1
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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2
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Liu T, Marcinko TM, Vachet RW. Protein-Ligand Affinity Determinations Using Covalent Labeling-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1544-1553. [PMID: 32501685 PMCID: PMC7332385 DOI: 10.1021/jasms.0c00131] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Determining the binding affinity is an important aspect of characterizing protein-ligand complexes. Here, we describe an approach based on covalent labeling (CL)-mass spectrometry (MS) that can accurately provide protein-ligand dissociation constants (Kd values) using diethylpyrocarbonate (DEPC) as the labeling reagent. Even though DEPC labeling reactions occur on a time scale that is similar to the dissociation/reassociation rates of many protein-ligand complexes, we demonstrate that relatively accurate binding constants can still be obtained as long as the extent of protein labeling is kept below 30%. Using two well-established model systems and one insufficiently characterized system, we find that Kd values can be determined that are close to values obtained in previous measurements. The CL-MS-based strategy that is described here should serve as an alternative for characterizing protein-ligand complexes that are challenging to measure by other methods. Moreover, this method has the potential to provide, simultaneously, the affinity and binding site information.
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Affiliation(s)
| | | | - Richard W. Vachet
- Corresponding author: Prof. Richard W. Vachet, Department of Chemistry, University of Massachusetts, Amherst, MA 01003, , Phone: (413) 545-2733
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3
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Liu XR, Zhang MM, Gross ML. Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications. Chem Rev 2020; 120:4355-4454. [PMID: 32319757 PMCID: PMC7531764 DOI: 10.1021/acs.chemrev.9b00815] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Proteins adopt different higher-order structures (HOS) to enable their unique biological functions. Understanding the complexities of protein higher-order structures and dynamics requires integrated approaches, where mass spectrometry (MS) is now positioned to play a key role. One of those approaches is protein footprinting. Although the initial demonstration of footprinting was for the HOS determination of protein/nucleic acid binding, the concept was later adapted to MS-based protein HOS analysis, through which different covalent labeling approaches "mark" the solvent accessible surface area (SASA) of proteins to reflect protein HOS. Hydrogen-deuterium exchange (HDX), where deuterium in D2O replaces hydrogen of the backbone amides, is the most common example of footprinting. Its advantage is that the footprint reflects SASA and hydrogen bonding, whereas one drawback is the labeling is reversible. Another example of footprinting is slow irreversible labeling of functional groups on amino acid side chains by targeted reagents with high specificity, probing structural changes at selected sites. A third footprinting approach is by reactions with fast, irreversible labeling species that are highly reactive and footprint broadly several amino acid residue side chains on the time scale of submilliseconds. All of these covalent labeling approaches combine to constitute a problem-solving toolbox that enables mass spectrometry as a valuable tool for HOS elucidation. As there has been a growing need for MS-based protein footprinting in both academia and industry owing to its high throughput capability, prompt availability, and high spatial resolution, we present a summary of the history, descriptions, principles, mechanisms, and applications of these covalent labeling approaches. Moreover, their applications are highlighted according to the biological questions they can answer. This review is intended as a tutorial for MS-based protein HOS elucidation and as a reference for investigators seeking a MS-based tool to address structural questions in protein science.
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Affiliation(s)
| | | | - Michael L. Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO, USA, 63130
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4
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Arden BG, Borotto NB, Burant B, Warren W, Akiki C, Vachet RW. Measuring the Energy Barrier of the Structural Change That Initiates Amyloid Formation. Anal Chem 2020; 92:4731-4735. [PMID: 32159946 DOI: 10.1021/acs.analchem.0c00368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Obtaining kinetic and thermodynamic information for protein amyloid formation can yield new insight into the mechanistic details of this biomedically important process. The kinetics of the structural change that initiates the amyloid pathway, however, has been challenging to access for any amyloid protein system. Here, using the protein β-2-microglobulin (β2m) as a model, we measure the kinetics and energy barrier associated with an initial amyloidogenic structural change. Using covalent labeling and mass spectrometry, we measure the decrease in solvent accessibility of one of β2m's Trp residues, which is buried during the initial structural change, as a way to probe the kinetics of this structural change at different temperatures and under different amyloid forming conditions. Our results provide the first-ever measure of the activation barrier for a structural change that initiates the amyloid formation pathway. The results also yield new mechanistic insight into β2m's amyloidogenic structural change, especially the role of Pro32 isomerization in this reaction.
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Affiliation(s)
- Blaise G Arden
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Nicholas B Borotto
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Brittney Burant
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - William Warren
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Christine Akiki
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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5
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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
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6
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Marcinko TM, Dong J, LeBlanc R, Daborowski KV, Vachet RW. Small molecule-mediated inhibition of β-2-microglobulin-based amyloid fibril formation. J Biol Chem 2017; 292:10630-10638. [PMID: 28468825 DOI: 10.1074/jbc.m116.774083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 05/02/2017] [Indexed: 12/26/2022] Open
Abstract
In dialysis patients, β-2 microglobulin (β2m) can aggregate and eventually form amyloid fibrils in a condition known as dialysis-related amyloidosis, which deleteriously affects joint and bone function. Recently, several small molecules have been identified as potential inhibitors of β2m amyloid formation in vitro Here we investigated whether these molecules are more broadly applicable inhibitors of β2m amyloid formation by studying their effect on Cu(II)-induced β2m amyloid formation. Using a variety of biophysical techniques, we also examined their inhibitory mechanisms. We found that two molecules, doxycycline and rifamycin SV, can inhibit β2m amyloid formation in vitro by causing the formation of amorphous, redissolvable aggregates. Rather than interfering with β2m amyloid formation at the monomer stage, we found that doxycycline and rifamycin SV exert their effect by binding to oligomeric species both in solution and in gas phase. Their binding results in a diversion of the expected Cu(II)-induced progression of oligomers toward a heterogeneous collection of oligomers, including trimers and pentamers, that ultimately matures into amorphous aggregates. Using ion mobility mass spectrometry, we show that both inhibitors promote the compaction of the initially formed β2m dimer, which causes the formation of other off-pathway and amyloid-incompetent oligomers that are isomeric with amyloid-competent oligomers in some cases. Overall, our results suggest that doxycycline and rifamycin are general inhibitors of Cu(II)-induced β2m amyloid formation. Interestingly, the putative mechanism of their activity is different depending on how amyloid formation is initiated with β2m, which underscores the complexity of how these structures assemble in vitro.
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Affiliation(s)
- Tyler M Marcinko
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Jia Dong
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Raquel LeBlanc
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Kate V Daborowski
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
| | - Richard W Vachet
- From the Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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7
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Ugur Z, Gronert S. A Robust Analytical Approach for the Identification of Specific Protein Carbonylation Sites: Metal-Catalyzed Oxidations of Human Serum Albumin. ANAL LETT 2016; 50:567-579. [PMID: 28303033 DOI: 10.1080/00032719.2016.1186171] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The formation of protein carbonyls in the metal-catalyzed oxidation of human serum albumin (HSA) is characterized using a new analytical approach that involves tagging the modification site with multiple hydrazide reagents. Protein carbonyl formation at lysine and arginine residues was catalyzed with copper and iron ions, and the resulting oxidation patterns in HSA are contrasted. A total of 18 modification sites were identified with iron ion catalysis and 14 with copper ion catalysis. However, with the more stringent requirement of identification with at least two tagging reagents, the number of validated modification sites drops to 10 for iron and 9 for copper. Of the 14 total validated sites, there were only five in common for the two metal ions. The results illustrate the value of using multiple tagging agents and highlight the selective and specific nature of metal-catalyzed protein oxidations.
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Affiliation(s)
- Zafer Ugur
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284 USA
| | - Scott Gronert
- Department of Chemistry, Virginia Commonwealth University, Richmond, VA 23284 USA
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8
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Phillips AS, Gomes AF, Kalapothakis JMD, Gillam JE, Gasparavicius J, Gozzo FC, Kunath T, MacPhee C, Barran PE. Conformational dynamics of α-synuclein: insights from mass spectrometry. Analyst 2015; 140:3070-81. [DOI: 10.1039/c4an02306d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Different mass spectrometry approaches are combined to investigate the conformational flexibility of α-synuclein.
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Affiliation(s)
- Ashley S. Phillips
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | - Alexandre F. Gomes
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | | | - Jay E. Gillam
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | | | - Fabio C. Gozzo
- Dalton Mass Spectrometry Laboratory
- University of Campinas – UNICAMP
- Brazil
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine
- University of Edinburgh
- Edinburgh
- UK
| | - Cait MacPhee
- School of Physics and Astronomy
- University of Edinburgh
- Edinburgh
- UK
| | - Perdita E. Barran
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
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9
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Liuni P, Zhu S, Wilson DJ. Oxidative protein labeling with analysis by mass spectrometry for the study of structure, folding, and dynamics. Antioxid Redox Signal 2014; 21:497-510. [PMID: 24512178 DOI: 10.1089/ars.2014.5850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
SIGNIFICANCE Analytical approaches that can provide insights into the mechanistic processes underlying protein folding and dynamics are few since the target analytes-high-energy structural intermediates-are short lived and often difficult to distinguish from coexisting structures. Folding "intermediates" can be populated at equilibrium using weakly denaturing solvents, but it is not clear that these species are identical to those that are transiently populated during folding under "native" conditions. Oxidative labeling with mass spectrometric analysis is a powerful alternative for structural characterization of proteins and transient protein species based on solvent exposure at specific sites. RECENT ADVANCES Oxidative labeling is increasingly used with exceedingly short (μs) labeling pulses, both to minimize the occurrence of artifactual structural changes due to the incorporation of label and to detect short-lived species. The recent introduction of facile photolytic approaches for producing reactive oxygen species is an important technological advance that will enable more widespread adoption of the technique. CRITICAL ISSUES The most common critique of oxidative labeling data is that even with brief labeling pulses, covalent modification of the protein may cause significant artifactual structural changes. FUTURE DIRECTIONS While the oxidative labeling with the analysis by mass spectrometry is mature enough that most basic methodological issues have been addressed, a complete systematic understanding of side chain reactivity in the context of intact proteins is an avenue for future work. Specifically, there remain issues around the impact of primary sequence and side chain interactions on the reactivity of "solvent-exposed" residues. Due to its analytical power, wide range of applications, and relative ease of implementation, oxidative labeling is an increasingly important technique in the bioanalytical toolbox.
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Affiliation(s)
- Peter Liuni
- 1 Department of Chemistry, York University , Toronto, Canada
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10
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Kojima A, Konishi M, Akizawa T. Prion fragment peptides are digested with membrane type matrix metalloproteinases and acquire enzyme resistance through Cu²⁺-binding. Biomolecules 2014; 4:510-26. [PMID: 24970228 PMCID: PMC4101495 DOI: 10.3390/biom4020510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 04/02/2014] [Accepted: 04/11/2014] [Indexed: 11/16/2022] Open
Abstract
Prions are the cause of neurodegenerative disease in humans and other mammals. The structural conversion of the prion protein (PrP) from a normal cellular protein (PrPC) to a protease-resistant isoform (PrPSc) is thought to relate to Cu2+ binding to histidine residues. In this study, we focused on the membrane-type matrix metalloproteinases (MT-MMPs) such as MT1-MMP and MT3-MMP, which are expressed in the brain as PrPC-degrading proteases. We synthesized 21 prion fragment peptides. Each purified peptide was individually incubated with recombinant MT1-MMP or MT3-MMP in the presence or absence of Cu2+ and the cleavage sites determined by LC-ESI-MS analysis. Recombinant MMP-7 and human serum (HS) were also tested as control. hPrP61-90, from the octapeptide-repeat region, was cleaved by HS but not by the MMPs tested here. On the other hand, hPrP92-168 from the central region was cleaved by MT1-MMP and MT3-MMP at various sites. These cleavages were inhibited by treatment with Cu2+. The C-terminal peptides had higher resistance than the central region. The data obtained from this study suggest that MT-MMPs expressed in the brain might possess PrPC-degrading activity.
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Affiliation(s)
- Aya Kojima
- Analytical Chemistry, Pharmaceutical Science, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan.
| | - Motomi Konishi
- Analytical Chemistry, Pharmaceutical Science, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan.
| | - Toshifumi Akizawa
- Analytical Chemistry, Pharmaceutical Science, Setsunan University, 45-1 Nagaotoge-cho, Hirakata, Osaka 573-0101, Japan.
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11
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Zhang N, Cui M, Du Y, Liu Z, Liu S. Exploring the interaction of cisplatin with β2-microglobulin: new insights into a chemotherapeutic drug. RSC Adv 2014. [DOI: 10.1039/c3ra44096f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Fukuda M, Takao T. Quantitative analysis of deamidation and isomerization in β2-microglobulin by 18O labeling. Anal Chem 2012; 84:10388-94. [PMID: 23126476 DOI: 10.1021/ac302603b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deamidation of asparagine residues in proteins via the formation of a 5-membered succinimide ring intermediate is a nonenzymatic intramolecular reaction and, in general, occurs most rapidly at an Asn-Gly sequence. A protein containing this sequence would, therefore, be susceptible to modification, and the result would produce a structural alteration in the molecule. An Asn would be replaced with an Asp, resulting in an increase in the overall negative charge on the molecule but also an isomerization to isoAsp. Despite the fact that such a structural replacement could affect the functional properties of a protein, estimating the susceptibility of the Asn-Gly sequence to deamidation/isomerization remains a difficult task. This is especially true for proteins that are subjected to enzymatic digestion during their characterization, since the above transformation could occur spontaneously during this treatment. To address this issue, we applied a stable-isotope (18)O-labeling method combined with nano-LC-MS/MS to examine the susceptibility of two Asn-Gly sites in β2-microglobulin (β2m) to the reaction. The method permits the reaction occurring in a protein to be distinguished from that during enzymatic treatment. When β2m was incubated for 60 days at 37 °C, deamidation at Asn17-Gly and Asn42-Gly with half-lives of 33 and 347 days occurred, respectively. Moreover, a comparison of the deamidated products to synthetic peptides revealed that 44% of the Asp17 and 96% of the Asp42 had been converted into isoAsp forms. Interestingly, such structurally altered β2m showed a specific affinity for divalent Cu(2+) ions, which is thought to be a candidate for initiating fibril formation.
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Affiliation(s)
- Masafumi Fukuda
- Laboratory of Protein Profiling and Functional Proteomics, Institute for Protein Research, Osaka University, Yamadaoka, Japan
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13
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Kojima A, Mabuchi Y, Konishi M, Okihara R, Nagano M, Akizawa T. Metal-binding ability of human prion protein fragment peptides analyzed by column switch HPLC. Chem Pharm Bull (Tokyo) 2011; 59:965-71. [PMID: 21804240 DOI: 10.1248/cpb.59.965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structural conversion of the prion protein (PrP) from the normal cellular isoform (PrP(C)) to the posttranslationally modified form (PrP(Sc)) is thought to relate to Cu²⁺ binding to histidine (H) residues. Traditionally, the binding of metals to PrP has been investigated by monitoring the conformational conversion using circular dichroism (CD). In this study, the metal-binding ability of 21 synthetic peptides representing regions of human PrP(C) was investigated by column switch high-performance liquid chromatography (CS-HPLC). The CS-HPLC system is composed of a metal chelate affinity column and an octadecylsilica (ODS) reversed-phase column that together enable the identification of metal-binding regardless of conformational conversion. Synthetic peptides were designed with respect to the position of H residues as well as the secondary structure of human PrP (hPrP). The ability of the octapeptide (PHGGGWGQ)-repeating region (OP-repeat) to bind metals was analyzed by CS-HPLC and supported by CD analysis, and indicated that CS-HPLC is a reliable and useful method for measuring peptide metal-binding. Peptides from the middle region of hPrP showed a high affinity for Cu²⁺, but binding to Zn²⁺, Ni²⁺, and Co²⁺ was dependent on peptide length. C-Terminal peptides had a lower affinity for Cu²⁺, Zn²⁺, Ni²⁺, and Co²⁺ than OP-repeat region peptides. Interestingly, hPrP193-230, which contained no H residues, also bound to Cu²⁺, Zn²⁺, Ni²⁺, and Co²⁺, indicating that this region is a novel metal-binding site in the C-terminal region of PrP(C). The CS-HPLC method described in this study is useful and convenient for assessing metal-binding affinity and characterizing metal-binding peptides or proteins.
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Affiliation(s)
- Aya Kojima
- Department of Analytical Chemistry, Pharmaceutical Science, Setsunan University, Japan
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14
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Schorzman AN, Perera L, Cutalo-Patterson JM, Pedersen LC, Pedersen LG, Kunkel TA, Tomer KB. Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry. DNA Repair (Amst) 2011; 10:454-65. [PMID: 21354867 PMCID: PMC3084373 DOI: 10.1016/j.dnarep.2011.01.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 01/07/2011] [Accepted: 01/24/2011] [Indexed: 11/26/2022]
Abstract
Mismatch repair (MMR) corrects replication errors that would otherwise lead to mutations and, potentially, various forms of cancer. Among several proteins required for eukaryotic MMR, MutLα is a heterodimer comprised of Mlh1 and Pms1. The two proteins dimerize along their C-terminal domains (CTDs), and the CTD of Pms1 houses a latent endonuclease that is required for MMR. The highly conserved N-terminal domains (NTDs) independently bind DNA and possess ATPase active sites. Here we use two protein footprinting techniques, limited proteolysis and oxidative surface mapping, coupled with mass spectrometry to identify amino acids involved along the DNA-binding surface of the Pms1-NTD. Limited proteolysis experiments elucidated several basic residues that were protected in the presence of DNA, while oxidative surface mapping revealed one residue that is uniquely protected from oxidation. Furthermore, additional amino acids distributed throughout the Pms1-NTD were protected from oxidation either in the presence of a non-hydrolyzable analog of ATP or DNA, indicating that each ligand stabilizes the protein in a similar conformation. Based on the recently published X-ray crystal structure of yeast Pms1-NTD, a model of the Pms1-NTD/DNA complex was generated using the mass spectrometric data as constraints. The proposed model defines the DNA-binding interface along a positively charged groove of the Pms1-NTD and complements prior mutagenesis studies of Escherichia coli and eukaryotic MutL.
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Affiliation(s)
- Allison N. Schorzman
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lalith Perera
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Jenny M. Cutalo-Patterson
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lars C. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Lee G. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Thomas A. Kunkel
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Kenneth B. Tomer
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709
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15
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Inoue K, Nakagawa A, Hino T, Oka H. Screening assay for metal-catalyzed oxidation inhibitors using liquid chromatography-mass spectrometry with an N-terminal beta-amyloid peptide. Anal Chem 2010; 81:1819-25. [PMID: 19173589 DOI: 10.1021/ac802162n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Production of microregional catalytic reactive oxygen species (ROS) by metal-binding amyloid-beta (Abeta) peptides mediates the neurotoxicity of Alzheimer's disease, and inhibitors of this activity may be of therapeutic value. No current analytical methods target specific ROS inhibitors produced by metal-binding peptides. We report a screening assay for metal-catalyzed oxidation (MCO) inhibitors based on liquid chromatography-mass spectrometry (LC-MS) with a model N-terminal Abeta peptide (Abeta(1-6)). When subjected to MCO by Cu(II)/ascorbic acid, singly and doubly charged Abeta(1-6) molecules were observed at m/z 729.2 and 364.8 and m/z 685.3 and 343.3, respectively, corresponding to a decrease in mass of 45 and 89 Da compared with the model peptide. In contrast, H(2)O(2) did not modify the Abeta(1-6) peptide. Modified peptides were characterized by a specific MCO of Abeta(1-6), which contains both His and N-terminal Asp residues. LC-MS detection of the modified peptides allowed us to identify antioxidants that inhibit MCO of Abeta(1-6). MCO of the model peptide was inhibited by curcumin, but not dibutylhydroxytoluene, carotene, tocopherol, estradiol or nicotine, revealing a clear difference between curcumin and other antioxidants. This novel assay may allow for the identification of antioxidants that protect against MCO of peptides and proteins related to degenerative diseases.
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Affiliation(s)
- Koichi Inoue
- Department of Physical and Analytical Chemistry, School of Pharmacy, Kinjo Gakuin University, 2-1723 Omori, Moriyama-ku, Nagoya 463-8521, Japan.
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16
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Sydnes MO, Miyazaki A, Isobe M, Ohinata H, Miyazu M, Takai A. Development of a new protein labeling strategy, oxidation labeling. part 1: Preliminary evaluation and synthesis of tautomycin containing a metal coordinating unit. Tetrahedron 2010. [DOI: 10.1016/j.tet.2009.12.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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17
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Miyazaki A, Sydnes MO, Isobe M, Ohinata H, Miyazu M, Takai A. Oxidatively induced Cu for Mn exchange in protein phosphatase 1γ: A new method for active site analysis. Bioorg Med Chem 2009; 17:7978-86. [DOI: 10.1016/j.bmc.2009.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2009] [Revised: 10/06/2009] [Accepted: 10/07/2009] [Indexed: 11/26/2022]
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18
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Srikanth R, Mendoza VL, Bridgewater JD, Zhang G, Vachet RW. Copper binding to beta-2-microglobulin and its pre-amyloid oligomers. Biochemistry 2009; 48:9871-81. [PMID: 19754160 DOI: 10.1021/bi901172y] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta-2-microglobulin (beta2m) deposits as amyloid fibrils in the musculoskeletal system of patients undergoing long-term dialysis treatment as a result of kidney failure. Previous work has shown that Cu(II) binding causes beta2m to organize into nativelike dimers and tetramers that precede amyloid formation. Cu(II) is then released from higher-order oligomers before mature Cu(II)-free amyloid fibrils are formed. While some of the Cu(II)-induced structural changes that enable beta2m self-assembly are starting to be revealed, the details of how the Cu(II) binding site evolves from the monomer to the dimers and tetramers are not known. Here, we report results from three mass spectrometry (MS)-based methods that provide insight into the changing Cu-beta2m interactions. We find that monomeric beta2m binds Cu(II) via the N-terminal amine, the amide of Gln2, His31, and Asp59. In the dimer and tetramer, Asp59 is no longer bound to Cu(II), but the other residues still comprise a well-defined albeit weaker binding site that is better able to release Cu(II). Consistent with this is the observation that a fraction of the tetrameric species no longer binds Cu(II) at this weakened binding site, which agrees with a previous report that suggested the tetramer as the first Cu(II)-free oligomer. Our results also provide some insight into structural changes caused by Cu(II) binding that facilitate oligomer formation. Specifically, binding by Asp59 in the monomer requires significant movement of this residue, and we propose that this repositioning is important for establishing a pair of dimer-stabilizing salt bridges between this residue and Lys19. We also find evidence that Cu(II) binding in the N-terminal region of the monomer repels Arg3, which likely allows this residue to form a pair of dimer-stabilizing salt bridges with Glu16. Overall, our measurements suggest that the previously proposed conformational switch caused by Cu(II) binding includes not only a cis-trans isomerization at Pro32 but also the repositioning of residues that are critical for the formation of new electrostatic interactions.
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Affiliation(s)
- Rapole Srikanth
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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19
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Blaho DV, Miranker AD. Delineating the conformational elements responsible for Cu(2+)-induced oligomerization of beta-2 microglobulin. Biochemistry 2009; 48:6610-7. [PMID: 19518133 DOI: 10.1021/bi900540j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Beta-2 microglobulin (beta2m) is a small globular protein implicated in amyloid fiber formation in renal patients on long-term hemodialysis therapy. In vitro, under physiological conditions, beta2m is not aggregation prone. However, in the presence of stoichiometric Cu(2+), beta2m readily self-associates ultimately leading to heterogeneously sized aggregates. As this process occurs under near physiological solution conditions where the fold is >or=20 kJ/mol stabilized over the unfolded state, local conformational rearrangements are critical to understanding the oligomerization of beta2m. The isomerization of a conserved cis proline at residue 32 is a recognized step in this process that can be initiated by Cu(2+) binding. To better understand the structural basis of metal-induced oligomerization of beta2m, we set out to determine the role of individual imidazole side chains in mediating metal binding affinity, native state stability, and oligomerization in the framework of P32A beta2m. We find that P32A in the presence of Cu(2+) forms a tetramer in an apparently cooperative manner. One interface of this tetramer appears to reside along an edge strand as H51 is a key residue in mediating oligomerization. Furthermore, H31 is the main Cu(2+) binding residue in P32A and has an important role in stabilizing the protein in its holo form. Importantly, Cu(2+) binding affinity in P32A is much greater than in WT. Here, we show that this strong binding affinity need not be directly coupled to oligomerization. We interpret our results in terms of the known structures of beta2m(apo) and a reversible hexameric state of beta2m(holo).
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Affiliation(s)
- Dorottya V Blaho
- Department of Molecular Biophysics and Biochemistry Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520-8114, USA
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20
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Srikanth R, Wilson J, Vachet RW. Correct identification of oxidized histidine residues using electron-transfer dissociation. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:755-62. [PMID: 19160434 PMCID: PMC2737336 DOI: 10.1002/jms.1552] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Oxidative modification to the side chain of histidine can noticeably change the collision-induced dissociation (CID) pathways of peptides containing this oxidized residue. In cases where an oxidized peptide consists two or more isomers differing only in the site of modification, oxidation to histidine usually causes the other oxidized sites to be mis-assigned in CID spectra. These spectral misassignments can sometimes be avoided by using multiple stages of MS/MS (MS(n)) or via specially optimized liquid chromatographic separation conditions. In this manuscript, we demonstrate that these misassignments can be more readily and easily avoided by using electron-transfer dissociation (ETD) to dissociate the oxidized peptides. Furthermore, we find that the relative insensitivity of ETD to side-chain chemistry allows the extent of oxidative modification to be determined readily for peptide isomers having more than one site of oxidation. The current results along with previous studies of oxidized peptides suggest that ETD is probably a better technique than CID for obtaining correct sequence and modification information for oxidized peptides.
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Affiliation(s)
- Rapole Srikanth
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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21
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Abstract
Beta-2 microglobulin (beta2m) is a globular protein that self-associates into fibrillar amyloid deposits in patients undergoing hemodialysis therapy. Formation of these beta-sheet-rich assemblies is a fundamental property of polypeptides that can be triggered by diverse conditions. For beta2m, oligomerization into pre-amyloidogenic states occurs in specific response to coordination by Cu2+. Here we report the basis for this self-association at atomic resolution. Metal is not a direct participant in the molecular interface. Rather, binding results in distal alterations enabling the formation of two new surfaces. These interact to form a closed hexameric species. The origins of this include isomerization of a buried and conserved cis-proline previously implicated in the beta2m aggregation pathway. The consequences of this isomerization are evident and reveal a molecular basis for the conversion of this robust monomeric protein into an amyloid-competent state.
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22
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Abstract
Beta-2 microglobulin (beta2m) is the protein responsible for amyloid deposition in Dialysis-Related Amyloidosis (DRA). Aggregation can be induced by various solution conditions including exposure to divalent metal, incubation at acidic pH, and limited proteolysis. Using Cu(2+) as a trigger, we have trapped, isolated, and crystallized a stable oligomer of beta2m that is populated under amyloidogenic solution conditions (Calabrese et al. Nat Struct Mol Biol 2008; 15:965-71). This structure reveals that Cu(2+)-binding is associated with dramatic conformational rearrangements. This has allowed us to postulate a set of structural changes common to all beta2m aggregation pathways. Cu(2+) serves as a potential trigger in other aggregation systems such as Abeta, alpha-synuclein, and mammalian Prion (PrP). A comparison of Cu(2+) binding to beta2m and PrP reveals common features. Therefore, in addition to providing insight into DRA, induction of structure by Cu(2+) binding appears to be a recurring structural motif for pathological changes in conformation.
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Affiliation(s)
- Matthew F Calabrese
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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23
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Abstract
beta(2)-microglobulin (beta(2)m) is capable of forming amyloid in osteoarticular structures in kidney failure patients that undergo chronic hemodialysis treatment. Although sophisticated analytical methods have yielded comprehensive data about the conformation of the native protein both as a monomer and as the light chain of the type I major histocompatibility complex, the cause and mechanisms leading to the transformation of beta(2)m into amyloid deposits in patients with dialysis-related amyloidosis are unsettled. The impact on conformational stability of various truncations, cleavages, amino acid substitutions, and divalent cations, especially Cu(2+), however, are highly relevant for understanding beta(2)m unfolding pathways leading to amyloid formation. This review describes the current knowledge about such conformationally destabilizing and amyloidogenic factors and links these to the structure and function of beta(2)m in normal physiology and pathology. Tables listing modifications of beta(2)m found in amyloid from patients and a systematic overview of laboratory conditions conducive to beta(2)m-fibrillogenesis are also included.
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24
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Srikanth R, Wilson J, Burns CS, Vachet RW. Identification of the copper(II) coordinating residues in the prion protein by metal-catalyzed oxidation mass spectrometry: evidence for multiple isomers at low copper(II) loadings. Biochemistry 2008; 47:9258-68. [PMID: 18690704 DOI: 10.1021/bi800970m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the Cu(II) binding sites of the prion protein have been well studied under Cu-saturation conditions, the identity of the residues involved in coordinating Cu(II) at low stoichiometries and the order in which the binding sites load with Cu(II) remain unresolved. In this study, we have used two mass spectrometry based methods to gather insight into Cu(II)-prion binding under different stoichiometric loadings of Cu(II). The first method uses metal-catalyzed oxidation reactions to site specifically modify the residues bound to Cu(II) in solution, and the second method determines Cu binding sites based on the protection of His from modification by diethyl pyrocarbonate when this residue binds Cu(II) in solution. For both methods, the residues that are labeled by these reactions can then be unambiguously identified using tandem mass spectrometry. Upon applying these two complementary methods to a construct of the prion protein that contains residues 23-28 and 57-98, several noteworthy observations are made. Coordination of Cu(II) by multiple His imidazoles is found at 1:1 and 1:2 PrP:Cu(II) ratios. Notably, there appear to be four to seven isomers of this multiple histidine coordination mode in the 1:1 complex. Furthermore, our data clearly show that His96 is the dominant Cu(II) binding ligand, as in every isomer His96 is bound to Cu(II). The individual octarepeat binding sites begin to fill at ratios of 1:3 PrP:Cu(II) with no clear preference for the order in which they load with Cu(II), although the His77 octarepeat appears to saturate last. The existence of several "degenerate" Cu binding modes at low PrP:Cu(II) ratios may allow it to more readily accept additional Cu(II) ions, thus allowing PrP to transition from a singly Cu(II) bound state to a multiply Cu(II) bound state as a function of cellular Cu(II) concentration.
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Affiliation(s)
- Rapole Srikanth
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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25
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De Lorenzi E, Colombo R, Sabella S, Corlin DB, Heegaard NHH. The influence of Cu2+ on the unfolding and refolding of intact and proteolytically processed β2-microglobulin. Electrophoresis 2008; 29:1734-40. [DOI: 10.1002/elps.200700506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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26
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Mendoza VL, Vachet RW. Protein surface mapping using diethylpyrocarbonate with mass spectrometric detection. Anal Chem 2008; 80:2895-904. [PMID: 18338903 DOI: 10.1021/ac701999b] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reliability and information content of diethylpyrocarbonate (DEPC) as a covalent probe of protein surface structure has been improved when used appropriately with mass spectrometric detection. Using myoglobin, cytochrome c, and beta-2-microglobulin as model protein systems, we demonstrate for the first time that DEPC can modify Ser and Thr residues in addition to His and Tyr residues. This result expands the capability of DEPC as a structural probe because about 25% of the sequence of the average protein can now be covered using this covalent labeling reagent. In addition, we establish a new approach based on mass spectrometry to ensure the structural integrity of proteins during amino acid-specific covalent labeling reactions. This approach involves monitoring the extent of modification as a function of reagent concentration and allows any small-scale or local perturbations caused by the covalent label to be readily identified and avoided. Results indicate that these dose-response plots are much more reliable and generally applicable probes of possible protein structural changes than fluorescence or circular dichroism spectroscopies. These dose-response plots also provide a means of quantitatively comparing the reactivity of each modified residue. On the basis of comparisons to known X-ray crystal structures, we find that the solvent accessibility of the reactive atom in the side chain and the presence of a nearby charged residue most affect modification rates. Finally, this improved surface mapping method has been used to determine the effect of Cu(II) binding on the structure of beta-2-microglobulin. Results confirm that Cu(II) binds His31, but not any of the other three His residues, and changes the solvent accessibility of residues near His31 and near the N-terminus.
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Affiliation(s)
- Vanessa Leah Mendoza
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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27
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Antwi K, Mahar M, Srikanth R, Olbris MR, Tyson JF, Vachet RW. Cu(II) organizes beta-2-microglobulin oligomers but is released upon amyloid formation. Protein Sci 2008; 17:748-59. [PMID: 18305198 DOI: 10.1110/ps.073249008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
beta-2-Microglobulin (beta2m) is deposited as amyloid fibrils in the bones and joints of patients undergoing long-term dialysis treatment as a result of kidney failure. Previous work has shown that biologically relevant amounts of Cu(II) can cause beta2m to be converted to amyloid fibrils under physiological conditions in vitro. In this work, dynamic light scattering, mass spectrometry, and size-exclusion chromatography are used to characterize the role that Cu plays in the formation of oligomeric intermediates that precede fibril formation. Cu(II) is found to be necessary for the stability of the dimer and an initial form of the tetramer. The initially formed tetramer then undergoes a structural change to a state that no longer binds Cu(II) before progressing to a hexameric state. Based on these results, we propose that the lag phase associated with beta2m fibril formation is partially accounted for by the structural transition of the tetramer that results in Cu(II) loss. Consistent with this observation is the determination that the mature beta2m amyloid fibrils do not contain Cu. Thus, Cu(II) appears to play a catalytic role by enabling the organization of the necessary oligomeric intermediates that precede beta2m amyloid formation.
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Affiliation(s)
- Kwasi Antwi
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
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28
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Xu G, Chance MR. Hydroxyl Radical-Mediated Modification of Proteins as Probes for Structural Proteomics. Chem Rev 2007; 107:3514-43. [PMID: 17683160 DOI: 10.1021/cr0682047] [Citation(s) in RCA: 513] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guozhong Xu
- Center for Proteomics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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29
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Srikanth R, Wilson J, Bridgewater JD, Numbers JR, Lim J, Olbris MR, Kettani A, Vachet RW. Improved sequencing of oxidized cysteine and methionine containing peptides using electron transfer dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1499-506. [PMID: 17583533 DOI: 10.1016/j.jasms.2007.05.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 05/14/2007] [Accepted: 05/14/2007] [Indexed: 05/15/2023]
Abstract
Oxidative modifications to the side chains of sulfur-containing amino acids often limit the number of product ions formed during collision-induced dissociation (CID) and thus make it difficult to obtain sequence information for oxidized peptides. In this work, we demonstrate that electron-transfer dissociation (ETD) can be used to improve the sequence information obtained from peptides with oxidized cysteine and methionine residues. In contrast to CID, ETD is found to be much less sensitive to the side-chain chemistry, enabling extensive sequence information to be obtained in cases where CID fails to provide this information. These results indicate that ETD is a valuable technique for studying oxidatively modified peptides and proteins. In addition, we report a unique and very abundant product ion that is formed in the CID spectra of peptides having N-terminal cysteine sulfinic acid residues. The mechanism for this unique dissociation pathway involves a six-membered cyclic intermediate and leads to the facile loss of NH(3) and SO(2), which corresponds to a mass loss of 81 Da. While the facile nature of this dissociation pathway limits the sequence information present in CID spectra of peptides with N-terminal cysteine sulfinic acid residues, extensive sequence information for these peptides can be obtained with ETD.
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Affiliation(s)
- R Srikanth
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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30
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Bridgewater JD, Srikanth R, Lim J, Vachet RW. The effect of histidine oxidation on the dissociation patterns of peptide ions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:553-62. [PMID: 17157528 PMCID: PMC1839887 DOI: 10.1016/j.jasms.2006.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 10/31/2006] [Accepted: 11/01/2006] [Indexed: 05/12/2023]
Abstract
Oxidative modifications to amino acid side chains can change the dissociation pathways of peptide ions, although these variations are most commonly observed when cysteine and methionine residues are oxidized. In this work we describe the very noticeable effect that oxidation of histidine residues can have on the dissociation patterns of peptide ions containing this residue. A common product ion spectral feature of doubly charged tryptic peptides is enhanced cleavage at the C-terminal side of histidine residues. This preferential cleavage arises as a result of the unique acid/base character of the imidazole side chain that initiates cleavage of a proximal peptide bond for ions in which the number of protons does not exceed the number of basic residues. We demonstrate here that this enhanced cleavage is eliminated when histidine is oxidized to 2-oxo-histidine because the proton affinity and nucleophilicity of the imidazole side chain are lowered. Furthermore, we find that oxidation of histidine to 2-oxo-histidine can cause the misassignment of oxidized residues when more than one oxidized isomer is simultaneously subjected to tandem mass spectrometry (MS/MS). These spectral misinterpretations can usually be avoided by using multiple stages of MS/MS (MS(n)) or by specially optimized liquid chromatographic separation conditions. When these approaches are not accessible or do not work, N-terminal derivatization with sulfobenzoic acid avoids the problem of mistakenly assigning oxidized residues.
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Affiliation(s)
| | | | | | - Richard W. Vachet
- *Corresponding author: Department of Chemistry, Lederle GRT 701, 710 N. Pleasant St., University of Massachusetts, Amherst, MA 01003, , Phone: 413-545-2733, Fax: 413-545-4490
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31
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Bridgewater JD, Lim J, Vachet RW. Using metal-catalyzed oxidation reactions and mass spectrometry to identify amino acid residues within 10 A of the metal in Cu-binding proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1552-9. [PMID: 16872838 DOI: 10.1016/j.jasms.2006.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2006] [Revised: 06/07/2006] [Accepted: 06/08/2006] [Indexed: 05/11/2023]
Abstract
Metal-catalyzed oxidation (MCO) reactions and mass spectrometry (MS) can be used together to determine the amino acids bound to Cu in a metalloprotein. Selective oxidation of only amino acids bound to Cu during the MCO/MS approach relies on proper choice of the types and concentrations of the reducing and oxidizing agents. We show here that if these MCO reagent concentrations are "detuned" or varied slightly from optimal conditions, nonmetal-bound amino acids close to Cu can also be oxidized in a controlled manner. Using Cu/Zn superoxide dismutase as a model system, we demonstrate that amino acids up to 10 A from Cu can be modified as long as they are readily accessible to diffusing reactive oxygen species. UV/VIS spectroscopy and measurements of oxidation kinetics provide evidence that the protein's structural integrity around Cu is maintained during the detuned MCO reactions. Because this method can identify amino acids around Cu that have low solvent accessibility, it should complement other radical-based protein surface-mapping techniques.
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Affiliation(s)
- Juma D Bridgewater
- Department of Chemistry, University of Massachusetts, Amherst, Massachusetts 01003, USA
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32
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Temple A, Yen TY, Gronert S. Identification of specific protein carbonylation sites in model oxidations of human serum albumin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1172-80. [PMID: 16750385 DOI: 10.1016/j.jasms.2006.04.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2006] [Revised: 04/10/2006] [Accepted: 04/10/2006] [Indexed: 05/10/2023]
Abstract
Human serum albumin (HSA) was subjected to oxidative stress and the locations of the resulting protein carbonyls were determined using mass spectrometry in conjunction with a hydrazide labeling scheme. To model oxidative stress, HSA samples were subjected to metal-catalyzed oxidation (MCO) conditions or treated with hypochlorous acid (HOCl). Oxidation led to the conversion of lysine residues to 2-aminoadipic semi-aldehyde residues, which were subsequently labeled with biotin hydrazide. Analysis of the tryptic peptides from the samples indicates that the oxidations are highly selective. Under MCO conditions, only two of the 59 lysine residues appeared to be modified (Lys-97 and Lys-186). With HOCl, five different lysine modification sites were identified (Lys-130, Lys-257, Lys-438, Lys-499, and Lys-598). These results strongly suggest that the preferred site of modification is dependent on the nature of the oxidant and that the process relies on specific structural motifs in the protein to direct the oxidation. The high selectivity seen here provides insights into the factors that in vivo drive the selective carbonylation of specific proteins in systems under oxidative stress.
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Affiliation(s)
- Ani Temple
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
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33
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Takamoto K, Chance MR. RADIOLYTIC PROTEIN FOOTPRINTING WITH MASS SPECTROMETRY TO PROBE THE STRUCTURE OF MACROMOLECULAR COMPLEXES. ACTA ACUST UNITED AC 2006; 35:251-76. [PMID: 16689636 DOI: 10.1146/annurev.biophys.35.040405.102050] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Structural proteomics approaches using mass spectrometry are increasingly used in biology to examine the composition and structure of macromolecules. Hydroxyl radical-mediated protein footprinting using mass spectrometry has recently been developed to define structure, assembly, and conformational changes of macromolecules in solution based on measurements of reactivity of amino acid side chain groups with covalent modification reagents. Accurate measurements of side chain reactivity are achieved using quantitative liquid-chromatography-coupled mass spectrometry, whereas the side chain modification sites are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunction with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes. In this review, we discuss the basic chemistry of hydroxyl radical reactions with peptides and proteins, highlight various approaches to map protein structure using radical oxidation methods, and describe state-of-the-art approaches to combine computational and footprinting data.
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Affiliation(s)
- Keiji Takamoto
- Case Center for Proteomics, Case Western Reserve University, Cleveland, Ohio 44106, USA
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34
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Inoue K, Garner C, Ackermann BL, Oe T, Blair IA. Liquid chromatography/tandem mass spectrometry characterization of oxidized amyloid beta peptides as potential biomarkers of Alzheimer's disease. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2006; 20:911-8. [PMID: 16470704 DOI: 10.1002/rcm.2395] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Alzheimer's disease is characterized by the deposition of senile plaques that consist primarily of amyloid beta peptides. There is substantial evidence that amyloid beta is oxidized in vivo, which has led to the suggestion that oxidative stress is an important mediator of Alzheimer's disease. Metal-catalyzed oxidation can mimic in vivo oxidation of amyloid beta because the metal ion binds to the amino acid residues at the site of oxidation, which then deliver reactive oxygen species to that site. Based on electrospray mass spectrometry, it has been suggested that metal-catalyzed oxidation occurs on histidines-13 and -14. Unfortunately, the amyloid beta peptides provide complex spectra, so it is difficult to definitively characterize the sites of oxidation. Trypsin digestion of both native and oxidized amyloid beta1-16 and amyloid beta1-40 resulted in the formation of tryptic peptides corresponding to amyloid beta6-16, which could be separated by liquid chromatography (LC). Sites of oxidation were then unequivocally characterized as histidine-13 and histidine-14 by LC/tandem mass spectrometric (MS/MS) analysis of the tryptic peptides. The ability to analyze the specific amyloid beta6-16 tryptic fragments derived from full-length amyloid beta peptides will make it possible to determine whether oxidation in vivo occurs at specific histidine residues and/or at other amino acid residues such as methionine-35. Using methodology based on LC/MS/MS it will also be possible to analyze the relative amounts of oxidized peptides and native peptide in cerebrospinal fluid from patients with Alzheimer's disease as biomarkers of oxidative stress.
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Affiliation(s)
- Koichi Inoue
- Center for Cancer Pharmacology, University of Pennsylvania School of Medicine, 854 BRB II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6160, USA
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35
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Guan JQ, Chance MR. Structural proteomics of macromolecular assemblies using oxidative footprinting and mass spectrometry. Trends Biochem Sci 2005; 30:583-92. [PMID: 16126388 DOI: 10.1016/j.tibs.2005.08.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 07/14/2005] [Accepted: 08/16/2005] [Indexed: 11/20/2022]
Abstract
Understanding the composition, structure and dynamics of macromolecules and their assemblies is at the forefront of biological science today. Hydroxyl-radical-mediated protein footprinting using mass spectrometry can define macromolecular structure, macromolecular assembly and conformational changes of macromolecules in solution based on measurements of reactivity of amino acid side-chain groups with covalent-modification reagents. Subsequent to oxidation by reactive oxygen species, proteins are digested by specific proteases to generate peptides for analysis by mass spectrometry. Accurate measurements of side-chain reactivity are achieved using quantitative liquid-chromatography-coupled mass spectrometry, whereas the side-chain sites within the macromolecular probes are identified using tandem mass spectrometry. In addition, the use of footprinting data in conjunction with computational modeling approaches is a powerful new method for testing and refining structural models of macromolecules and their complexes.
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Affiliation(s)
- Jing-Qu Guan
- Case Center for Proteomics and Mass Spectrometry, 930 BRB, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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36
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Heegaard NHH, De Lorenzi E. Interactions of charged ligands with β2-microglobulin conformers in affinity capillary electrophoresis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1753:131-40. [PMID: 16112627 DOI: 10.1016/j.bbapap.2005.07.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Revised: 07/08/2005] [Accepted: 07/12/2005] [Indexed: 10/25/2022]
Abstract
Alternative conformations of beta(2)-microglobulin (beta(2)m) are involved in its transformation from soluble monomeric precursor molecules to the insoluble polymeric material that constitutes beta(2)m amyloid. Accordingly, non-native conditions such as low pH or high ionic strength promote beta(2)m amyloid formation in vitro. The early events in these processes are not well known, partly because of the paucity of techniques available for the characterization of transient folding intermediates in proteins. We have used high-resolution separations in capillaries (capillary electrophoresis, CE) to resolve putative conformer fractions in native and structurally modified beta(2)m and to show the induction of alternatively folded beta(2)m under different experimental conditions. The conformer fractions are observed as distinct peaks in the separation profiles and thus it is possible to probe for the reactivity of these individual beta(2)m species with specific ligands that, upon binding, alter analyte mobility in affinity capillary electrophoresis experiments. Interactions were shown in this way for the negatively charged substances heparin, Congo red, and suramin, as well as for Cu(2+) ions. Marked differences in the binding behavior of the beta(2)m conformational variants compared with native beta(2)m could be demonstrated. This approach for conformer separation and binding characterization is a valuable starting point for the assessment of various ligand molecules, or analogues thereof, as agents capable of perturbing the mechanisms of fibril formation.
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Affiliation(s)
- Niels H H Heegaard
- Department of Autoimmunology, Statens Serum Institute, Bldg. 81, Rm. 536, Artillerivej 5, DK-2300 Copenhagen S, Denmark.
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Bridgewater JD, Vachet RW. Metal-catalyzed oxidation reactions and mass spectrometry: The roles of ascorbate and different oxidizing agents in determining Cu–protein-binding sites. Anal Biochem 2005; 341:122-30. [PMID: 15866536 DOI: 10.1016/j.ab.2005.02.034] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2005] [Indexed: 11/26/2022]
Abstract
Further study has been made of metal-catalyzed oxidation (MCO) reactions and mass spectrometry as a method to determine the binding site of copper in metalloproteins. The role of ascorbate and a variety of oxidizing agents, including O2, H2O2, and S2O8(2-), have been investigated using Cu/Zn superoxide dismutase (SOD) as a model system. Ascorbate is found to play two competing roles in the MCO reactions. It reduces Cu(II), which initiates and maintains the generation of reactive oxygen species, and it scavenges radicals, which helps to localize oxidation products to amino acids near the metal center. An ascorbate concentration of 100 mM is found to be optimal with regard to localizing oxidation products to only the Cu-binding residues (His44, His46, His61, and His118) of Cu/Zn SOD. This concentration of ascorbate is very similar to the optimum concentration found in our previous studies of different Cu-binding proteins. Another notable result from this study is the observation that S2O8(2-) is more effective as an oxidant than O2 or H2O2 in the MCO reactions. Because S2O8(2-) is more stable in solution than H2O2, using it as an oxidizing agent results in much less nonspecific oxidation to the protein. The overall results of this study suggest that general MCO reaction conditions may exist for determining the metal-binding site of a wide range of Cu-binding proteins.
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Affiliation(s)
- Juma D Bridgewater
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
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