network analyses) and the characterization of biological states.
Collapse
Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - He Meng
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | | | - Renze Ma
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Ryenne N Ogburn
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Julia H R Johnson
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Michael C Fitzgerald
- Department of Chemistry , Duke University , Durham , North Carolina 27708-0346 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| |
Collapse
|
21
|
Abolhasani Khaje N, Mobley CK, Misra SK, Miller L, Li Z, Nudler E, Sharp JS. Variation in FPOP Measurements Is Primarily Caused by Poor Peptide Signal Intensity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1901-1907. [PMID: 29943081 PMCID: PMC6087495 DOI: 10.1007/s13361-018-1994-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 05/27/2023]
Abstract
Fast photochemical oxidation of proteins (FPOP) may be used to characterize changes in protein structure by measuring differences in the apparent rate of peptide oxidation by hydroxyl radicals. The variability between replicates is high for some peptides and limits the statistical power of the technique, even using modern methods controlling variability in radical dose and quenching. Currently, the root cause of this variability has not been systematically explored, and it is unknown if the major source(s) of variability are structural heterogeneity in samples, remaining irreproducibility in FPOP oxidation, or errors in LC-MS quantification of oxidation. In this work, we demonstrate that coefficient of variation of FPOP measurements varies widely at low peptide signal intensity, but stabilizes to ≈ 0.13 at higher peptide signal intensity. We dramatically reduced FPOP variability by increasing the total sample loaded onto the LC column, indicating that the major source of variability in FPOP measurements is the difficulties in quantifying oxidation at low peptide signal intensities. This simple method greatly increases the sensitivity of FPOP structural comparisons, an important step in applying the technique to study subtle conformational changes and protein-ligand interactions. Graphical Abstract ᅟ.
Collapse
Affiliation(s)
- Niloofar Abolhasani Khaje
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, 38655, USA
| | - Charles K Mobley
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, 38655, USA
| | - Sandeep K Misra
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, 38655, USA
| | - Lindsey Miller
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, 38655, USA
| | - Zixuan Li
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Evgeny Nudler
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, NY, 10016, USA
| | - Joshua S Sharp
- Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, University, MS, 38655, USA.
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Kukacka Z, Iurascu M, Lupu L, Rusche H, Murphy M, Altamore L, Borri F, Maeser S, Papini AM, Hennermann J, Przybylski M. Antibody Epitope of Human α-Galactosidase A Revealed by Affinity Mass Spectrometry: A Basis for Reversing Immunoreactivity in Enzyme Replacement Therapy of Fabry Disease. ChemMedChem 2018; 13:909-915. [DOI: 10.1002/cmdc.201800094] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Zdenek Kukacka
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry; 65428 Rüsselsheim am Main Germany
- Department of Chemistry; University of Konstanz; 78457 Konstanz Germany
| | - Marius Iurascu
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry; 65428 Rüsselsheim am Main Germany
- Department of Chemistry; University of Konstanz; 78457 Konstanz Germany
| | - Loredana Lupu
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry; 65428 Rüsselsheim am Main Germany
- Department of Chemistry; University of Konstanz; 78457 Konstanz Germany
| | - Hendrik Rusche
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry; 65428 Rüsselsheim am Main Germany
- Department of Chemistry; University of Konstanz; 78457 Konstanz Germany
| | - Mary Murphy
- Ametek Reichert Technologies; Depew NY 14043 USA
| | - Lorenzo Altamore
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology; Università degli Studi di Firenze; 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 13 50019 Sesto Fiorentino Italy
- PeptLab@UCP and Laboratory of Chemical Biology EA4505; Université Paris-Seine; 5 Mail Gay-Lussac 95031 Cergy-Pontoise France
| | - Fabio Borri
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology; Università degli Studi di Firenze; 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 13 50019 Sesto Fiorentino Italy
- PeptLab@UCP and Laboratory of Chemical Biology EA4505; Université Paris-Seine; 5 Mail Gay-Lussac 95031 Cergy-Pontoise France
| | - Stefan Maeser
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry; 65428 Rüsselsheim am Main Germany
- Department of Chemistry; University of Konstanz; 78457 Konstanz Germany
| | - Anna Maria Papini
- French-Italian Interdepartmental Laboratory of Peptide and Protein Chemistry and Biology; Università degli Studi di Firenze; 50019 Sesto Fiorentino Italy
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 13 50019 Sesto Fiorentino Italy
- PeptLab@UCP and Laboratory of Chemical Biology EA4505; Université Paris-Seine; 5 Mail Gay-Lussac 95031 Cergy-Pontoise France
| | - Julia Hennermann
- Department of Pediatrics, Villa Metabolica; Universitätsmedizin Mainz; 55130 Mainz Germany
| | - Michael Przybylski
- Steinbeis Centre for Biopolymer Analysis and Biomedical Mass Spectrometry; 65428 Rüsselsheim am Main Germany
- Department of Chemistry; University of Konstanz; 78457 Konstanz Germany
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Quantitative Protein Topography Measurements by High Resolution Hydroxyl Radical Protein Footprinting Enable Accurate Molecular Model Selection. Sci Rep 2017; 7:4552. [PMID: 28674401 PMCID: PMC5495787 DOI: 10.1038/s41598-017-04689-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/18/2017] [Indexed: 11/23/2022] Open
Abstract
We report an integrated workflow that allows mass spectrometry-based high-resolution hydroxyl radical protein footprinting (HR-HRPF) measurements to accurately measure the absolute average solvent accessible surface area (<SASA>) of amino acid side chains. This approach is based on application of multi-point HR-HRPF, electron-transfer dissociation (ETD) tandem MS (MS/MS) acquisition, measurement of effective radical doses by radical dosimetry, and proper normalization of the inherent reactivity of the amino acids. The accuracy of the resulting <SASA> measurements was tested by using well-characterized protein models. Moreover, we demonstrated the ability to use <SASA> measurements from HR-HRPF to differentiate molecular models of high accuracy (<3 Å backbone RMSD) from models of lower accuracy (>4 Å backbone RMSD). The ability of <SASA> data from HR-HRPF to differentiate molecular model quality was found to be comparable to that of <SASA> data obtained from X-ray crystal structures, indicating the accuracy and utility of HR-HRPF for evaluating the accuracy of computational models.
Collapse
|
26
|
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
| |
Collapse
|
27
|
Malhotra P, Udgaonkar JB. How cooperative are protein folding and unfolding transitions? Protein Sci 2016; 25:1924-1941. [PMID: 27522064 PMCID: PMC5079258 DOI: 10.1002/pro.3015] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/09/2016] [Accepted: 08/09/2016] [Indexed: 11/12/2022]
Abstract
A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two-state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non-cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier-less "downhill" folding, as well as for continuous "uphill" unfolding transitions, indicate that gradual non-cooperative processes may be ubiquitous features on the free energy landscape of protein folding.
Collapse
Affiliation(s)
- Pooja Malhotra
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India
| | - Jayant B Udgaonkar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, India.
| |
Collapse
|
28
|
Rinas A, Espino JA, Jones LM. An efficient quantitation strategy for hydroxyl radical-mediated protein footprinting using Proteome Discoverer. Anal Bioanal Chem 2016; 408:3021-31. [PMID: 26873216 DOI: 10.1007/s00216-016-9369-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 01/17/2016] [Accepted: 01/27/2016] [Indexed: 01/12/2023]
Abstract
Hydroxyl radical protein footprinting coupled with mass spectrometry has become an invaluable technique for protein structural characterization. In this method, hydroxyl radicals react with solvent exposed amino acid side chains producing stable, covalently attached labels. Although this technique yields beneficial information, the extensive list of known oxidation products produced make the identification and quantitation process considerably complex. Currently, the methods available for analysis either involve manual analysis steps, or limit the amount of searchable modifications or the size of sequence database. This creates a bottleneck which can result in a long and arduous analysis process, which is further compounded in a complex sample. Here, we report the use of a new footprinting analysis method for both peptide and residue-level analysis, demonstrated on the GCaMP2 synthetic construct in calcium free and calcium bound states. This method utilizes a customized multi-search node workflow developed for an on-market search platform in conjunction with a quantitation platform developed using a free Excel add-in. Moreover, the method expedites the analysis process, requiring only two post-search hours to complete quantitation, regardless of the size of the experiment or the sample complexity.
Collapse
Affiliation(s)
- Aimee Rinas
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St LD326, Indianapolis, IN, 46202, USA
| | - Jessica A Espino
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St LD326, Indianapolis, IN, 46202, USA
| | - Lisa M Jones
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N. Blackford St LD326, Indianapolis, IN, 46202, USA.
| |
Collapse
|
29
|
Yefremova Y, Al-Majdoub M, Opuni KF, Koy C, Yan Y, Gross M, Glocker MO. A Dynamic Model of pH-Induced Protein G'e Higher Order Structure Changes derived from Mass Spectrometric Analyses. Anal Chem 2016; 88:890-7. [PMID: 26606592 PMCID: PMC5201196 DOI: 10.1021/acs.analchem.5b03536] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To obtain insight into pH change-driven molecular dynamics, we studied the higher order structure changes of protein G'e at the molecular and amino acid residue levels in solution by using nanoESI- and IM-mass spectrometry, CD spectroscopy, and protein chemical modification reactions (protein footprinting). We found a dramatic change of the overall tertiary structure of protein G'e when the pH was changed from neutral to acidic, whereas its secondary structure features remained nearly invariable. Limited proteolysis and surface-topology mapping of protein G'e by fast photochemical oxidation of proteins (FPOP) under neutral and acidic conditions reveal areas where higher order conformational changes occur on the amino-acid residue level. Under neutral solution conditions, lower oxidation occurs for residues of the first linker region, whereas greater oxidative modifications occur for amino-acid residues of the IgG-binding domains I and II. We propose a dynamic model of pH-induced structural changes in which protein G'e at neutral pH adopts an overall tight conformation with all four domains packed in a firm assembly, whereas at acidic pH, the three IgG-binding domains form an elongated alignment, and the N-terminal, His-tag-carrying domain unfolds. At the same time the individual IgG-binding domains themselves seem to adopt a more compacted fold. As the secondary structure features are nearly unchanged at either pH, interchange between both conformations is highly reversible, explaining the high reconditioning power of protein G'e-based affinity chromatography columns.
Collapse
Affiliation(s)
- Yelena Yefremova
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | | | | | - Cornelia Koy
- Proteome Center Rostock, University Medicine Rostock, Rostock, Germany
| | - Yuetian Yan
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 USA
| | - Michael Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130 USA
| | | |
Collapse
|
30
|
Calabrese AN, Ault JR, Radford SE, Ashcroft AE. Using hydroxyl radical footprinting to explore the free energy landscape of protein folding. Methods 2015; 89:38-44. [PMID: 25746386 PMCID: PMC4651025 DOI: 10.1016/j.ymeth.2015.02.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 02/17/2015] [Accepted: 02/23/2015] [Indexed: 01/26/2023] Open
Abstract
Characterisation of the conformational states adopted during protein folding, including globally unfolded/disordered structures and partially folded intermediate species, is vital to gain fundamental insights into how a protein folds. In this work we employ fast photochemical oxidation of proteins (FPOP) to map the structural changes that occur in the folding of the four-helical bacterial immunity protein, Im7. Oxidative footprinting coupled with mass spectrometry (MS) is used to probe changes in the solvent accessibility of amino acid side-chains concurrent with the folding process, by quantifying the degree of oxidation experienced by the wild-type protein relative to a kinetically trapped, three-helical folding intermediate and an unfolded variant that lacks secondary structure. Analysis of the unfolded variant by FPOP-MS shows oxidative modifications consistent with the species adopting a solution conformation with a high degree of solvent accessibility. The folding intermediate, by contrast, experiences increased levels of oxidation relative to the wild-type, native protein only in regions destabilised by the amino acid substitutions introduced. The results demonstrate the utility of FPOP-MS to characterise protein variants in different conformational states and to provide insights into protein folding mechanisms that are complementary to measurements such as hydrogen/deuterium exchange labelling and Φ-value analysis.
Collapse
Affiliation(s)
- Antonio N Calabrese
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - James R Ault
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sheena E Radford
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| | - Alison E Ashcroft
- School of Molecular and Cellular Biology, Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
| |
Collapse
|
31
|
Xie B, Sharp JS. Hydroxyl Radical Dosimetry for High Flux Hydroxyl Radical Protein Footprinting Applications Using a Simple Optical Detection Method. Anal Chem 2015; 87:10719-23. [PMID: 26455423 DOI: 10.1021/acs.analchem.5b02865] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) by fast photochemical oxidation of proteins (FPOP) is a powerful benchtop tool used to probe protein structure, interactions, and conformational changes in solution. However, the reproducibility of all HRPF techniques is limited by the ability to deliver a defined concentration of hydroxyl radicals to the protein. This ability is impacted by both the amount of radical generated and the presence of radical scavengers in solution. In order to compare HRPF data from sample to sample, a hydroxyl radical dosimeter is needed that can measure the effective concentration of radical that is delivered to the protein, after accounting for both differences in hydroxyl radical generation and nonanalyte radical consumption. Here, we test three radical dosimeters (Alexa Fluor 488, terepthalic acid, and adenine) for their ability to quantitatively measure the effective radical dose under the high radical concentration conditions of FPOP. Adenine has a quantitative relationship between UV spectrophotometric response, effective hydroxyl radical dose delivered, and peptide and protein oxidation levels over the range of radical concentrations typically encountered in FPOP. The simplicity of an adenine-based dosimeter allows for convenient and flexible incorporation into FPOP applications, and the ability to accurately measure the delivered radical dose will enable reproducible and reliable FPOP across a variety of platforms and applications.
Collapse
Affiliation(s)
- Boer Xie
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| | - Joshua S Sharp
- Complex Carbohydrate Research Center, University of Georgia , Athens, Georgia 30602, United States
| |
Collapse
|
32
|
Quantitative mapping of protein structure by hydroxyl radical footprinting-mediated structural mass spectrometry: a protection factor analysis. Biophys J 2015; 108:107-15. [PMID: 25564857 DOI: 10.1016/j.bpj.2014.11.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Revised: 11/06/2014] [Accepted: 11/10/2014] [Indexed: 11/23/2022] Open
Abstract
Measurements from hydroxyl radical footprinting (HRF) provide rich information about the solvent accessibility of amino acid side chains of a protein. Traditional HRF data analyses focus on comparing the difference in the modification/footprinting rate of a specific site to infer structural changes across two protein states, e.g., between a free and ligand-bound state. However, the rate information itself is not fully used for the purpose of comparing different protein sites within a protein on an absolute scale. To provide such a cross-site comparison, we present a new, to our knowledge, data analysis algorithm to convert the measured footprinting rate constant to a protection factor (PF) by taking into account the known intrinsic reactivity of amino acid side chain. To examine the extent to which PFs can be used for structural interpretation, this PF analysis is applied to three model systems where radiolytic footprinting data are reported in the literature. By visualizing structures colored with the PF values for individual peptides, a rational view of the structural features of various protein sites regarding their solvent accessibility is revealed, where high-PF regions are buried and low-PF regions are more exposed to the solvent. Furthermore, a detailed analysis correlating solvent accessibility and local structural contacts for gelsolin shows a statistically significant agreement between PF values and various structure measures, demonstrating that the PFs derived from this PF analysis readily explain fundamental HRF rate measurements. We also tested this PF analysis on alternative, chemical-based HRF data, showing improved correlations of structural properties of a model protein barstar compared to examining HRF rate data alone. Together, this PF analysis not only permits a novel, to our knowledge, approach of mapping protein structures by using footprinting data, but also elevates the use of HRF measurements from a qualitative, cross-state comparison to a quantitative, cross-site assessment of protein structures in the context of individual conformational states of interest.
Collapse
|
33
|
Farrokhi V, Bajrami B, Nemati R, McShane AJ, Rueckert F, Wells B, Yao X. Development of Structural Marker Peptides for Cystic Fibrosis Transmembrane Conductance Regulator in Cell Plasma Membrane by Reversed-Footprinting Mass Spectrometry. Anal Chem 2015; 87:8603-7. [DOI: 10.1021/acs.analchem.5b01962] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
| | | | | | | | - Franz Rueckert
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Barrett Wells
- Department
of Physics, University of Connecticut, Storrs, Connecticut 06269, United States
| | | |
Collapse
|
34
|
Espino JA, Mali VS, Jones LM. In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells. Anal Chem 2015; 87:7971-8. [DOI: 10.1021/acs.analchem.5b01888] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jessica A. Espino
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46204, United States
| | | | - Lisa M. Jones
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46204, United States
| |
Collapse
|
35
|
Kaur P, Kiselar J, Yang S, Chance MR. Quantitative protein topography analysis and high-resolution structure prediction using hydroxyl radical labeling and tandem-ion mass spectrometry (MS). Mol Cell Proteomics 2015; 14:1159-68. [PMID: 25687570 DOI: 10.1074/mcp.o114.044362] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Indexed: 11/06/2022] Open
Abstract
Hydroxyl radical footprinting based MS for protein structure assessment has the goal of understanding ligand induced conformational changes and macromolecular interactions, for example, protein tertiary and quaternary structure, but the structural resolution provided by typical peptide-level quantification is limiting. In this work, we present experimental strategies using tandem-MS fragmentation to increase the spatial resolution of the technique to the single residue level to provide a high precision tool for molecular biophysics research. Overall, in this study we demonstrated an eightfold increase in structural resolution compared with peptide level assessments. In addition, to provide a quantitative analysis of residue based solvent accessibility and protein topography as a basis for high-resolution structure prediction; we illustrate strategies of data transformation using the relative reactivity of side chains as a normalization strategy and predict side-chain surface area from the footprinting data. We tested the methods by examination of Ca(+2)-calmodulin showing highly significant correlations between surface area and side-chain contact predictions for individual side chains and the crystal structure. Tandem ion based hydroxyl radical footprinting-MS provides quantitative high-resolution protein topology information in solution that can fill existing gaps in structure determination for large proteins and macromolecular complexes.
Collapse
Affiliation(s)
- Parminder Kaur
- From the ‡Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10009 Euclid Ave, Cleveland, Ohio, 44109
| | - Janna Kiselar
- From the ‡Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10009 Euclid Ave, Cleveland, Ohio, 44109
| | - Sichun Yang
- From the ‡Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10009 Euclid Ave, Cleveland, Ohio, 44109
| | - Mark R Chance
- From the ‡Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10009 Euclid Ave, Cleveland, Ohio, 44109
| |
Collapse
|
36
|
Brody DL, Gross ML. The remarkable properties of amyloid-β derived from human Alzheimer’s disease brain: swinging the streetlight. Brain 2014; 137:2874-5. [DOI: 10.1093/brain/awu261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
37
|
Probing the paramyxovirus fusion (F) protein-refolding event from pre- to postfusion by oxidative footprinting. Proc Natl Acad Sci U S A 2014; 111:E2596-605. [PMID: 24927585 DOI: 10.1073/pnas.1408983111] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To infect a cell, the Paramyxoviridae family of enveloped viruses relies on the coordinated action of a receptor-binding protein (variably HN, H, or G) and a more conserved metastable fusion protein (F) to effect membrane fusion and allow genomic transfer. Upon receptor binding, HN (H or G) triggers F to undergo an extensive refolding event to form a stable postfusion state. Little is known about the intermediate states of the F refolding process. Here, a soluble form of parainfluenza virus 5 F was triggered to refold using temperature and was footprinted along the refolding pathway using fast photochemical oxidation of proteins (FPOP). Localization of the oxidative label to solvent-exposed side chains was determined by high-resolution MS/MS. Globally, metastable prefusion F is oxidized more extensively than postfusion F, indicating that the prefusion state is more exposed to solvent and is more flexible. Among the first peptides to be oxidatively labeled after temperature-induced triggering is the hydrophobic fusion peptide. A comparison of peptide oxidation levels with the values of solvent-accessible surface area calculated from molecular dynamics simulations of available structural data reveals regions of the F protein that lie at the heart of its prefusion metastability. The strong correlation between the regions of F that experience greater-than-expected oxidative labeling and epitopes for neutralizing antibodies suggests that FPOP has a role in guiding the development of targeted therapeutics. Analysis of the residue levels of labeled F intermediates provides detailed insights into the mechanics of this critical refolding event.
Collapse
|
38
|
Konermann L, Vahidi S, Sowole MA. Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules. Anal Chem 2013; 86:213-32. [DOI: 10.1021/ac4039306] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Siavash Vahidi
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| | - Modupeola A. Sowole
- Department of Chemistry, The University of Western Ontario, London, Ontario, N6A 5B7 Canada
| |
Collapse
|
39
|
Kathuria SV, Chan A, Graceffa R, Nobrega RP, Matthews CR, Irving TC, Perot B, Bilsel O. Advances in turbulent mixing techniques to study microsecond protein folding reactions. Biopolymers 2013; 99:888-96. [PMID: 23868289 PMCID: PMC3843316 DOI: 10.1002/bip.22355] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Accepted: 07/03/2013] [Indexed: 02/01/2023]
Abstract
Recent experimental and computational advances in the protein folding arena have shown that the readout of the one-dimensional sequence information into three-dimensional structure begins within the first few microseconds of folding. The initiation of refolding reactions has been achieved by several means, including temperature jumps, flash photolysis, pressure jumps, and rapid mixing methods. One of the most commonly used means of initiating refolding of chemically denatured proteins is by turbulent flow mixing with refolding dilution buffer, where greater than 99% mixing efficiency has been achieved within 10's of microseconds. Successful interfacing of turbulent flow mixers with complementary detection methods, including time-resolved Fluorescence Spectroscopy (trFL), Förster Resonance Energy Transfer, Circular Dichroism, Small-Angle X-ray Scattering, Hydrogen Exchange followed by Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy, Infrared Spectroscopy (IR), and Fourier Transform IR Spectroscopy, has made this technique very attractive for monitoring various aspects of structure formation during folding. Although continuous-flow (CF) mixing devices interfaced with trFL detection have a dead time of only 30 µs, burst phases have been detected in this time scale during folding of peptides and of large proteins (e.g., CheY and TIM barrels). Furthermore, a major limitation of the CF mixing technique has been the requirement of large quantities of sample. In this brief communication, we will discuss the recent flurry of activity in micromachining and microfluidics, guided by computational simulations, which are likely to lead to dramatic improvements in time resolution and sample consumption for CF mixers over the next few years.
Collapse
Affiliation(s)
- Sagar V. Kathuria
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| | - Alexander Chan
- Department of Mechanical and Industrial Engineering, Engineering Laboratory, University of Massachusetts, Box 32210-219, Amherst, MA, 01003-2210
| | - Rita Graceffa
- BioCAT, Department of Biological and Chemical Science, Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616
| | - R. Paul Nobrega
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| | - C. Robert Matthews
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| | - Thomas C. Irving
- BioCAT, Department of Biological and Chemical Science, Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616
| | - Blair Perot
- Department of Mechanical and Industrial Engineering, Engineering Laboratory, University of Massachusetts, Box 32210-219, Amherst, MA, 01003-2210
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605
| |
Collapse
|
40
|
Li X, Li Z, Xie B, Sharp JS. Improved identification and relative quantification of sites of peptide and protein oxidation for hydroxyl radical footprinting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1767-76. [PMID: 24014150 PMCID: PMC3814024 DOI: 10.1007/s13361-013-0719-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/25/2013] [Accepted: 07/29/2013] [Indexed: 05/08/2023]
Abstract
Protein oxidation is typically associated with oxidative stress and aging and affects protein function in normal and pathological processes. Additionally, deliberate oxidative labeling is used to probe protein structure and protein-ligand interactions in hydroxyl radical protein footprinting (HRPF). Oxidation often occurs at multiple sites, leading to mixtures of oxidation isomers that differ only by the site of modification. We utilized sets of synthetic, isomeric "oxidized" peptides to test and compare the ability of electron-transfer dissociation (ETD) and collision-induced dissociation (CID), as well as nano-ultra high performance liquid chromatography (nanoUPLC) separation, to quantitate oxidation isomers with one oxidation at multiple adjacent sites in mixtures of peptides. Tandem mass spectrometry by ETD generates fragment ion ratios that accurately report on relative oxidative modification extent on specific sites, regardless of the charge state of the precursor ion. Conversely, CID was found to generate quantitative MS/MS product ions only at the higher precursor charge state. Oxidized isomers having multiple sites of oxidation in each of two peptide sequences in HRPF product of protein Robo-1 Ig1-2, a protein involved in nervous system axon guidance, were also identified and the oxidation extent at each residue was quantified by ETD without prior liquid chromatography (LC) separation. ETD has proven to be a reliable technique for simultaneous identification and relative quantification of a variety of functionally different oxidation isomers, and is a valuable tool for the study of oxidative stress, as well as for improving spatial resolution for HRPF studies.
Collapse
Affiliation(s)
- Xiaoyan Li
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | | | | | | |
Collapse
|
41
|
Collier TS, Diraviyam K, Monsey J, Shen W, Sept D, Bose R. Carboxyl group footprinting mass spectrometry and molecular dynamics identify key interactions in the HER2-HER3 receptor tyrosine kinase interface. J Biol Chem 2013; 288:25254-25264. [PMID: 23843458 DOI: 10.1074/jbc.m113.474882] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The HER2 receptor tyrosine kinase is a driver oncogene in many human cancers, including breast and gastric cancer. Under physiologic levels of expression, HER2 heterodimerizes with other members of the EGF receptor/HER/ErbB family, and the HER2-HER3 dimer forms one of the most potent oncogenic receptor pairs. Previous structural biology studies have individually crystallized the kinase domains of HER2 and HER3, but the HER2-HER3 kinase domain heterodimer structure has yet to be solved. Using a reconstituted membrane system to form HER2-HER3 kinase domain heterodimers and carboxyl group footprinting mass spectrometry, we observed that HER2 and HER3 kinase domains preferentially form asymmetric heterodimers with HER3 and HER2 monomers occupying the donor and acceptor kinase positions, respectively. Conformational changes in the HER2 activation loop, as measured by changes in carboxyl group labeling, required both dimerization and nucleotide binding but did not require activation loop phosphorylation at Tyr-877. Molecular dynamics simulations on HER2-HER3 kinase dimers identify specific inter- and intramolecular interactions and were in good agreement with MS measurements. Specifically, several intermolecular ionic interactions between HER2 Lys-716-HER3 Glu-909, HER2 Glu-717-HER3 Lys-907, and HER2 Asp-871-HER3 Arg-948 were identified by molecular dynamics. We also evaluated the effect of the cancer-associated mutations HER2 D769H/D769Y, HER3 E909G, and HER3 R948K (also numbered HER3 E928G and R967K) on kinase activity in the context of this new structural model. This study provides valuable insights into the EGF receptor/HER/ErbB kinase structure and interactions, which can guide the design of future therapies.
Collapse
Affiliation(s)
| | - Karthikeyan Diraviyam
- the Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109
| | - John Monsey
- From the Division of Oncology, Department of Medicine, and
| | - Wei Shen
- From the Division of Oncology, Department of Medicine, and
| | - David Sept
- the Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109
| | - Ron Bose
- From the Division of Oncology, Department of Medicine, and; the Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri 63110 and.
| |
Collapse
|