1
|
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: 11] [Impact Index Per Article: 3.7] [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
|
2
|
Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
Collapse
Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
| |
Collapse
|
3
|
Johnson DT, Punshon-Smith B, Espino JA, Gershenson A, Jones LM. Implementing In-Cell Fast Photochemical Oxidation of Proteins in a Platform Incubator with a Movable XY Stage. Anal Chem 2020; 92:1691-1696. [PMID: 31860269 PMCID: PMC7944481 DOI: 10.1021/acs.analchem.9b04933] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Fast
photochemical oxidation of proteins (FPOP) is a protein footprinting
technique that is being increasingly used in MS-based proteomics.
FPOP is utilized to study protein–protein interactions, protein–ligand
interactions, and protein conformational dynamics. This method has
recently been extended to protein labeling in live cells (IC-FPOP),
allowing the study of protein conformations in the complex cellular
environment. Traditionally, IC-FPOP has been executed using a single
cell flow system, in which hydrodynamic focusing drives cells along
in a single file line, keeping the cells from clumping and thus ensuring
equal exposure to the laser irradiation required for photochemical
oxidation. Here, we introduce a novel platform that allows IC-FPOP
to occur in a sterile incubation system complete with a mobile stage
for XY movement, peristaltic pumps equipped with perfusion lines for
chemical transport, and mirrors for laser beam guidance. This new
system, called Platform Incubator with movable XY stage (PIXY), also
utilizes software enabling automated communication between equipment
and execution of the entire system. Further, comparison with a standard
IC-FPOP flow system results reveal that this platform can successfully
be used in lieu of the flow system while also decreasing the time
to complete analysis of a single sample.
Collapse
Affiliation(s)
- Danté T Johnson
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Benjamin Punshon-Smith
- Technology Research Center , University of Maryland Baltimore County , Catonsville , Maryland 21250 , United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Anne Gershenson
- Department of Biochemistry and Molecular Biology , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| |
Collapse
|
4
|
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
|
5
|
Sharp JS, Misra SK, Persoff JJ, Egan RW, Weinberger SR. Real Time Normalization of Fast Photochemical Oxidation of Proteins Experiments by Inline Adenine Radical Dosimetry. Anal Chem 2018; 90:12625-12630. [PMID: 30290117 PMCID: PMC7811273 DOI: 10.1021/acs.analchem.8b02787] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hydroxyl radical protein footprinting (HRPF) is a powerful method for measuring protein topography, allowing researchers to monitor events that alter the solvent accessible surface of a protein (e.g., ligand binding, aggregation, conformational changes, etc.) by measuring changes in the apparent rate of reaction of portions of the protein to hydroxyl radicals diffusing in solution. Fast Photochemical Oxidation of Proteins (FPOP) offers an ultrafast benchtop method for radical generation for HRPF, photolyzing hydrogen peroxide using a UV laser to generate high concentrations of hydroxyl radicals that are consumed on roughly a microsecond time scale. The broad reactivity of hydroxyl radicals means that almost anything added to the solution (e.g., ligands, buffers, excipients, etc.) will scavenge hydroxyl radicals, altering their half-life and changing the effective radical concentration experienced by the protein. Similarly, minute changes in peroxide concentration, laser fluence, and buffer composition can alter the effective radical concentration, making reproduction of data challenging. Here, we present a simple method for radical dosimetry that can be carried out as part of the FPOP workflow, allowing for measurement of effective radical concentration in real time. Additionally, by modulating the amount of radical generated, we demonstrate that effective hydroxyl radical yields in FPOP HRPF experiments carried out in buffers with widely differing levels of hydroxyl radical scavenging capacity can be compensated on the fly, yielding statistically indistinguishable results for the same conformer. This method represents a major step in transforming FPOP into a robust and reproducible technology capable of probing protein structure in a wide variety of contexts.
Collapse
Affiliation(s)
- Joshua S. Sharp
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677
- GenNext Technologies, Inc., Montara, CA 94037
| | - Sandeep K. Misra
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677
| | | | | | | |
Collapse
|
6
|
Yin V, Shaw GS, Konermann L. Cytochrome c as a Peroxidase: Activation of the Precatalytic Native State by H2O2-Induced Covalent Modifications. J Am Chem Soc 2017; 139:15701-15709. [DOI: 10.1021/jacs.7b07106] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Victor Yin
- Department of Chemistry and Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Gary S. Shaw
- Department of Chemistry and Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Lars Konermann
- Department of Chemistry and Department
of Biochemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| |
Collapse
|
7
|
Ishii K, Noda M, Uchiyama S. Mass spectrometric analysis of protein-ligand interactions. Biophys Physicobiol 2016; 13:87-95. [PMID: 27924262 PMCID: PMC5042164 DOI: 10.2142/biophysico.13.0_87] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 12/01/2022] Open
Abstract
The interactions of small molecules with proteins (protein–ligand interactions) mediate various biological phenomena including signal transduction and protein transcription and translation. Synthetic compounds such as drugs can also bind to target proteins, leading to the inhibition of protein–ligand interactions. These interactions typically accompany association–dissociation equilibrium according to the free energy difference between free and bound states; therefore, the quantitative biophysical analysis of the interactions, which uncovers the stoichiometry and dissociation constant, is important for understanding biological reactions as well as for rational drug development. Mass spectrometry (MS) has been used to determine the precise molecular masses of molecules. Recent advancements in MS enable us to determine the molecular masses of protein–ligand complexes without disrupting the non-covalent interactions through the gentle desolvation of the complexes by increasing the vacuum pressure of a chamber in a mass spectrometer. This method is called MS under non-denaturing conditions or native MS and allows the unambiguous determination of protein–ligand interactions. Under a few assumptions, MS has also been applied to determine the dissociation constants for protein–ligand interactions. The structural information of a protein–ligand interaction, such as the location of the interaction and conformational change in a protein, can also be analyzed using hydrogen/deuterium exchange MS. In this paper, we briefly describe the history, principle, and recent applications of MS for the study of protein–ligand interactions.
Collapse
Affiliation(s)
- Kentaro Ishii
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
8
|
Rajabi K, Ashcroft AE, Radford SE. Mass spectrometric methods to analyze the structural organization of macromolecular complexes. Methods 2015; 89:13-21. [DOI: 10.1016/j.ymeth.2015.03.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 02/25/2015] [Accepted: 03/06/2015] [Indexed: 01/14/2023] Open
|
9
|
Heinkel F, Gsponer J. Determination of Protein Folding Intermediate Structures Consistent with Data from Oxidative Footprinting Mass Spectrometry. J Mol Biol 2015; 428:365-371. [PMID: 26523679 DOI: 10.1016/j.jmb.2015.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 11/29/2022]
Abstract
The mapping of folding landscapes remains an important challenge in protein chemistry. Pulsed oxidative labeling of exposed residues and their detection via mass spectrometry provide new means of taking time-resolved "snapshots" of the structural changes that occur during protein folding. However, such experiments have been so far only interpreted qualitatively. Here, we report the detailed structural interpretation of mass spectrometry data from fast photochemical oxidation of proteins (FPOP) experiments at atomic resolution in a biased molecular dynamics approach. We are able to calculate structures of the early folding intermediate of the model system barstar that are fully consistent with FPOP data and Φ values. Furthermore, structures calculated with both FPOP data and Φ values are significantly less compact and have fewer helical residues than intermediate structures calculated with Φ values only. This improves the agreement with the experimental β-Tanford value and CD measurements. The restraints that we introduce facilitate the structural interpretation of FPOP data and provide new means for refined structure calculations of transiently sampled states on protein folding landscapes.
Collapse
Affiliation(s)
- Florian Heinkel
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jörg Gsponer
- Centre for High-Throughput Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
10
|
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
|
11
|
Maillot S, Carvalho A, Vola JP, Boudier C, Mély Y, Haacke S, Léonard J. Out-of-equilibrium biomolecular interactions monitored by picosecond fluorescence in microfluidic droplets. LAB ON A CHIP 2014; 14:1767-1774. [PMID: 24683603 DOI: 10.1039/c3lc51283e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We developed a new experimental approach combining Time-Resolved Fluorescence (TRF) spectroscopy and Droplet Microfluidics (DμF) to investigate the relaxation dynamics of structurally heterogeneous biomolecular systems. Here DμF was used to produce with minimal material consumption an out-of-equilibrium, fluorescently labeled biomolecular complex by rapid mixing within the droplets. TRF detection was implemented with a streak camera to monitor the time evolution of the structural heterogeneity of the complex along its relaxation towards equilibrium while it propagates inside the microfluidic channel. The approach was validated by investigating the fluorescence decay kinetics of a model interacting system of bovine serum albumin and Patent Blue V. Fluorescence decay kinetics are acquired with very good signal-to-noise ratio and allow for global, multicomponent fluorescence decay analysis, evidencing heterogeneous structural relaxation over several 100 ms.
Collapse
Affiliation(s)
- Sacha Maillot
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504, F-67034 Strasbourg Cedex 2, France.
| | | | | | | | | | | | | |
Collapse
|
12
|
Schmidt C, Robinson CV. Dynamic protein ligand interactions--insights from MS. FEBS J 2014; 281:1950-64. [PMID: 24393119 PMCID: PMC4154455 DOI: 10.1111/febs.12707] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/19/2013] [Accepted: 12/30/2013] [Indexed: 12/31/2022]
Abstract
Proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine‐tuned for different cellular actions. The study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. During the last two decades MS, and its associated techniques, has become accepted as a method for the study of protein–ligand interactions, not only for covalent complexes, where the use of MS is well established, but also, and significantly for protein–ligand interactions, for noncovalent assemblies. In this review, we employ a broad definition of a ligand to encompass protein subunits, drug molecules, oligonucleotides, carbohydrates, and lipids. Under the appropriate conditions, MS can reveal the composition, heterogeneity and dynamics of these protein–ligand interactions, and in some cases their structural arrangements and binding affinities. Herein, we highlight MS approaches for studying protein–ligand complexes, including those containing integral membrane subunits, and showcase examples from recent literature. Specifically, we tabulate the myriad of methodologies, including hydrogen exchange, proteomics, hydroxyl radical footprinting, intact complexes, and crosslinking, which, when combined with MS, provide insights into conformational changes and subtle modifications in response to ligand‐binding interactions.
Collapse
|
13
|
Serpa JJ, Makepeace KAT, Borchers TH, Wishart DS, Petrotchenko EV, Borchers CH. Using isotopically-coded hydrogen peroxide as a surface modification reagent for the structural characterization of prion protein aggregates. J Proteomics 2013; 100:160-6. [PMID: 24316355 DOI: 10.1016/j.jprot.2013.11.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 10/29/2013] [Accepted: 11/25/2013] [Indexed: 12/20/2022]
Abstract
UNLABELLED The conversion of the cellular prion protein (PrP(C)) into aggregated ß-oligomeric (PrP(ß)) and fibril (PrP(Sc)) forms is the central element in the development of prion diseases. Here we report the first use of isotopically-coded hydrogen peroxide surface modification combined with mass spectrometry (MS) for the differential characterization of PrP(C) and PrP(β). (16)O and (18)O hydrogen peroxide were used to oxidize methionine and tryptophan residues in PrP(C) and PrP(β), allowing for the relative quantitation of the extent of modification of each form of the prion protein. After modification with either light or heavy forms of hydrogen peroxide (H2(16)O2 and H2(18)O2), the PrP(C) and PrP(β) forms of the protein were then combined, digested with trypsin, and analysed by LC-MS. The (18)O/(16)O signal intensity ratios were used to determine the relative levels of oxidation of specific amino acids in the PrP(C) and PrP(β) forms. Using this approach we have detected several residues that are differentially-oxidized between the native and β-oligomeric prion forms, allowing determination of the regions of PrP(C) involved in the formation of PrP(β) aggregates. Modification of these residues in the β-oligomeric form is compatible with a flip of the β1-H1-β2 loop away from amphipathic helices 2 and 3 during conversion. BIOLOGICAL SIGNIFICANCE Surface modification using isotopically-coded hydrogen peroxide has allowed quantitative comparison of the exposure of methionine and tryptophan residues in PrP(C) and PrP(ß) forms of prion protein. Detected changes in surface exposure of a number of residues have indicated portions of the PrP structure which undergo conformational transition upon conversion. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
Collapse
Affiliation(s)
- Jason J Serpa
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Karl A T Makepeace
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Tristan H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - David S Wishart
- Departments of Biological Sciences and Computing Science, University of Alberta, Edmonton, Alberta, T6G 2E8, Canada
| | - Evgeniy V Petrotchenko
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada
| | - Christoph H Borchers
- University of Victoria, Genome British Columbia Proteomics Centre, #3101-4464 Markham Street, Vancouver Island Technology Park, Victoria, BC V8Z7X8, Canada; University of Victoria, Department of Biochemistry & Microbiology, Petch Building Room 207, 3800 Finnerty Rd., Victoria, BC V8P 5C2, Canada.
| |
Collapse
|
14
|
Wu L, Lapidus LJ. Combining Ultrarapid Mixing with Photochemical Oxidation to Probe Protein Folding. Anal Chem 2013; 85:4920-4. [DOI: 10.1021/ac3033646] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ling Wu
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United
States
| | - Lisa J. Lapidus
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, United
States
| |
Collapse
|
15
|
Shin S, Yang HJ, Kim JH, Kim J, Lee JH, Park KH, Kim HS, Kim J. Clarification of a peak at m/z 1634 from tryptically digested cytochrome c. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:1576-1581. [PMID: 23280746 DOI: 10.1002/jms.3119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/03/2012] [Accepted: 10/04/2012] [Indexed: 06/01/2023]
Abstract
A peptide peak at m/z 1634 in the mass spectrum of tryptically digested cytochrome c has been ambiguously assigned to either a peptide IFVQKCAQCHTVEK or a peptide CAQCHTVEK combined with a heme group (CAQCHTVEK + heme (Fe(III))). A comprehensive investigation was performed to clearly identify the origin of the peak. Tryptic digests of cytochrome c were analyzed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), liquid chromatography-tandem MS (LC-MS/MS), LC-ultraviolet (LC-UV), and MALDI Fourier transform-ion cyclotron resonance (FT-ICR) MS. The use of instruments with extremely high mass accuracy revealed the mass difference between the IFVQKCAQCHTVEK and the (CAQCHTVEK + heme (Fe(III))) ions. Fragmentation of the peptide associated with the unknown peak yielded a heme ion and other fragment ions originating from a (CAQCHTVEK + heme (Fe(III))) ion. Furthermore, an absorption peak at 395 nm confirmed the presence of a heme group in the unknown peptide. High mass accuracy analyses of MS and MS/MS spectra, in addition to three-dimensional UV contour mapping, showed that the peak at m/z 1634 is due to a (CAQCHTVEK + heme (Fe(III))) ion and not from protonated IFVQKCAQCHTVEK.
Collapse
|
16
|
Chen J, Rempel DL, Gau BC, Gross ML. Fast photochemical oxidation of proteins and mass spectrometry follow submillisecond protein folding at the amino-acid level. J Am Chem Soc 2012; 134:18724-31. [PMID: 23075429 DOI: 10.1021/ja307606f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a study of submillisecond protein folding with amino-acid residue resolution achieved with a two-laser pump/probe experiment with analysis by mass spectrometry. The folding of a test protein, barstar, can be triggered by a laser-induced temperature jump (T jump) from ∼0 °C to ∼room temperature. Subsequent reactions via fast photochemical oxidation of proteins (FPOP) at various fractional millisecond points after the T jump lead to oxidative modification of solvent-accessible side chains whose "protection" changes with time and extent of folding. The modifications are identified and quantified by LC-MS/MS following proteolysis. Among all the segments that form secondary structure in the native state, helix(1) shows a decreasing trend of oxidative modification during the first 0.1-1 ms of folding while others do not change in this time range. Residues I5, H17, L20, L24 and F74 are modified less in the intermediate state than the denatured state, likely due to full or partial protection of these residues as folding occurs. We propose that in the early folding stage, barstar forms a partially solvent-accessible hydrophobic core consisting of several residues that have long-range interaction with other, more remote residues in the protein sequence. Our data not only are consistent with the previous conclusion that barstar fast folding follows the nucleation-condensation mechanism with the nucleus centered on helix(1) formed in a folding intermediate but also show the efficacy of this new approach to following protein folding on the submillisecond time range.
Collapse
Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University in St. Louis, Missouri 63130, United States
| | | | | | | |
Collapse
|
17
|
Konermann L, Pan Y, Stocks BB. Protein folding mechanisms studied by pulsed oxidative labeling and mass spectrometry. Curr Opin Struct Biol 2011; 21:634-40. [PMID: 21703846 DOI: 10.1016/j.sbi.2011.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Revised: 05/21/2011] [Accepted: 05/26/2011] [Indexed: 12/14/2022]
Abstract
Deciphering the mechanisms of protein folding remains a considerable challenge. In this review we discuss the application of pulsed oxidative labeling for tracking protein structural changes in a time-resolved fashion. Exposure to a microsecond OH pulse at selected time points during folding induces the oxidation of solvent-accessible side chains, whereas buried residues are protected. Oxidative modifications can be detected by mass spectrometry. Folding is associated with dramatic accessibility changes, and therefore this method can provide detailed mechanistic insights. Solvent accessibility patterns are complementary to H/D exchange investigations, which report on the extent of hydrogen bonding. This review highlights the application of pulsed OH labeling to soluble proteins as well as membrane proteins.
Collapse
Affiliation(s)
- Lars Konermann
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada.
| | | | | |
Collapse
|
18
|
Stocks BB, Rezvanpour A, Shaw GS, Konermann L. Temporal Development of Protein Structure during S100A11 Folding and Dimerization Probed by Oxidative Labeling and Mass Spectrometry. J Mol Biol 2011; 409:669-79. [DOI: 10.1016/j.jmb.2011.04.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Revised: 04/01/2011] [Accepted: 04/11/2011] [Indexed: 10/18/2022]
|
19
|
Kinetic folding mechanism of an integral membrane protein examined by pulsed oxidative labeling and mass spectrometry. J Mol Biol 2011; 410:146-58. [PMID: 21570983 DOI: 10.1016/j.jmb.2011.04.074] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 04/26/2011] [Accepted: 04/29/2011] [Indexed: 11/21/2022]
Abstract
We report the application of pulsed oxidative labeling for deciphering the folding mechanism of a membrane protein. SDS-denatured bacteriorhodopsin (BR) was refolded by mixing with bicelles in the presence of free retinal. At various time points (20 ms to 1 day), the protein was exposed to a microsecond ·OH pulse that induces oxidative modifications at solvent-accessible methionine side chains. The extent of labeling was determined by mass spectrometry. These measurements were complemented by stopped-flow spectroscopy. Major time-dependent changes in solvent accessibility were detected for M20 (helix A) and M118 (helix D). Our kinetic data indicate a sequential folding mechanism, consistent with models previously suggested by others on the basis of optical data. Yet, ·OH labeling provides additional structural insights. An initial folding intermediate I(1) gets populated within 20 ms, concomitantly with formation of helix A. Subsequent structural consolidation leads to a transient species I(2). Noncovalent retinal binding to I(2) induces folding of helix D, thereby generating an intermediate I(R). In the absence of retinal, the latter transition does not take place. Hence, formation of helix D depends on retinal binding, whereas this is not the case for helix A. As the cofactor settles deeper into its binding pocket, a final transient species I(R) is generated. This intermediate converts into native BR within minutes by formation of the retinal-K216 Schiff base linkage. The combination of pulsed covalent labeling and optical spectroscopy employed here should also be suitable for exploring the folding mechanisms of other membrane proteins.
Collapse
|
20
|
Chen J, Rempel DL, Gross ML. Temperature jump and fast photochemical oxidation probe submillisecond protein folding. J Am Chem Soc 2011; 132:15502-4. [PMID: 20958033 DOI: 10.1021/ja106518d] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a new mass-spectrometry-based approach for studying protein-folding dynamics on the submillisecond time scale. The strategy couples a temperature jump with fast photochemical oxidation of proteins (FPOP), whereby folding/unfolding is followed by changes in oxidative modifications by OH radical reactions. Using a flow system containing the protein barstar as a model, we altered the protein's equilibrium conformation by applying the temperature jump and demonstrated that its reactivity with OH free radicals serves as a reporter of the conformational change. Furthermore, we found that the time-dependent increase in mass resulting from free-radical oxidation is a measure of the rate constant for the transition from the unfolded to the first intermediate state. This advance offers the promise that, when extended with mass-spectrometry-based proteomic analysis, the sites and kinetics of folding/unfolding can also be followed on the submillisecond time scale.
Collapse
Affiliation(s)
- Jiawei Chen
- Department of Chemistry, Washington University, One Brookings Drive, Saint Louis, Missouri 63130, United States
| | | | | |
Collapse
|
21
|
Ben-Nissan G, Sharon M. Capturing protein structural kinetics by mass spectrometry. Chem Soc Rev 2011; 40:3627-37. [DOI: 10.1039/c1cs15052a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
22
|
Kiselar JG, Chance MR. Future directions of structural mass spectrometry using hydroxyl radical footprinting. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:1373-82. [PMID: 20812376 PMCID: PMC3012749 DOI: 10.1002/jms.1808] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein-protein and protein-DNA interactions. Using synchrotron radiolysis, exposure of proteins to a 'white' X-ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time-resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium-dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time-resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)-based method can be utilized for quantification of oxidized species, improving the signal-to-noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis-driven structural mass spectrometry experiments.
Collapse
Affiliation(s)
- Janna G Kiselar
- Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| | | |
Collapse
|
23
|
Pan Y, Brown L, Konermann L. Site-directed mutagenesis combined with oxidative methionine labeling for probing structural transitions of a membrane protein by mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2010; 21:1947-1956. [PMID: 20829064 DOI: 10.1016/j.jasms.2010.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2010] [Revised: 08/06/2010] [Accepted: 08/09/2010] [Indexed: 05/29/2023]
Abstract
Exposure of the membrane protein bacteriorhodopsin (BR) to SDS induces partial breakdown of the native conformation. The exact structural properties of this SDS state remain a matter of debate, despite its widespread use in BR folding experiments. The current work employs hydroxyl radical (·OH) labeling in conjunction with mass spectrometry (MS)-based peptide mapping for probing the solvent accessibility of individual BR segments in the presence of SDS. Previous work revealed methionine sulfoxide formation to be the dominant oxidative pathway. Those data suggested extensive unfolding of helices A and D in SDS. Unfortunately, the lack of Met residues in helices C and F implies that no direct information on the behavior of the latter two elements could be obtained. Here, we address this problem by employing two variants with additional Met residues, L93M (helix C) and V179M (helix F). The oxidation behavior of the resulting 11 methionines can be grouped into three categories: (1) extensively labeled both in native BR and in SDS (loop residues M32, M68, and M163); (2) protected in the native state but not in SDS (M20, M118); (3) always protected (M56, M60, M93, M145, M179, M209). These data show that a solvent-inaccessible core is retained in SDS. This core consists of partially intact helices B, C, E, F, and G. The termini of these helices are highly dynamic and/or unraveled, particularly on the cytoplasmic side. Overall, this work demonstrates how the use of engineered ·OH labeling sites can provide insights into structural properties of membrane proteins.
Collapse
Affiliation(s)
- Yan Pan
- Department of Chemistry, University of Western Ontario, London, Ontario, Canada
| | | | | |
Collapse
|
24
|
Konermann L, Stocks BB, Czarny T. Laminar Flow Effects During Laser-Induced Oxidative Labeling for Protein Structural Studies by Mass Spectrometry. Anal Chem 2010; 82:6667-74. [DOI: 10.1021/ac101326f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lars Konermann
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Bradley B. Stocks
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Tomasz Czarny
- Departments of Chemistry and Biochemistry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| |
Collapse
|