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Maurer J, Grouzmann E, Eugster PJ. Tutorial review for peptide assays: An ounce of pre-analytics is worth a pound of cure. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1229:123904. [PMID: 37832388 DOI: 10.1016/j.jchromb.2023.123904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
The recent increase in peptidomimetic-based medications and the growing interest in peptide hormones has brought new attention to the quantification of peptides for diagnostic purposes. Indeed, the circulating concentrations of peptide hormones in the blood provide a snapshot of the state of the body and could eventually lead to detecting a particular health condition. Although extremely useful, the quantification of such molecules, preferably by liquid chromatography coupled to mass spectrometry, might be quite tricky. First, peptides are subjected to hydrolysis, oxidation, and other post-translational modifications, and, most importantly, they are substrates of specific and nonspecific proteases in biological matrixes. All these events might continue after sampling, changing the peptide hormone concentrations. Second, because they include positively and negatively charged groups and hydrophilic and hydrophobic residues, they interact with their environment; these interactions might lead to a local change in the measured concentrations. A phenomenon such as nonspecific adsorption to lab glassware or materials has often a tremendous effect on the concentration and needs to be controlled with particular care. Finally, the circulating levels of peptides might be low (pico- or femtomolar range), increasing the impact of the aforementioned effects and inducing the need for highly sensitive instruments and well-optimized methods. Thus, despite the extreme diversity of these peptides and their matrixes, there is a common challenge for all the assays: the need to keep concentrations unchanged from sampling to analysis. While significant efforts are often placed on optimizing the analysis, few studies consider in depth the impact of pre-analytical steps on the results. By working through practical examples, this solution-oriented tutorial review addresses typical pre-analytical challenges encountered during the development of a peptide assay from the standpoint of a clinical laboratory. We provide tips and tricks to avoid pitfalls as well as strategies to guide all new developments. Our ultimate goal is to increase pre-analytical awareness to ensure that newly developed peptide assays produce robust and accurate results.
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Affiliation(s)
- Jonathan Maurer
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Eric Grouzmann
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Philippe J Eugster
- Service of Clinical Pharmacology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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2
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Lloyd-Jones C, Dos Santos Seckler H, DiStefano N, Sniderman A, Compton PD, Kelleher NL, Wilkins JT. Preparative Electrophoresis for HDL Particle Size Separation and Intact-Mass Apolipoprotein Proteoform Analysis. J Proteome Res 2023; 22:1455-1465. [PMID: 37053489 PMCID: PMC10436667 DOI: 10.1021/acs.jproteome.2c00804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The most abundant proteins on high-density lipoproteins (HDLs), apolipoproteins A-I (APOA1) and A-II (APOA2), are determinants of HDL function with 15 and 9 proteoforms (chemical-structure variants), respectively. The relative abundance of these proteoforms in human serum is associated with HDL cholesterol efflux capacity, and cholesterol content. However, the association between proteoform concentrations and HDL size is unknown. We employed a novel native-gel electrophoresis technique, clear native gel-eluted liquid fraction entrapment electrophoresis (CN-GELFrEE) paired with mass spectrometry of intact proteins to investigate this association. Pooled serum was fractionated using acrylamide gels of lengths 8 and 25 cm. Western blotting determined molecular diameter and intact-mass spectrometry determined proteoform profiles of each fraction. The 8- and 25 cm experiments generated 19 and 36 differently sized HDL fractions, respectively. The proteoform distribution varied across size. Fatty-acylated APOA1 proteoforms were associated with larger HDL sizes (Pearson's R = 0.94, p = 4 × 10-7) and were approximately four times more abundant in particles larger than 9.6 nm than in total serum; HDL-unbound APOA1 was acylation-free and contained the pro-peptide proAPOA1. APOA2 proteoform abundance was similar across HDL sizes. Our results establish CN-GELFrEE as an effective lipid-particle separation technique and suggest that acylated proteoforms of APOA1 are associated with larger HDL particles.
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Affiliation(s)
- Cameron Lloyd-Jones
- Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Henrique Dos Santos Seckler
- Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Nicholas DiStefano
- Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Allan Sniderman
- Royal Victoria Hospital-McGill University Health Centre, Montreal, Quebec H3A 1W9, Canada
| | - Phillip D Compton
- Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Department of Chemistry, Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - John T Wilkins
- Departments of Medicine (Cardiology) and Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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3
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Ozgul M, Nesburn AB, Nasralla N, Katz B, Taylan E, Kuppermann BD, Kenney MC. Stability Determination of Intact Humanin-G with Characterizations of Oxidation and Dimerization Patterns. Biomolecules 2023; 13:biom13030515. [PMID: 36979450 PMCID: PMC10046509 DOI: 10.3390/biom13030515] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/14/2023] Open
Abstract
Humanin is the first identified mitochondrial-derived peptide. Humanin-G (HNG) is a variant of Humanin that has significantly higher cytoprotective properties. Here, we describe the stability features of HNG in different conditions and characterize HNG degradation, oxidation, and dimerization patterns over short-term and long-term periods. HNG solutions were prepared in high-performance liquid chromatography (HPLC) water or MO formulation and stored at either 4 °C or 37 °C. Stored HNG samples were analyzed using HPLC and high-resolution mass spectrometry (HRMS). Using HPLC, full-length HNG peptides in HPLC water decreased significantly with time and higher temperature, while HNG in MO formulation remained stable up to 95% at 4 °C on day 28. HNG peptides in HPLC water, phosphate-buffered saline (PBS) and MO formulation were incubated at 37 °C and analyzed at day 1, day 7 and day 14 using HRMS. Concentrations of full-length HNG peptide in HPLC water and PBS declined over time with a corresponding appearance of new peaks that increased over time. These new peaks were identified to be singly oxidized HNG, doubly oxidized HNG, homodimerized HNG, singly oxidized homodimerized HNG, and doubly oxidized homodimerized HNG. Our results may help researchers improve the experimental design to further understand the critical role of HNG in human diseases.
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Affiliation(s)
- Mustafa Ozgul
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92617, USA
- Correspondence: (M.O.); (M.C.K.)
| | - Anthony B. Nesburn
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92617, USA
- Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | | | - Benjamin Katz
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Enes Taylan
- Department of Obstetrics and Gynecology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Baruch D. Kuppermann
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92617, USA
| | - Maria Cristina Kenney
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA 92617, USA
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA 92617, USA
- Correspondence: (M.O.); (M.C.K.)
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4
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Zhang L, Li Q, Bao Y, Tan Y, Lametsch R, Hong H, Luo Y. Recent advances on characterization of protein oxidation in aquatic products: A comprehensive review. Crit Rev Food Sci Nutr 2022; 64:1572-1591. [PMID: 36122384 DOI: 10.1080/10408398.2022.2117788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In addition to microbial spoilage and lipid peroxidation, protein oxidation is increasingly recognized as a major cause for quality deterioration of muscle-based foods. Although protein oxidation in muscle-based foods has attracted tremendous interest in the past decade, specific oxidative pathways and underlying mechanisms of protein oxidation in aquatic products remain largely unexplored. The present review covers the aspects of the origin and site-specific nature of protein oxidation, progress on the characterization of protein oxidation, oxidized proteins in aquatic products, and impact of protein oxidation on protein functionalities. Compared to meat protein oxidation, aquatic proteins demonstrate a less extent of oxidation on aromatic amino acids and are more susceptible to be indirectly oxidized by lipid peroxidation products. Different from traditional measurement of protein carbonyls and thiols, proteomics-based strategy better characterizes the targeted oxidation sites within proteins. The future trends using more robust and accurate targeted proteomics, such as parallel reaction monitoring strategy, to characterize protein oxidation in aquatic products are also given.
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Affiliation(s)
- Longteng Zhang
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Qian Li
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Yulong Bao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Yuqing Tan
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - René Lametsch
- Department of Food Science, University of Copenhagen, Frederiksberg C, Denmark
| | - Hui Hong
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yongkang Luo
- Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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5
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Wang H, Wu F, Xu F, Liu Y, Ding CF. Identification of Bi-2-naphthol and Its Phosphate Derivatives Complexed with Cyclodextrin and Metal Ions Using Trapped Ion Mobility Spectrometry. Anal Chem 2021; 93:15096-15104. [PMID: 34726389 DOI: 10.1021/acs.analchem.1c03378] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The separation of chiral enantiomers has gained increasing importance in many research fields, becoming a major research hotspot. 1,1'-Bi (2-naphthol) (BINOL) and 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate (BNP) are referred to as atropisomer chiral molecules, which are essential chiral catalysts and intermediates in several reactions. In this work, BINOL and BNP atropisomers are separated and identified using trapped ion mobility spectrometry (TIMS) to monitor the different mobilities of their derivative complexes. The latter are obtained by the simple mixing of BINOL/BNP, cyclodextrin (CD), and the metal ions through noncovalent interactions. The results indicate that the enantiomer complexes of BINOL/BNP can be separated with a certain specificity, showing that R-, S-BINOL can be separated by the ternary complexes of [BINOL+γ-CD + Rb]+, [BINOL+γ-CD + Cu-H]+, and [BINOL+β-CD + Cu-H]+ based on the difference in their mobility; similarly, the R-, S-BNP enantiomer can be isolated by the formed ternary complexes of [BNP+α-CD + Ba-H]+, [BNP+β-CD + Co-H]+, [BNP+β-CD + Ca-H]+, [BNP+β-CD + Cu-H]+, [BNP+β-CD + Fe-H]+, [BNP+β-CD + Li]+, and [BNP+β-CD + Sr-H]+. Furthermore, the peak separation rate (Rp-p) of the complexes was calculated, with the Rp-p of the three enantiomers of BINOL being 1.130 and the Rp-p of the seven complexes of BNP reaching 2.089. At last, the different survival yields for the collision energies were found for the enantiomer complexes, revealing the rigid structural differences in the stereospecificity of the enantiomer complexes that result in the separation by the TIMS. Additionally, due to the advantages of simple operation, fast speed, and high sensitivity and because chemical derivatization and chromatographic separation are not required, the developed method can provide a promising and powerful strategy for the separation and identification of binaphthyl derivatives or even other enantiomers of the reaction intermediates.
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Affiliation(s)
- Huanhuan Wang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211 Zhejiang, P. R. China
| | - Fangling Wu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211 Zhejiang, P. R. China
| | - Fuxing Xu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211 Zhejiang, P. R. China
| | - Yiyi Liu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211 Zhejiang, P. R. China
| | - Chuan-Fan Ding
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo 315211 Zhejiang, P. R. China
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6
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Carman PJ, Barrie KR, Dominguez R. Novel human cell expression method reveals the role and prevalence of posttranslational modification in nonmuscle tropomyosins. J Biol Chem 2021; 297:101154. [PMID: 34478714 PMCID: PMC8463859 DOI: 10.1016/j.jbc.2021.101154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/29/2022] Open
Abstract
Biochemical studies require large quantities of proteins, which are typically obtained using bacterial overexpression. However, the folding machinery in bacteria is inadequate for expressing many mammalian proteins, which additionally undergo posttranslational modifications (PTMs) that bacteria, yeast, or insect cells cannot perform. Many proteins also require native N- and C-termini and cannot tolerate extra tag amino acids for proper function. Tropomyosin (Tpm), a coiled coil protein that decorates most actin filaments in cells, requires both native N- and C-termini and PTMs, specifically N-terminal acetylation (Nt-acetylation), to polymerize along actin filaments. Here, we describe a new method that combines native protein expression in human cells with an intein-based purification tag that can be precisely removed after purification. Using this method, we expressed several nonmuscle Tpm isoforms (Tpm1.6, Tpm1.7, Tpm2.1, Tpm3.1, Tpm3.2, and Tpm4.2) and the muscle isoform Tpm1.1. Proteomics analysis revealed that human-cell-expressed Tpms present various PTMs, including Nt-acetylation, Ser/Thr phosphorylation, Tyr phosphorylation, and Lys acetylation. Depending on the Tpm isoform (humans express up to 40 Tpm isoforms), Nt-acetylation occurs on either the initiator methionine or on the second residue after removal of the initiator methionine. Human-cell-expressed Tpms bind F-actin differently than their Escherichia coli-expressed counterparts, with or without N-terminal extensions intended to mimic Nt-acetylation, and they can form heterodimers in cells and in vitro. The expression method described here reveals previously unknown features of nonmuscle Tpms and can be used in future structural and biochemical studies with Tpms and other proteins, as shown here for α-synuclein.
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Affiliation(s)
- Peter J Carman
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle R Barrie
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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7
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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8
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Enhancement of hydrogen peroxide tolerance of lipase LipA from Bacillus subtilis using semi-rational design. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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9
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Welch NG, Mukherjee S, Hossain MA, Praveen P, Werkmeister JA, Wade JD, Bathgate RAD, Winkler DA, Thissen H. Coatings Releasing the Relaxin Peptide Analogue B7-33 Reduce Fibrotic Encapsulation. ACS APPLIED MATERIALS & INTERFACES 2019; 11:45511-45519. [PMID: 31713411 DOI: 10.1021/acsami.9b17859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The development of antifibrotic materials and coatings that can resist the foreign body response (FBR) continues to present a major hurdle in the advancement of current and next-generation implantable medical devices, biosensors, and cell therapies. From an implant perspective, the most important issue associated with the FBR is the prolonged inflammatory response leading to a collagenous capsule that ultimately blocks mass transport and communication between the implant and the surrounding tissue. Up to now, most attempts to reduce the capsule thickness have focused on providing surface coatings that reduce protein fouling and cell attachment. Here, we present an approach that is based on the sustained release of a peptide drug interfering with the FBR. In this study, the biodegradable polymer poly(lactic-co-glycolic) acid (PLGA) was used as a coating releasing the relaxin peptide analogue B7-33, which has been demonstrated to reduce organ fibrosis in animal models. While in vitro protein quantification was used to demonstrate controlled release of the antifibrotic peptide B7-33 from PLGA coatings, an in vitro reporter cell assay was used to demonstrate that B7-33 retains activity against the relaxin family peptide receptor 1 (RXFP1). Subcutaneous implantation of PLGA-coated polypropylene samples in mice with and without the peptide demonstrated a marked reduction in capsule thickness (49.2%) over a 6 week period. It is expected that this novel approach will open the door to a range of new and improved implantable medical devices.
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Affiliation(s)
- Nicholas G Welch
- CSIRO Manufacturing , Research Way , Clayton , VIC 3168 , Australia
| | - Shayanti Mukherjee
- The Ritchie Centre , Hudson Institute of Medical Research , Clayton , VIC 3168 , Australia
| | - Mohammed A Hossain
- The Florey Institute of Neuroscience and Mental Health , Parkville , VIC 3052 , Australia
| | - Praveen Praveen
- The Florey Institute of Neuroscience and Mental Health , Parkville , VIC 3052 , Australia
| | - Jerome A Werkmeister
- The Ritchie Centre , Hudson Institute of Medical Research , Clayton , VIC 3168 , Australia
| | - John D Wade
- The Florey Institute of Neuroscience and Mental Health , Parkville , VIC 3052 , Australia
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health , Parkville , VIC 3052 , Australia
| | - David A Winkler
- CSIRO Manufacturing , Research Way , Clayton , VIC 3168 , Australia
- La Trobe Institute for Molecular Science , La Trobe University , Kingsbury Drive , Bundoora , VIC 3083 , Australia
- Monash Institute of Pharmaceutical Sciences , Royal Parade , Parkville , VIC 3052 , Australia
- School of Pharmacy , The University of Nottingham , Nottingham NG7 2RD , U.K
| | - Helmut Thissen
- CSIRO Manufacturing , Research Way , Clayton , VIC 3168 , Australia
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10
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Bikaki M, Kuhnert N. Identification of Products from Thermal Degradation of Tryptophan Containing Pentapeptides: Oxidation and Decarboxylation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:7448-7454. [PMID: 31244194 DOI: 10.1021/acs.jafc.9b01056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this contribution, we investigate the thermal decomposition of four pentapeptides containing a tryptophan moiety. Pentapeptides were heated at 220 °C, and the resulting reaction mixtures were investigated by HPLC coupled to high-resolution mass spectrometry and tandem mass spectrometry. A total of 95 thermal decomposition products could be observed and resolved by chromatography. In detail, we report on the structure assignment of two types of reaction products common to investigated peptides and introduce two decomposition mechanisms. Pentapeptides react with oxygen to produce hydroxyl-tryptophan derivatives. In addition, we observe the C-terminal decarboxylation of two peptides to form N-acyl tryptamine derivatives.
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Affiliation(s)
- Maria Bikaki
- Department of Life Sciences & Chemistry , Jacobs University Bremen , Campus Ring 1 , 28759 Bremen , Germany
| | - Nikolai Kuhnert
- Department of Life Sciences & Chemistry , Jacobs University Bremen , Campus Ring 1 , 28759 Bremen , Germany
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11
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Differences in peptide oxidation between muscles in 12 months Spanish dry-cured ham. Food Res Int 2018; 109:343-349. [DOI: 10.1016/j.foodres.2018.04.045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 11/24/2022]
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12
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dos Santos Seckler H, Fornelli L, Mutharasan RK, Thaxton CS, Fellers R, Daviglus M, Sniderman A, Rader D, Kelleher NL, Lloyd-Jones DM, Compton PD, Wilkins JT. A Targeted, Differential Top-Down Proteomic Methodology for Comparison of ApoA-I Proteoforms in Individuals with High and Low HDL Efflux Capacity. J Proteome Res 2018; 17:2156-2164. [PMID: 29649363 PMCID: PMC6162093 DOI: 10.1021/acs.jproteome.8b00100] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Top-down proteomics (TDP) allows precise determination/characterization of the different proteoforms derived from the expression of a single gene. In this study, we targeted apolipoprotein A-I (ApoA-I), a mediator of high-density-lipoprotein cholesterol efflux (HDL-E), which is inversely associated with coronary heart disease risk. Absolute ApoA-I concentration and allelic variation only partially explain interindividual HDL-E variation. Therefore, we hypothesize that differences in HDL-E are associated with the abundances of different ApoA-I proteoforms. Here, we present a targeted TDP methodology to characterize ApoA-I proteoforms in serum samples and compare their abundances between individuals. We characterized 18 ApoA-I proteoforms using selected-ion monitoring coupled to electron-transfer dissociation mass spectrometry. We then compared the abundances of these proteoforms between two groups of four participants, representing the individuals with highest and lowest HDL-E values within the Chicago Healthy Aging Study ( n = 420). Six proteoforms showed significantly ( p < 0.0005) higher intensity in high HDL-E individuals: canonical ApoA-I [fold difference (fd) = 1.17], carboxymethylated ApoA-I (fd = 1.24) and, with highest difference, four fatty acylated forms: palmitoylated (fd = 2.16), oleoylated (fd = 2.08), arachidonoylated (fd = 2.31) and one bearing two modifications: palmitoylation and truncation (fd = 2.13). These results demonstrate translational potential for targeted TDP in revealing, with high sensitivity, associations between interindividual proteoform variation and physiological differences underlying disease risk.
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Affiliation(s)
- Henrique dos Santos Seckler
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - R. Kannan Mutharasan
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Chicago, IL, USA; The Department of Medicine (Cardiology), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - C. Shad Thaxton
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- International Institute for Nanotechnology (IIN), Northwestern University, Evanston, IL, USA
- Feinberg School of Medicine, Department of Urology, Northwestern University, Chicago, IL, USA
| | - Ryan Fellers
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
| | - Martha Daviglus
- Northwestern University Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
- University of Illinois at Chicago, Institute for Minority Health Research, Chicago, IL, USA
| | - Allan Sniderman
- Royal Victoria Hospital–McGill University Health Centre, Montreal, QC, Canada
| | - Daniel Rader
- Department of Medicine and Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Neil L. Kelleher
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - Donald M. Lloyd-Jones
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Chicago, IL, USA; The Department of Medicine (Cardiology), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern University Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
| | - Philip D. Compton
- Departments of Chemistry and Molecular Biosciences and the Proteomics Center of Excellence, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
| | - John T. Wilkins
- Bluhm Cardiovascular Institute, Northwestern Memorial Hospital, Chicago, IL, USA; The Department of Medicine (Cardiology), Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Northwestern University Feinberg School of Medicine, Department of Preventive Medicine, Chicago, IL, USA
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13
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Development of an analytical method to assess the occupational health risk of therapeutic monoclonal antibodies using LC-HRMS. Anal Bioanal Chem 2018; 410:2829-2836. [DOI: 10.1007/s00216-018-0966-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/07/2018] [Accepted: 02/14/2018] [Indexed: 01/30/2023]
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14
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Taniguchi A. [Amyloid-selective Photooxygenation toward Treatment for Amyloid Diseases]. YAKUGAKU ZASSHI 2018; 138:47-53. [PMID: 29311465 DOI: 10.1248/yakushi.17-00186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Amyloid proteins and peptides form aggregates which lead to amyloid diseases. For example, Alzheimer's disease-related amyloid β (Aβ) forms oligomers, protofibrils, and amyloid fibrils, which exhibit neurotoxicity. Controlling the aggregation and toxicity of Aβ would be a therapeutic strategy for the treatment of Alzheimer's disease. Recently, we have investigated an artificial oxygenative modification (chemical introduction of oxygen atoms) of amyloid proteins using a photocatalyst, which attenuated the aggregation potency and toxicity of these proteins. The oxygenation of Aβ1-42 was efficiently induced using a riboflavin catalyst (1). The oxygenated Aβ was less aggregative and cytotoxic than native Aβ. The oxygenated Aβ also showed inhibitory activity against aggregation and the onset of toxicity of native Aβ. Flavin catalyst 2, bearing an Aβ-binding peptide, allowed the selective oxygenation of Aβ even in the presence of living cells, due to its Aβ-affinity. Furthermore, "On/Off" switchable photooxygenation catalysts 3 and 4, which can sense a higher-order amyloid structure (i.e., cross-β-sheet structure), were developed based on the amyloid fluorescence probe thioflavin-T. The photo-excited catalysts generated singlet oxygens to induce oxygenation when binding to the amyloid structure ("On"). In contrast, the free catalysts, without binding to the amyloid structure, produced no singlet oxygen, even if photo-excited ("Off"). This "On/Off" switchable function enabled highly Aβ-selective oxygenation. Catalyst 3 was successfully used for the selective oxygenation of other amyloid proteins and peptides. These findings suggest that amyloid-selective oxygenation could provide a versatile system in developing effective new treatments for amyloid diseases.
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Affiliation(s)
- Atsuhiko Taniguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Japan Science and Technology Agency (JST), ERATO, Kanai Life Science Catalysis Project
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15
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Gallego M, Mora L, Toldrá F. Evolution of oxidised peptides during the processing of 9 months Spanish dry-cured ham. Food Chem 2018; 239:823-830. [DOI: 10.1016/j.foodchem.2017.06.159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 06/15/2017] [Accepted: 06/29/2017] [Indexed: 01/25/2023]
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16
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Hedayati MH, Norouzian D, Aminian M, Teimourian S, Ahangari Cohan R, Khorramizadeh MR. Identification of methionine oxidation in human recombinant erythropoietin by mass spectrometry: Comparative isoform distribution and biological activity analysis. Prep Biochem Biotechnol 2017; 47:990-997. [PMID: 28825868 DOI: 10.1080/10826068.2017.1365243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
BACKGROUND Oxidative degradation of human recombinant erythropoietin (hrEPO) may occur in manufacturing process or therapeutic applications. This unfavorable alteration may render EPO inefficient or inactive. We investigated the effect of methionine/54 oxidative changes on the amino acid sequences, glycoform distribution and biological activity of hrEPO. METHODS Mass spectrometry was applied to verify the sequence and determine the methionine oxidation level of hrEPO. Isoform distribution was studied by capillary zone electrophoresis method. In vivo normocythemic mice assay was used to assess the biological activity of three different batches (A, B, and C) of the proteins. RESULTS Nano-LC/ESI/MS/MS data analyses confirmed the amino acid sequences of all samples. The calculated area percent of three isoforms (2-4 of the 8 obtained isoforms) were decreased in samples of C, B, and A with 27.3, 16.7, and 6.8% of oxidation, respectively. Specific activities were estimated as 53671.54, 95826.47, and 112994.93 mg/mL for the samples of A, B, and C, respectively. CONCLUSION The observed decrease in hrEPO biological activity, caused by increasing methionine oxidation levels, was rather independent of its amino acid structure and mainly associated with the higher contents of acidic isoforms.
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Affiliation(s)
- Mohammad Hossein Hedayati
- a Department of Medical Biotechnology, School of Advanced Technologies in Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Dariush Norouzian
- b Department of Pilot Nanobiotechnology , Pasteur Institute of Iran , Tehran , Iran
| | - Mahdi Aminian
- c Department of Clinical Biochemistry, School of Medicine , Tehran University of Medical Sciences , Tehran , Iran
| | - Shahram Teimourian
- d Department of Medical Genetics , Iran University of Medical sciences , Tehran , Iran
| | - Reza Ahangari Cohan
- b Department of Pilot Nanobiotechnology , Pasteur Institute of Iran , Tehran , Iran
| | - M Reza Khorramizadeh
- e Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute , University of Medical Sciences , Tehran , Iran
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17
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Pilo AL, Zhao F, McLuckey SA. Gas-Phase Oxidation via Ion/Ion Reactions: Pathways and Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:991-1004. [PMID: 28050870 PMCID: PMC5438755 DOI: 10.1007/s13361-016-1554-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 10/31/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Here, we provide an overview of pathways available upon the gas-phase oxidation of peptides and DNA via ion/ion reactions and explore potential applications of these chemistries. The oxidation of thioethers (i.e., methionine residues and S-alkyl cysteine residues), disulfide bonds, S-nitrosylated cysteine residues, and DNA to the [M+H+O]+ derivative via ion/ion reactions with periodate and peroxymono-sulfate anions is demonstrated. The oxidation of neutral basic sites to various oxidized structures, including the [M+H+O]+, [M-H]+, and [M-H-NH3]+ species, via ion/ion reactions is illustrated and the oxidation characteristics of two different oxidizing reagents, periodate and persulfate anions, are compared. Lastly, the highly efficient generation of molecular radical cations via ion/ion reactions with sulfate radical anion is summarized. Activation of the newly generated molecular radical peptide cations results in losses of various neutral side chains, several of which generate dehydroalanine residues that can be used to localize the amino acid from which the dehydroalanine was generated. The chemistries presented herein result in a diverse range of structures that can be used for a variety of applications, including the identification and localization of S-alkyl cysteine residues, the oxidative cleavage of disulfide bonds, and the generation of molecular radical cations from even-electron doubly protonated peptides. Graphical Abstract ᅟ.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Feifei Zhao
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
| | - Scott A McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
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18
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Sen KI, Hepler R, Nanda H. Detection and Measurement of Methionine Oxidation in Proteins. ACTA ACUST UNITED AC 2017; 87:14.16.1-14.16.11. [DOI: 10.1002/cpps.25] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Robert Hepler
- Janssen Research & Development LLC, Spring House Pennsylvania
| | - Hirsh Nanda
- Janssen Research & Development LLC, Spring House Pennsylvania
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19
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Kang J, Lee SJC, Nam JS, Lee HJ, Kang MG, Korshavn KJ, Kim HT, Cho J, Ramamoorthy A, Rhee HW, Kwon TH, Lim MH. An Iridium(III) Complex as a Photoactivatable Tool for Oxidation of Amyloidogenic Peptides with Subsequent Modulation of Peptide Aggregation. Chemistry 2017; 23:1645-1653. [PMID: 27862428 DOI: 10.1002/chem.201604751] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 02/03/2023]
Abstract
Aggregates of amyloidogenic peptides are involved in the pathogenesis of several degenerative disorders. Herein, an iridium(III) complex, Ir-1, is reported as a chemical tool for oxidizing amyloidogenic peptides upon photoactivation and subsequently modulating their aggregation pathways. Ir-1 was rationally designed based on multiple characteristics, including 1) photoproperties leading to excitation by low-energy radiation; 2) generation of reactive oxygen species responsible for peptide oxidation upon photoactivation under mild conditions; and 3) relatively easy incorporation of a ligand on the IrIII center for specific interactions with amyloidogenic peptides. Biochemical and biophysical investigations illuminate that the oxidation of representative amyloidogenic peptides (i.e., amyloid-β, α-synuclein, and human islet amyloid polypeptide) is promoted by light-activated Ir-1, which alters the conformations and aggregation pathways of the peptides. Additionally, their potential oxidation sites are identified as methionine, histidine, or tyrosine residues. Overall, our studies on Ir-1 demonstrate the feasibility of devising metal complexes as chemical tools suitable for elucidating the nature of amyloidogenic peptides at the molecular level, as well as controlling their aggregation.
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Affiliation(s)
- Juhye Kang
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Shin Jung C Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jung Seung Nam
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyuck Jin Lee
- School of Life Sciences, UNIST, Ulsan, 44919, Republic of Korea
| | - Myeong-Gyun Kang
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kyle J Korshavn
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hyun-Tak Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jaeheung Cho
- Department of Emerging Materials Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
| | - Ayyalusamy Ramamoorthy
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.,Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hyun-Woo Rhee
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tae-Hyuk Kwon
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Mi Hee Lim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
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20
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Pilo AL, Zhao F, McLuckey SA. Selective Gas-Phase Oxidation and Localization of Alkylated Cysteine Residues in Polypeptide Ions via Ion/Ion Chemistry. J Proteome Res 2016; 15:3139-46. [PMID: 27476698 DOI: 10.1021/acs.jproteome.6b00266] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The thiol group in cysteine residues is susceptible to several post-translational modifications (PTMs), including prenylation, nitrosylation, palmitoylation, and the formation of disulfide bonds. Additionally, cysteine residues involved in disulfide bonds are commonly reduced and alkylated prior to mass spectrometric analysis. Several of these cysteine modifications, specifically S-alkyl modifications, are susceptible to gas-phase oxidation via selective ion/ion reactions with periodate anions. Multiply protonated peptides containing modified cysteine residues undergo complex formation upon ion/ion reaction with periodate anions. Activation of the ion/ion complexes results in oxygen transfer from the reagent to the modified sulfur residue to create a sulfoxide functionality. Further activation of the sulfoxide derivative yields abundant losses of the modification with the oxidized sulfur as a sulfenic acid (namely, XSOH) to generate a dehydroalanine residue. This loss immediately indicates the presence of an S-alkyl cysteine residue, and the mass of the loss can be used to easily deduce the type of modification. An additional step of activation can be used to localize the modification to a specific residue within the peptide. Selective cleavage to create c- and z-ions N-terminal to the dehydroalanine residue is often noted. As these types of ions are not typically observed upon collision-induced dissociation (CID), they can be used to immediately indicate where in the peptide the PTM was originally located.
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Affiliation(s)
- Alice L Pilo
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Feifei Zhao
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Scott A McLuckey
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
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21
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Cerni FA, Pucca MB, Amorim FG, de Castro Figueiredo Bordon K, Echterbille J, Quinton L, De Pauw E, Peigneur S, Tytgat J, Arantes EC. Isolation and characterization of Ts19 Fragment II, a new long-chain potassium channel toxin from Tityus serrulatus venom. Peptides 2016; 80:9-17. [PMID: 26116782 DOI: 10.1016/j.peptides.2015.06.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/05/2015] [Accepted: 06/08/2015] [Indexed: 01/13/2023]
Abstract
Ts19 Fragment II (Ts19 Frag-II) was first isolated from the venom of the scorpion Tityus serrulatus (Ts). It is a protein presenting 49 amino acid residues, three disulfide bridges, Mr 5534Da and was classified as a new member of class (subfamily) 2 of the β-KTxs, the second one described for Ts scorpion. The β-KTx family is composed by two-domain peptides: N-terminal helical domain (NHD), with cytolytic activity, and a C-terminal CSαβ domain (CCD), with Kv blocking activity. The extensive electrophysiological screening (16 Kv channels and 5 Nav channels) showed that Ts19 Frag-II presents a specific and significant blocking effect on Kv1.2 (IC50 value of 544±32nM). However, no cytolytic activity was observed with this toxin. We conclude that the absence of 9 amino acid residues from the N-terminal sequence (compared to Ts19 Frag-I) is responsible for the absence of cytolytic activity. In order to prove this hypothesis, we synthesized the peptide with these 9 amino acid residues, called Ts19 Frag-III. As expected, Ts19 Frag-III showed to be cytolytic and did not block the Kv1.2 channel. The post-translational modifications of Ts19 and its fragments (I-III) are also discussed here. A mechanism of post-translational processing (post-splitting) is suggested to explain Ts19 fragments production. In addition to the discovery of this new toxin, this report provides further evidence for the existence of several compounds in the scorpion venom contributing to the diversity of the venom arsenal.
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Affiliation(s)
- Felipe Augusto Cerni
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Manuela Berto Pucca
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Fernanda Gobbi Amorim
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Karla de Castro Figueiredo Bordon
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil
| | - Julien Echterbille
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, Allée de la chimie 6, B6c, B-4000 Liège, Belgium
| | - Loïc Quinton
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, Allée de la chimie 6, B6c, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liège, Allée de la chimie 6, B6c, B-4000 Liège, Belgium
| | - Steve Peigneur
- Toxicology and Pharmacology, University of Leuven, O&N 2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium
| | - Jan Tytgat
- Toxicology and Pharmacology, University of Leuven, O&N 2, Herestraat 49, P.O. Box 922, 3000 Leuven, Belgium
| | - Eliane Candiani Arantes
- Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, SP, Brazil.
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22
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Design of protease-resistant peptide ligands for the purification of antibodies from human plasma. J Chromatogr A 2016; 1445:93-104. [DOI: 10.1016/j.chroma.2016.03.087] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/24/2016] [Accepted: 03/31/2016] [Indexed: 11/20/2022]
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23
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Rombouts I, Lagrain B, Scherf KA, Koehler P, Delcour JA. Formation and reshuffling of disulfide bonds in bovine serum albumin demonstrated using tandem mass spectrometry with collision-induced and electron-transfer dissociation. Sci Rep 2015; 5:12210. [PMID: 26193081 PMCID: PMC4507448 DOI: 10.1038/srep12210] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 06/18/2015] [Indexed: 12/28/2022] Open
Abstract
Thermolysin hydrolyzates of freshly isolated, extensively stored (6 years, 6 °C, dry) and heated (60 min, 90 °C, in excess water) bovine serum albumin (BSA) samples were analyzed with liquid chromatography (LC) electrospray ionization (ESI) tandem mass spectrometry (MS/MS) using alternating electron-transfer dissociation (ETD) and collision-induced dissociation (CID). The positions of disulfide bonds and free thiol groups in the different samples were compared to those deduced from the crystal structure of native BSA. Results revealed non-enzymatic posttranslational modifications of cysteine during isolation, extensive dry storage, and heating. Heat-induced extractability loss of BSA was linked to the impact of protein unfolding on the involvement of specific cysteine residues in intermolecular and intramolecular thiol-disulfide interchange and thiol oxidation reactions. The here developed approach holds promise for exploring disulfide bond formation and reshuffling in various proteins under conditions relevant for chemical, biochemical, pharmaceutical and food processing.
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Affiliation(s)
- Ine Rombouts
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, box 2463, B-3001 Leuven, Belgium
| | - Bert Lagrain
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, box 2463, B-3001 Leuven, Belgium
| | - Katharina A. Scherf
- Deutsche Forschungsanstalt für Lebensmittelchemie, Leibniz Institut, Lise-Meitner-Straβe 34, D-85354 Freising, Germany
| | - Peter Koehler
- Deutsche Forschungsanstalt für Lebensmittelchemie, Leibniz Institut, Lise-Meitner-Straβe 34, D-85354 Freising, Germany
| | - Jan A. Delcour
- Laboratory of Food Chemistry and Biochemistry, Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, box 2463, B-3001 Leuven, Belgium
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24
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Pilo AL, Bu J, McLuckey SA. Transformation of [M + 2H](2+) Peptide Cations to [M - H](+), [M + H + O](+), and M(+•) Cations via Ion/Ion Reactions: Reagent Anions Derived from Persulfate. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1103-14. [PMID: 25944366 PMCID: PMC4475491 DOI: 10.1007/s13361-015-1125-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 05/25/2023]
Abstract
The gas-phase oxidation of doubly protonated peptides is demonstrated here using ion/ion reactions with a suite of reagents derived from persulfate. Intact persulfate anion (HS2O8(-)), peroxymonosulfate anion (HSO5(-)), and sulfate radical anion (SO4(-•)) are all either observed directly upon negative nanoelectrospray ionization (nESI) or easily obtained via beam-type collisional activation of persulfate into the mass spectrometer. Ion/ion reactions between each of these reagents and doubly protonated peptides result in the formation of a long-lived complex. Collisional activation of the complex containing a peroxymonosulfate anion results in oxygen transfer from the reagent to the peptide to generate the [M + H + O](+) species. Activation of the complex containing intact persulfate anion either results in oxygen transfer to generate the [M + H + O](+) species or abstraction of two hydrogen atoms and a proton to generate the [M - H](+) species. Activation of the complex containing sulfate radical anion results in abstraction of one hydrogen atom and a proton to form the peptide radical cation, [M](+•). This suite of reagents allows for the facile transformation of the multiply protonated peptides obtained via nESI into a variety of oxidized species capable of providing complementary information about the sequence and structure of the peptide.
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Affiliation(s)
- Alice L. Pilo
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084
| | - Jiexun Bu
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, IN 47907-2084
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25
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Güzel Y, Rainer M, Messner CB, Hussain S, Meischl F, Sasse M, Tessadri R, Bonn GK. Development of erbium phosphate doped poly(glycidyl methacrylate/ethylene dimethacrylate) spin columns for selective enrichment of phosphopeptides. J Sep Sci 2015; 38:1334-43. [DOI: 10.1002/jssc.201401409] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 01/15/2015] [Accepted: 01/15/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Yüksel Güzel
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
- ADSI-Austrian Drug Screening Institute; Innsbruck Austria
| | - Matthias Rainer
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Christoph B. Messner
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Shah Hussain
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Florian Meischl
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Michael Sasse
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
| | - Richard Tessadri
- Institute of Mineralogy and Petrography; Leopold-Franzens University; Innsbruck Austria
| | - Günther K. Bonn
- Institute of Analytical Chemistry and Radiochemistry; Leopold-Franzens University of Innsbruck; Innsbruck Austria
- ADSI-Austrian Drug Screening Institute; Innsbruck Austria
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26
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Pilo AL, McLuckey SA. Oxidation of methionine residues in polypeptide ions via gas-phase ion/ion chemistry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1049-57. [PMID: 24671696 PMCID: PMC4020970 DOI: 10.1007/s13361-014-0861-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/14/2014] [Accepted: 02/14/2014] [Indexed: 05/13/2023]
Abstract
The gas-phase oxidation of methionine residues is demonstrated here using ion/ion reactions with periodate anions. Periodate anions are observed to attach in varying degrees to all polypeptide ions irrespective of amino acid composition. Direct proton transfer yielding a charge-reduced peptide ion is also observed. In the case of methionine and, to a much lesser degree, tryptophan-containing peptide ions, collisional activation of the complex ion generated by periodate attachment yields an oxidized peptide product (i.e., [M + H + O](+)), in addition to periodic acid detachment. Detachment of periodic acid takes place exclusively for peptides that do not contain either a methionine or tryptophan side chain. In the case of methionine-containing peptides, the [M + H + O](+) product is observed at a much greater abundance than the proton transfer product (viz., [M + H](+)). Collisional activation of oxidized Met-containing peptides yields a signature loss of 64 Da from the precursor and/or product ions. This unique loss corresponds to the ejection of methanesulfenic acid from the oxidized methionine side chain and is commonly used in solution-phase proteomics studies to determine the presence of oxidized methionine residues. The present work shows that periodate anions can be used to 'label' methionine residues in polypeptides in the gas phase. The selectivity of the periodate anion for the methionine side chain suggests several applications including identification and location of methionine residues in sequencing applications.
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Affiliation(s)
| | - Scott A. McLuckey
- Address reprint requests to: Dr. S. A. McLuckey 560 Oval Drive Department of Chemistry Purdue University West Lafayette, IN 47907-2084, USA Phone: (765) 494-5270 Fax: (765) 494-0239
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27
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Tanabe K, Taniguchi A, Matsumoto T, Oisaki K, Sohma Y, Kanai M. Asparagine-selective cleavage of peptide bonds through hypervalent iodine-mediated Hofmann rearrangement in neutral aqueous solution. Chem Sci 2014. [DOI: 10.1039/c3sc53037j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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28
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Kerkaert B, Mestdagh F, Obando M, Cucu T, De Meulenaer B. Identification of modified lysozyme peptides upon photo-oxidation by LC-TOF-MS. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:12727-12736. [PMID: 24328178 DOI: 10.1021/jf404396c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Protein oxidation can have major implications on the quality and safety of foods, but the majority of methods to evaluate oxidative damage lack specificity. Therefore, this study aimed to identify specific markers for protein oxidation. A well-characterized protein, lysozyme, was modified by photo-oxidation and subsequently hydrolyzed prior to peptide analysis by LC-TOF-MS. A semiquantitative analysis of the peptides indicated that from the seven peptides containing sensitive amino acids, two peptides (HGLDNYR and WWCNDGR) were highly affected upon photo-oxidation and have the potential to serve as markers for protein oxidation. Site-specific modifications enabled the description of the degradation pathway of several lysozyme peptides but also indicated that the surrounding amino acids and the 3D structure of the protein have an impact on the induced modifications. It is therefore advisable to evaluate protein oxidation on the intact protein.
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Affiliation(s)
- Barbara Kerkaert
- NutriFOODchem Unit, Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University , Coupure links 653, B-9000 Ghent, Belgium
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29
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Taniguchi A, Sasaki D, Shiohara A, Iwatsubo T, Tomita T, Sohma Y, Kanai M. Attenuation of the Aggregation and Neurotoxicity of Amyloid-β Peptides by Catalytic Photooxygenation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201308001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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30
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Taniguchi A, Sasaki D, Shiohara A, Iwatsubo T, Tomita T, Sohma Y, Kanai M. Attenuation of the aggregation and neurotoxicity of amyloid-β peptides by catalytic photooxygenation. Angew Chem Int Ed Engl 2013; 53:1382-5. [PMID: 24339209 DOI: 10.1002/anie.201308001] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 10/30/2013] [Indexed: 11/06/2022]
Abstract
Alzheimer's disease (AD), a progressive severe neurodegenerative disorder, is currently incurable, despite intensive efforts worldwide. Herein, we demonstrate that catalytic oxygenation of amyloid-β peptides (Aβ) might be an effective approach to treat AD. Aβ1-42 was oxygenated under physiologically-relevant conditions (pH 7.4, 37 °C) using a riboflavin catalyst and visible light irradiation, with modifications at the Tyr(10) , His(13) , His(14) , and Met(35) residues. The oxygenated Aβ1-42 exhibited considerably lower aggregation potency and neurotoxicity compared with native Aβ. Photooxygenation of Aβ can be performed even in the presence of cells, by using a selective flavin catalyst attached to an Aβ-binding peptide; the Aβ cytotoxicity was attenuated in this case as well. Furthermore, oxygenated Aβ1-42 inhibited the aggregation and cytotoxicity of native Aβ.
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Affiliation(s)
- Atsuhiko Taniguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033 (Japan); Japan Science and Technology Agency (JST), ERATO, Kanai Life Science Catalysis Project, Bunkyo-ku, Tokyo 113-0033 (Japan)
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31
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Frankel LK, Sallans L, Limbach PA, Bricker TM. Oxidized amino acid residues in the vicinity of Q(A) and Pheo(D1) of the photosystem II reaction center: putative generation sites of reducing-side reactive oxygen species. PLoS One 2013; 8:e58042. [PMID: 23469138 PMCID: PMC3585169 DOI: 10.1371/journal.pone.0058042] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Accepted: 01/30/2013] [Indexed: 02/04/2023] Open
Abstract
Under a variety of stress conditions, Photosystem II produces reactive oxygen species on both the reducing and oxidizing sides of the photosystem. A number of different sites including the Mn4O5Ca cluster, P680, PheoD1, QA, QB and cytochrome b559 have been hypothesized to produce reactive oxygen species in the photosystem. In this communication using Fourier-transform ion cyclotron resonance mass spectrometry we have identified several residues on the D1 and D2 proteins from spinach which are oxidatively modified and in close proximity to QA (D1 residues 239F, 241Q, 242E and the D2 residues 238P, 239T, 242E and 247M) and PheoD1 (D1 residues 130E, 133L and 135F). These residues may be associated with reactive oxygen species exit pathways located on the reducing side of the photosystem, and their modification may indicate that both QA and PheoD1 are sources of reactive oxygen species on the reducing side of Photosystem II.
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Affiliation(s)
- Laurie K. Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Larry Sallans
- The Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Patrick A. Limbach
- The Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Terry M. Bricker
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, Louisiana, United States of America
- * E-mail:
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32
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Irani M, Törnvall U, Genheden S, Larsen MW, Hatti-Kaul R, Ryde U. Amino Acid Oxidation of Candida antarctica Lipase B Studied by Molecular Dynamics Simulations and Site-Directed Mutagenesis. Biochemistry 2013; 52:1280-9. [DOI: 10.1021/bi301298m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mehdi Irani
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221
00 Lund, Sweden
| | - Ulrika Törnvall
- Department
of Biotechnology, Lund University, Chemical
Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221
00 Lund, Sweden
| | - Marianne Wittrup Larsen
- Department of Biochemistry, School of Biotechnology, Royal Institute of Technology, AlbaNova University
Center, 106 91 Stockholm, Sweden
| | - Rajni Hatti-Kaul
- Department
of Biotechnology, Lund University, Chemical
Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221
00 Lund, Sweden
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33
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Targeted oxidation of Torpedo californica acetylcholinesterase by singlet oxygen: identification of N-formylkynurenine tryptophan derivatives within the active-site gorge of its complex with the photosensitizer methylene blue. Biochem J 2013; 448:83-91. [PMID: 22888904 DOI: 10.1042/bj20120992] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The principal role of AChE (acetylcholinesterase) is termination of impulse transmission at cholinergic synapses by rapid hydrolysis of the neurotransmitter acetylcholine. The active site of AChE is near the bottom of a long and narrow gorge lined with aromatic residues. It contains a CAS (catalytic 'anionic' subsite) and a second PAS (peripheral 'anionic' site), the gorge mouth, both of which bind acetylcholine via π-cation interactions, primarily with two conserved tryptophan residues. It was shown previously that generation of (1)O(2) by illumination of MB (Methylene Blue) causes irreversible inactivation of TcAChE (Torpedo californica AChE), and suggested that photo-oxidation of tryptophan residues might be responsible. In the present study, structural modification of the TcAChE tryptophan residues induced by MB-sensitized oxidation was investigated using anti-N-formylkynurenine antibodies and MS. From these analyses, we determined that N-formylkynurenine derivatives were specifically produced from Trp(84) and Trp(279), present at the CAS and PAS respectively. Peptides containing these two oxidized tryptophan residues were not detected when the competitive inhibitors, edrophonium and propidium (which should displace MB from the gorge) were present during illumination, in agreement with their efficient protection against the MB-induced photo-inactivation. Thus the bound MB elicited selective action of (1)O(2) on the tryptophan residues facing on to the water-filled active-site gorge. The findings of the present study thus demonstrate the localized action and high specificity of MB-sensitized photo-oxidation of TcAChE, as well as the value of this enzyme as a model system for studying the mechanism of action and specificity of photosensitizing agents.
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Güzel Y, Rainer M, Mirza MR, Messner CB, Bonn GK. Highly selective recovery of phosphopeptides using trypsin-assisted digestion of precipitated lanthanide–phosphoprotein complexes. Analyst 2013; 138:2897-905. [DOI: 10.1039/c3an00066d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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Kumar V, Calamaras TD, Haeussler D, Colucci WS, Cohen RA, McComb ME, Pimentel D, Bachschmid MM. Cardiovascular redox and ox stress proteomics. Antioxid Redox Signal 2012; 17:1528-59. [PMID: 22607061 PMCID: PMC3448941 DOI: 10.1089/ars.2012.4706] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SIGNIFICANCE Oxidative post-translational modifications (OPTMs) have been demonstrated as contributing to cardiovascular physiology and pathophysiology. These modifications have been identified using antibodies as well as advanced proteomic methods, and the functional importance of each is beginning to be understood using transgenic and gene deletion animal models. Given that OPTMs are involved in cardiovascular pathology, the use of these modifications as biomarkers and predictors of disease has significant therapeutic potential. Adequate understanding of the chemistry of the OPTMs is necessary to determine what may occur in vivo and which modifications would best serve as biomarkers. RECENT ADVANCES By using mass spectrometry, advanced labeling techniques, and antibody identification, OPTMs have become accessible to a larger proportion of the scientific community. Advancements in instrumentation, database search algorithms, and processing speed have allowed MS to fully expand on the proteome of OPTMs. In addition, the role of enzymatically reversible OPTMs has been further clarified in preclinical models. CRITICAL ISSUES The identification of OPTMs suffers from limitations in analytic detection based on the methodology, instrumentation, sample complexity, and bioinformatics. Currently, each type of OPTM requires a specific strategy for identification, and generalized approaches result in an incomplete assessment. FUTURE DIRECTIONS Novel types of highly sensitive MS instrumentation that allow for improved separation and detection of modified proteins and peptides have been crucial in the discovery of OPTMs and biomarkers. To further advance the identification of relevant OPTMs in advanced search algorithms, standardized methods for sample processing and depository of MS data will be required.
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Affiliation(s)
- Vikas Kumar
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA
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36
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Bachi A, Dalle-Donne I, Scaloni A. Redox Proteomics: Chemical Principles, Methodological Approaches and Biological/Biomedical Promises. Chem Rev 2012. [DOI: 10.1021/cr300073p] [Citation(s) in RCA: 189] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Angela Bachi
- Biological Mass Spectrometry Unit, San Raffaele Scientific Institute, 20132 Milan, Italy
| | | | - Andrea Scaloni
- Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, 80147 Naples, Italy
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37
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Frankel LK, Sallans L, Limbach PA, Bricker TM. Identification of oxidized amino acid residues in the vicinity of the Mn(4)CaO(5) cluster of Photosystem II: implications for the identification of oxygen channels within the Photosystem. Biochemistry 2012; 51:6371-7. [PMID: 22827410 DOI: 10.1021/bi300650n] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As a light-driven water-plastoquinone oxidoreductase, Photosystem II produces molecular oxygen as an enzymatic product. Additionally, under a variety of stress conditions, reactive oxygen species are produced at or near the active site for oxygen evolution. In this study, Fourier-transform ion cyclotron resonance mass spectrometry was used to identify oxidized amino acid residues located in several core Photosystem II proteins (D1, D2, CP43, and CP47) isolated from spinach Photosystem II membranes. While the majority of these oxidized residues (81%) are located on the oxygenated solvent-exposed surface of the complex, several residues on the CP43 protein ((354)E, (355)T, (356)M, and (357)R) which are in close proximity (<15 Å) to the Mn(4)CaO(5) active site are also modified. These residues appear to be associated with putative oxygen/reactive oxygen species exit channel(s) in the photosystem. These results are discussed within the context of a number of computational studies which have identified putative oxygen channels within the photosystem.
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Affiliation(s)
- Laurie K Frankel
- Department of Biological Sciences, Division of Biochemistry and Molecular Biology, Louisiana State University, Baton Rouge, LA 70803, USA
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38
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Lai P, Okazawa A, Izumi Y, Bamba T, Fukusaki E, Yoshikawa M, Kobayashi A. Gallic acid oxidizes Met residues in peptides released from bovine β-lactoglobulin by in vitro digestion. J Biosci Bioeng 2012; 114:297-305. [PMID: 22652084 DOI: 10.1016/j.jbiosc.2012.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 04/11/2012] [Accepted: 04/26/2012] [Indexed: 11/25/2022]
Abstract
Phenolic compounds (PCs) are frequently present in foods. However, little is known about the effect of PCs on enzymatic digestion process of food proteins and their products. In this study, the effect of gallic acid (GA) on in vitro digestion of β-lactoglobulin (β-LG) was investigated as a model system for analysis of the interaction between PCs and food proteins. GA showed no effect on the initial rate of β-LG digestion. However, after 1.5 h of digestion, the observed degree of hydrolysis of β-LG was lower in the presence than in the absence of GA. The peptides released from β-LG were characterized by LC/IT-TOF-MS and thirty peptides were identified. In particular, four new peaks were obtained following in vitro digestion of β-LG in the presence of GA. Met(7), Met(24) and Met(145) in the peptides corresponding to these peaks were oxidized to methionine sulfoxide residues.
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Affiliation(s)
- Ping Lai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Japan
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39
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Katsila T, Siskos AP, Tamvakopoulos C. Peptide and protein drugs: the study of their metabolism and catabolism by mass spectrometry. MASS SPECTROMETRY REVIEWS 2012; 31:110-133. [PMID: 21698655 DOI: 10.1002/mas.20340] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Peptide and protein drugs have evolved in recent years into mainstream therapeutics, representing a significant portion of the pharmaceutical market. Peptides and proteins exhibit highly diverse structures, broad biological activities as hormones, neurotransmitters, structural proteins, metabolic modulators and therefore have a significant role as both therapeutics and biomarkers. Understanding the metabolism of synthetic or biotechnologically derived peptide and protein drugs is critical for pharmaceutical development as metabolism has a significant impact on drug efficacy and safety. Although the same principles of pharmacokinetics and metabolism of small molecule drugs apply to peptide and protein drugs, there are few notable differences. Moreover, the study of peptide and protein drug metabolism is a rather complicated process which requires sophisticated analytical techniques, and mass spectrometry based approaches have provided the capabilities for efficient and reliable quantification, characterization, and metabolite identification. This review article will focus on the current use of mass spectrometry for the study of the metabolism of peptide and protein drugs.
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Affiliation(s)
- Theodora Katsila
- Biomedical Research Foundation, Academy of Athens, Division of Pharmacology-Pharmacotechnology, Soranou Efesiou Street 4, Athens GR-11527, Greece
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40
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Törnvall U, Hedström M, Schillén K, Hatti-Kaul R. Structural, functional and chemical changes in Pseudozyma antarctica lipase B on exposure to hydrogen peroxide. Biochimie 2010; 92:1867-75. [DOI: 10.1016/j.biochi.2010.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 07/12/2010] [Indexed: 11/29/2022]
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41
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Rubino JT, Chenkin MP, Keller M, Riggs-Gelasco P, Franz KJ. A comparison of methionine, histidine and cysteine in copper(I)-binding peptides reveals differences relevant to copper uptake by organisms in diverse environments. Metallomics 2010; 3:61-73. [PMID: 21305075 DOI: 10.1039/c0mt00044b] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The N-terminal, extracellular regions of eukaryotic high affinity copper transport (Ctr) proteins vary in composition of the Cu(i) binding amino acids: methionine, histidine, and cysteine. To examine why certain amino acids are exploited over others in Ctrs from different organisms, the relative Cu(i) binding affinity and the dependence of binding on pH were examined for 3 peptides of the sequence MG(2)XG(2)MK, where X is either Met, His, or Cys. Cu(i) affinity was examined using an ascorbic acid oxidation assay, an electrospray ionization mass spectrometry technique, and spectrophotometric titration with a competitive Cu(i) chelator. The relative affinities of the peptides with Cu(i) reveal a trend whereby Cys > His > Met at pH 7.4 and Cys > Met > His at pH 4.5. Ligand geometry and metric parameters were determined with X-ray absorption spectroscopy. Susceptibility of the peptides to oxidation by hydrogen peroxide and copper-catalyzed oxidative conditions was evaluated by mass spectrometry. These results support hypotheses as to why certain Cu(i) binding amino acids are preferred over others in proteins expressed at different pH and exposed to oxidative environments. The results also have implications for interpreting site-directed mutagenesis studies aimed at identifying copper binding amino acids in copper trafficking proteins.
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Affiliation(s)
- Jeffrey T Rubino
- Department of Chemistry, Duke University, P.O. Box 90346, Durham, NC 27708-0346, USA
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42
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A reductionist cell-free major histocompatibility complex class II antigen processing system identifies immunodominant epitopes. Nat Med 2010; 16:1333-40. [PMID: 21037588 PMCID: PMC3058316 DOI: 10.1038/nm.2248] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Accepted: 07/23/2010] [Indexed: 12/18/2022]
Abstract
Immunodominance is defined as restricted responsiveness of T cells to a few selected epitopes from complex antigens. Strategies currently used for elucidating CD4+ T cell epitopes are inadequate. To understand the mechanism of epitope selection for helper T cells, we established a cell-free antigen processing system composed of defined proteins: MHC class II, cathepsins, and HLA-DM. Our minimalist system successfully identified the physiologically selected immunodominant epitopes of model antigens, HA1 from influenza virus (A/Texas/1/77) and type II collagen. When applied for de novo epitope identification to a malaria antigen, or HA1 from H5N1 virus (Avian Flu), the system selected a single epitope from each protein that were confirmed to be immunodominant by their capacity to activate CD4+ T cells in HLA-DR1 positive human volunteers or transgenic mice immunized with the corresponding proteins. Thus, we provide a powerful new tool for the identification of physiologically relevant helper T cell epitopes from antigens.
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43
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Rule Wigginton K, Menin L, Montoya JP, Kohn T. Oxidation of virus proteins during UV(254) and singlet oxygen mediated inactivation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:5437-43. [PMID: 20553020 DOI: 10.1021/es100435a] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Despite the widespread use of UV(254) irradiation and solar disinfection for water treatment, little is known about the photochemical pathways that lead to virus inactivation by these treatments. The goal of this study was to identify reactions that occur in virus capsid proteins upon treatment by UV(254) irradiation and (1)O(2), an important oxidant involved in sunlight-mediated disinfection. Bacteriophage MS2 was inactivated via UV(254) irradiation and exposure to (1)O(2) in buffered water, and their capsid proteins were then analyzed with MALDI-TOF-TOF and ESI-TOF before and after digestion with protease enzymes. The results demonstrate that chemical modifications occur in the MS2 major capsid protein with both treatments. One oxidation event was detected following (1)O(2) treatment in an amino acid residue located on the capsid outer surface. UV(254) treatment caused three chemical reactions in the capsid proteins, two of which were oxidation reactions with residues on the capsid outer surface. A site-specific cleavage also occurred with UV(254) irradiation at a protein chain location on the inside face of the capsid shell. We attribute this UV(254) induced protein scission, which is nearly unprecedented in the literature, to a close association between the affected residues and viral RNA, an efficient UV(254) absorber. These results suggest that viral protein oxidation by UV(254) and (1)O(2) may play a role in virus inactivation and that viral inactivation may be tracked with mass spectrometric measurements.
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Affiliation(s)
- Krista Rule Wigginton
- Ecole Polytechnique Federale de Lausanne (EPFL), Laboratory of Environmental Chemistry, Institute of Environmental Engineering, Station 2, 1015 Lausanne, Switzerland
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44
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Ichiba H, Nakamoto M, Yajima T, Takayama M, Fukushima T. Analysis of oxidation process of cholecystokinin octapeptide with reactive oxygen species by high-performance liquid chromatography and subsequent electrospray ionization mass spectrometry. Biomed Chromatogr 2010; 24:140-7. [PMID: 19517450 DOI: 10.1002/bmc.1262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The C-terminal octapeptide of cholecystokinin (CCK8) includes some easily oxidizable amino acids. The oxidation of CCK8 by reactive oxygen species (ROS) such as hydrogen peroxide (H(2)O(2)) and hydroxyl radicals (OH(*)) was investigated using reversed-phase high performance liquid chromatography (RP-HPLC) and subsequent electrospray ionization mass spectrometry. The mechanism of oxidation of CCK8 in the H(2)O(2) system differed from that of CCK8 in the Fenton system, in which OH(*) are produced. In the H(2)O(2) system, (28)Met and (31)Met were oxidized to methionine sulfoxide, and no further oxidation or degradation/hydrolysis occurred. On the other hand, in the Fenton system, (28)Met and (31)Met residues were oxidized to methionine sulfone via the formation of methionine sulfoxide. In addition, the oxidized product was observed at the Trp residue but not at the Tyr residue, and small peptide fragments from CCK8 were observed in the Fenton system. From these results, it was concluded that (28)Met and (31)Met residues of CCK8 are susceptible to oxidation by ROS.
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Affiliation(s)
- Hideaki Ichiba
- Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba 274-8510, Japan
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45
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Tian Y, Liu R, Zong W, Sun F, Wang M, Zhang P. A new biomarker of protein oxidation degree and site using angiotensin as the target by MS. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 75:908-911. [PMID: 20045374 DOI: 10.1016/j.saa.2009.12.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Revised: 12/01/2009] [Accepted: 12/08/2009] [Indexed: 05/28/2023]
Abstract
Hydroxyl radicals generated from Fenton reaction were used to damage the angiotensin. The oxidative damage degree and sites of peptides were measured by HPLC-MS and MS/MS. Experimental results proved that the oxidative damage degree increased with longer reaction time. The results also showed that the side chains of phenylalanine and tyrosine in angiotension can be attacked by hydroxyl radicals to form the oxidative products. A new strategy was established to monitor the oxidative degree and sites of peptides and laid the foundation for protein oxidation. This method can be used to investigate the mechanism of protein oxidative damage caused by oxidative stress which is induced by environmental pollutants and physiological activities. There will also be a wide application in the research of pathogenesis of some disease related to oxidative stress.
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Affiliation(s)
- Yanmin Tian
- School of Environmental Science and Engineering, Shandong University, 27 Shanda South Road, Jinan 250100, PR China
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46
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Törnvall U, Fürst CM, Hatti-Kaul R, Hedström M. Mass spectrometric analysis of peptides from an immobilized lipase: focus on oxidative modifications. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:2959-2964. [PMID: 19681098 DOI: 10.1002/rcm.4208] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Liquid chromatography/tandem mass spectrometry (LC/MS/MS) was used to study the primary structure of immobilized Candida antarctica lipase B (Novozym(R)435) without detaching the enzyme from the carrier. The immobilized enzyme packed in a miniature column was subjected to proteolysis and the peptides released were injected into the mass spectrometer for analysis. The set-up was utilized to determine amino acid oxidation after treatment of the biocatalyst with hydrogen peroxide. In total, sequence coverage of more than 90% was obtained, containing almost all of the amino acids sensitive to oxidation. Oxidation of methionine, tryptophan and cystine residues was observed. The flow system also allowed evaluation of the enzyme activity prior to peptide analysis. The developed method is general and should be applicable to other immobilized enzyme systems and to different treatments.
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Affiliation(s)
- Ulrika Törnvall
- Department of Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden.
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47
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Fonseca C, Domingues MRM, Simões C, Amado F, Domingues P. Reactivity of Tyr-Leu and Leu-Tyr dipeptides: identification of oxidation products by liquid chromatography-tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:681-693. [PMID: 19125397 DOI: 10.1002/jms.1543] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The exposure of peptides and proteins to reactive hydroxyl radicals results in covalent modifications of amino acid side-chains and protein backbone. In this study we have investigated the oxidation the isomeric peptides tyrosine-leucine (YL) and leucine-tyrosine (LY), by the hydroxyl radical formed under Fenton reaction (Fe(2+)/H(2)O(2)). Through mass spectrometry (MS), high-performance liquid chromatography (HPLC-MS) and electrospray tandem mass spectrometry (HPLC-MS(n)) measurements, we have identified and characterized the oxidation products of these two dipeptides. This approach allowed observing and identifying a wide variety of oxidation products, including isomeric forms of the oxidized dipeptides. We detected oxidation products with 1, 2, 3 and 4 oxygen atoms for both peptides; however, oxidation products with 5 oxygen atoms were only present in LY. LY dipeptide oxidation leads to more isomers with 1 and 2 oxygen atoms than YL (3 vs 5 and 4 vs 5, respectively). Formation of the peroxy group occurred preferentially in the C-terminal residue. We have also detected oxidation products with double bonds or keto groups, dimers (YL-YL and LY-LY) and other products as a result of cross-linking. Both amino acids in the dipeptides were oxidized although the peptides showed different oxidation products. Also, amino acid residues have shown different oxidation products depending on the relative position on the dipeptide. Results suggest that amino acids in the C-terminal position are more prone to oxidation.
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Affiliation(s)
- Conceição Fonseca
- Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
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48
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Prudent M, Girault HH. The role of copper in cysteine oxidation: study of intra- and inter-molecular reactions in mass spectrometry. Metallomics 2009; 1:157-65. [DOI: 10.1039/b817061d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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49
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Zamani L, Andersson FO, Edebrink P, Yang Y, Jacobsson SP. Conformational studies of a monoclonal antibody, IgG1, by chemical oxidation: Structural analysis by ultrahigh-pressure LC–electrospray ionization time-of-flight MS and multivariate data analysis. Anal Biochem 2008; 380:155-63. [DOI: 10.1016/j.ab.2008.05.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2007] [Revised: 05/22/2008] [Accepted: 05/28/2008] [Indexed: 12/25/2022]
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Fonseca C, Domingues P, Reis A, Domingues MRM. Identification of leucine-enkephalin radical oxidation products by liquid chromatography tandem mass spectrometry. Biomed Chromatogr 2008; 22:947-59. [DOI: 10.1002/bmc.1014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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