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Smythers AL, Joseph KM, O'Dell HM, Clark TA, Crislip JR, Flinn BB, Daughtridge MH, Stair ER, Mubarek SN, Lewis HC, Salas AA, Hnilica ME, Kolling DRJ, Hicks LM. Chemobiosis reveals tardigrade tun formation is dependent on reversible cysteine oxidation. PLoS One 2024; 19:e0295062. [PMID: 38232097 DOI: 10.1371/journal.pone.0295062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024] Open
Abstract
Tardigrades, commonly known as 'waterbears', are eight-legged microscopic invertebrates renowned for their ability to withstand extreme stressors, including high osmotic pressure, freezing temperatures, and complete desiccation. Limb retraction and substantial decreases to their internal water stores results in the tun state, greatly increasing their ability to survive. Emergence from the tun state and/or activity regain follows stress removal, where resumption of life cycle occurs as if stasis never occurred. However, the mechanism(s) through which tardigrades initiate tun formation is yet to be uncovered. Herein, we use chemobiosis to demonstrate that tardigrade tun formation is mediated by reactive oxygen species (ROS). We further reveal that tuns are dependent on reversible cysteine oxidation, and that this reversible cysteine oxidation is facilitated by the release of intracellular reactive oxygen species (ROS). We provide the first empirical evidence of chemobiosis and map the initiation and survival of tardigrades via osmobiosis, chemobiosis, and cryobiosis. In vivo electron paramagnetic spectrometry suggests an intracellular release of reactive oxygen species following stress induction; when this release is quenched through the application of exogenous antioxidants, the tardigrades can no longer survive osmotic stress. Together, this work suggests a conserved dependence of reversible cysteine oxidation across distinct tardigrade cryptobioses.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Kara M Joseph
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Hayden M O'Dell
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Trace A Clark
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Jessica R Crislip
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Brendin B Flinn
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Meredith H Daughtridge
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Evan R Stair
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Saher N Mubarek
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Hailey C Lewis
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Abel A Salas
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Megan E Hnilica
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Derrick R J Kolling
- Department of Chemistry, Marshall University, Huntington, WV, United States of America
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
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2
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Engineering a disulfide-gated switch in streptavidin enables reversible binding without sacrificing binding affinity. Sci Rep 2020; 10:12483. [PMID: 32719366 PMCID: PMC7385176 DOI: 10.1038/s41598-020-69357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
Although high affinity binding between streptavidin and biotin is widely exploited, the accompanying low rate of dissociation prevents its use in many applications where rapid ligand release is also required. To combine extremely tight and reversible binding, we have introduced disulfide bonds into opposite sides of a flexible loop critical for biotin binding, creating streptavidin muteins (M88 and M112) with novel disulfide-switchable binding properties. Crystal structures reveal how each disulfide exerts opposing effects on structure and function. Whereas the disulfide in M112 disrupts the closed conformation to increase koff, the disulfide in M88 stabilizes the closed conformation, decreasing koff 260-fold relative to streptavidin. The simple and efficient reduction of this disulfide increases koff 19,000-fold, thus creating a reversible redox-dependent switch with 70-fold faster dissociation kinetics than streptavidin. The facile control of disulfide formation in M88 will enable the development of many new applications requiring high affinity and reversible binding.
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3
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McConnell EW, Smythers AL, Hicks LM. Maleimide-Based Chemical Proteomics for Quantitative Analysis of Cysteine Reactivity. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1697-1705. [PMID: 32573231 DOI: 10.1021/jasms.0c00116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cysteine is the most intrinsically nucleophilic residue in proteins and serves as a mediator against increasing reactive oxygen species (ROS) via reversible thiol oxidation. Despite the importance of cysteine oxidation in understanding biological stress response, cysteine sites most reactive toward ROS remain largely unknown and are a major analytical challenge. Herein, a chemical proteomic method to quantify site-specific cysteine reactivity using a maleimide-activated, thiol-reactive probe (N-propargylmaleimide, NPM) is described. Implementation of a gel-based approach via conjugation of rhodamine-azide to NPM-labeled cysteine residues by copper-catalyzed azide-alkyne cycloaddition (CuAAC) click chemistry allowed simple and highly sensitive fluorescence profiling. Relative quantification of >1500 unique cysteine sites from greater than 800 proteins was achieved by conjugating dialkoxydiphenylsilane (DADPS) biotin-azide by the CuAAC reaction and subsequently performing biotin-streptavidin affinity purification and mass-spectrometry-based proteomics. Taken together, this work defines a novel role for the NPM probe in chemical proteomics and presents a robust method for determination of cysteine reactivity during oxidative stress response.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Amanda L Smythers
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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4
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Zolochevska O, Bjorklund N, Woltjer R, Wiktorowicz JE, Taglialatela G. Postsynaptic Proteome of Non-Demented Individuals with Alzheimer's Disease Neuropathology. J Alzheimers Dis 2019; 65:659-682. [PMID: 30103319 PMCID: PMC6130411 DOI: 10.3233/jad-180179] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Some individuals, here referred to as Non-Demented with Alzheimer’s Neuropathology (NDAN), retain their cognitive function despite the presence of amyloid plaques and tau tangles typical of symptomatic Alzheimer’s disease (AD). In NDAN, unlike AD, toxic amyloid-β oligomers do not localize to the postsynaptic densities (PSDs). Synaptic resistance to amyloid-β in NDAN may thus enable these individuals to remain cognitively intact despite the AD-like pathology. The mechanism(s) responsible for this resistance remains unresolved and understanding such protective biological processes could reveal novel targets for the development of effective treatments for AD. The present study uses a proteomic approach to compare the hippocampal postsynaptic densities of NDAN, AD, and healthy age-matched persons to identify protein signatures characteristic for these groups. Subcellular fractionation followed by 2D gel electrophoresis and mass spectrometry were used to analyze the PSDs. We describe fifteen proteins which comprise the unique proteomic signature of NDAN PSDs, thus setting them apart from control subjects and AD patients.
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Affiliation(s)
- Olga Zolochevska
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
| | - Nicole Bjorklund
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
| | - Randall Woltjer
- Department of Pathology, Oregon Health and Science University, Portland, OR, USA
| | - John E Wiktorowicz
- Department of Biochemistry and Molecular Biology, Sealy Center for Molecular Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Giulio Taglialatela
- Department of Neurology, University of Texas Medical Branch, Galveston, TX, USA
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5
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Simulation of single-protein nanopore sensing shows feasibility for whole-proteome identification. PLoS Comput Biol 2019; 15:e1007067. [PMID: 31145734 PMCID: PMC6559672 DOI: 10.1371/journal.pcbi.1007067] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 06/11/2019] [Accepted: 05/02/2019] [Indexed: 11/25/2022] Open
Abstract
Single-molecule techniques for protein sequencing are making headway towards single-cell proteomics and are projected to propel our understanding of cellular biology and disease. Yet, single cell proteomics presents a substantial unmet challenge due to the unavailability of protein amplification techniques, and the vast dynamic-range of protein expression in cells. Here, we describe and computationally investigate the feasibility of a novel approach for single-protein identification using tri-color fluorescence and plasmonic-nanopore devices. Comprehensive computer simulations of denatured protein translocation processes through the nanopores show that the tri-color fluorescence time-traces retain sufficient information to permit pattern-recognition algorithms to correctly identify the vast majority of proteins in the human proteome. Importantly, even when taking into account realistic experimental conditions, which restrict the spatial and temporal resolutions as well as the labeling efficiency, and add substantial noise, a deep-learning protein classifier achieves 97% whole-proteome accuracies. Applying our approach for protein datasets of clinical relevancy, such as the plasma proteome or cytokine panels, we obtain ~98% correct protein identification. This study suggests the feasibility of a method for accurate and high-throughput protein identification, which is highly versatile and applicable. Macromolecules identification methods are central for most biological and biomedical studies, and while the field of genomics advanced to single-molecule resolution, the proteomic field still relies on bulk and costly techniques. We describe a solution for single protein identification, based on the analysis of optical traces obtained from fluorescently-labeled proteins threaded through a nanopore and processed by a pattern recognition algorithm. To evaluate the feasibility of our method we constructed computer simulations of the system, producing and analyzing nearly 108 individual protein translocations from the human Swiss-Prot database. Our results suggest protein identification of >95% for the whole human proteome, even under non-ideal conditions. These results constitute the basis for a novel whole proteome identification method, with single molecule resolution.
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Integrated Functional Analysis of the Nuclear Proteome of Classically and Alternatively Activated Macrophages. Mediators Inflamm 2019; 2019:3481430. [PMID: 31182931 PMCID: PMC6515079 DOI: 10.1155/2019/3481430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 12/31/2018] [Accepted: 03/06/2019] [Indexed: 02/03/2023] Open
Abstract
Macrophages (Mφ) play a central role in coordinating host response to pathogens, cellular injury, and environmental stimuli. Herein, we report multidimensional, nuclear proteomic analyses of protein expression and posttranslational modifications (PTMs) that control biological processes during Mφ activation. For this, Mφ were incubated with IFN-γ/LPS and IL-4, and their differentiation to proinflammatory (M1) and anti-inflammatory (M2a, referred as M2 for simplicity throughtout the manuscript) phenotypes was confirmed by detection of CD64 and CD206 surface markers and TNF-α, arginase I, and iNOS-dependent nitrite levels. We used a sequential method of organellar enrichment and labeling of nuclear fractions with BODIPY FL-maleimide fluorescence dye followed by two-dimensional electrophoresis (2DE) to capture quantitative changes in abundance and S-nitrosylated (SNO) proteome signatures. Exact same gels were then labeled with Pro-Q Diamond to detect protein phosphorylation. MALDI-TOF/TOF MS analysis of the protein spots with fold change of ≥|1.5| in any of the groups yielded 229 identifications. We found that 145, 78, and 173 protein spots in M1 Mφ and 105, 81, and 164 protein spots in M2 Mφ were changed in abundance, S-nitrosylation, and phosphorylation, respectively, with respect to M0 controls (fold change: ≥|1.5|, p ≤ 0.05). Targeted analysis by immunoprecipitation and Western blotting was performed to verify the differential abundance and phosphorylation levels of two of the proteins in M1 and M2 (vs. M0) Mφ. Ingenuity Pathway Analysis of the nuclear proteome datasets showed that the abundance and posttranslational (SNO and Phosphor) modifications of the proteins predicted to be involved in cytoskeletal organization/cell movement, phagocytosis/endocytosis, and cell proliferation/cell death were differentially regulated with proinflammatory and anti-inflammatory activation of Mφ.
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7
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Zago MP, Wiktorowicz JE, Spratt H, Koo SJ, Barrientos N, Nuñez Burgos A, Nuñez Burgos J, Iñiguez F, Botelli V, Leon de la Fuente R, Garg NJ. Potential Utility of Protein Targets of Cysteine-S-Nitrosylation in Identifying Clinical Disease Status in Human Chagas Disease. Front Microbiol 2019; 9:3320. [PMID: 30697201 PMCID: PMC6340995 DOI: 10.3389/fmicb.2018.03320] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 12/20/2018] [Indexed: 01/24/2023] Open
Abstract
Trypanosoma cruzi (Tc) infection causes Chagas disease (ChD) presented by dilated cardiomyopathy and heart failure. During infection, oxidative and nitrosative stresses are elicited by the immune cells for control the pathogen; however, excess nitric oxide and superoxide production can result in cysteine S-nitrosylation (SNO) of host proteins that affects cellular homeostasis and may contribute to disease development. To identify the proteins with changes in SNO modification levels as a hallmark of ChD, we obtained peripheral blood mononuclear cells (PBMC) from seronegative, normal healthy (NH, n = 30) subjects, and from seropositive clinically asymptomatic (ChD CA, n = 25) or clinically symptomatic (ChD CS, n = 28) ChD patients. All samples were treated (Asc+) or not-treated (Asc−) with ascorbate (reduces nitrosylated thiols), labeled with the thiol-labeling BODIPY FL-maleimide dye, resolved by two-dimensional electrophoresis (total 166 gels), and the protein spots that yielded significant differences in abundance or SNO level at p-value of ≤ 0.05t−test/Welch/BH were identified by MALDI-TOF/TOF MS or OrbiTrap LC-MS/MS. Targeted analysis of a new cohort of PBMC samples (n = 10–14/group) was conducted to verify the differential abundance/SNO levels of two of the proteins in ChD (vs. NH) subjects. The multivariate adaptive regression splines (MARS) modeling, comparing differences in relative SNO level (Asc−/Asc+ ratio) of the protein spots between any two groups yielded SNO biomarkers that exhibited ≥90% prediction success in classifying ChD CA (582-KRT1 and 884-TPM3) and ChD CS (426-PNP, 582-KRT1, 486-ALB, 662-ACTB) patients from NH controls. Ingenuity Pathway Analysis (IPA) of the SNO proteome dataset normalized to changes in protein abundance suggested the proteins belonging to the signaling networks of cell death and the recruitment and migration of immune cells were most affected in ChD CA and ChD CS (vs. NH) subjects. We propose that SNO modification of the select panel of proteins identified in this study have the potential to identify ChD severity in seropositive individuals exposed to Tc infection.
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Affiliation(s)
- Maria Paola Zago
- Instituto de Patología Experimental, CONICET-UNSa, Salta, Argentina
| | - John E Wiktorowicz
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | - Heidi Spratt
- Department of Preventive Medicine and Community Health, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | - Sue-Jie Koo
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | | | - Aida Nuñez Burgos
- Servicio de Cardiología, Programa de Medicina Interna, Hospital Papa Francisco, Salta, Argentina
| | - Julio Nuñez Burgos
- Servicio de Cardiología, Programa de Medicina Interna, Hospital Papa Francisco, Salta, Argentina
| | - Facundo Iñiguez
- Servicio de Cardiología, Hospital San Bernardo, Salta, Argentina
| | | | | | - Nisha Jain Garg
- Institute for Human Infections and Immunity, University of Texas Medical Branch (UTMB), Galveston, TX, United States.,Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX, United States.,Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, TX, United States
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8
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Structure and Conformational Studies of Aza-Crown 8-Amino-BODIPY Derivatives: Influence of Steric Hindrance on Their Photophysical Properties. European J Org Chem 2017. [DOI: 10.1002/ejoc.201701016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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9
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van Leeuwen LAG, Hinchy EC, Murphy MP, Robb EL, Cochemé HM. Click-PEGylation - A mobility shift approach to assess the redox state of cysteines in candidate proteins. Free Radic Biol Med 2017; 108:374-382. [PMID: 28366801 PMCID: PMC5488967 DOI: 10.1016/j.freeradbiomed.2017.03.037] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/16/2017] [Accepted: 03/29/2017] [Indexed: 12/12/2022]
Abstract
The redox state of cysteine thiols is critical for protein function. Whereas cysteines play an important role in the maintenance of protein structure through the formation of internal disulfides, their nucleophilic thiol groups can become oxidatively modified in response to diverse redox challenges and thereby function in signalling and antioxidant defences. These oxidative modifications occur in response to a range of agents and stimuli, and can lead to the existence of multiple redox states for a given protein. To assess the role(s) of a protein in redox signalling and antioxidant defence, it is thus vital to be able to assess which of the multiple thiol redox states are present and to investigate how these alter under different conditions. While this can be done by a range of mass spectrometric-based methods, these are time-consuming, costly, and best suited to study abundant proteins or to perform an unbiased proteomic screen. One approach that can facilitate a targeted assessment of candidate proteins, as well as proteins that are low in abundance or proteomically challenging, is by electrophoretic mobility shift assays. Redox-modified cysteine residues are selectively tagged with a large group, such as a polyethylene glycol (PEG) polymer, and then the proteins are separated by electrophoresis followed by immunoblotting, which allows the inference of redox changes based on band shifts. However, the applicability of this method has been impaired by the difficulty of cleanly modifying protein thiols by large PEG reagents. To establish a more robust method for redox-selective PEGylation, we have utilised a Click chemistry approach, where free thiol groups are first labelled with a reagent modified to contain an alkyne moiety, which is subsequently Click-reacted with a PEG molecule containing a complementary azide function. This strategy can be adapted to study reversibly reduced or oxidised cysteines. Separation of the thiol labelling step from the PEG conjugation greatly facilitates the fidelity and flexibility of this approach. Here we show how the Click-PEGylation technique can be used to interrogate the redox state of proteins.
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Affiliation(s)
- Lucie A G van Leeuwen
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Elizabeth C Hinchy
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Ellen L Robb
- MRC Mitochondrial Biology Unit, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
| | - Helena M Cochemé
- MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK; Institute of Clinical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.
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10
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Yudhistira T, Mulay SV, Lee KJ, Kim Y, Park HS, Churchill DG. Thiomaleimide Functionalization for Selective Biological Fluorescence Detection of Peroxynitrite as Tested in HeLa and RAW 264.7 Cells. Chem Asian J 2017; 12:1927-1934. [DOI: 10.1002/asia.201700527] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 05/08/2017] [Indexed: 01/22/2023]
Affiliation(s)
- Tesla Yudhistira
- Molecular Logic Gate Laboratory; Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Republic of Korea
| | - Sandip V. Mulay
- Molecular Logic Gate Laboratory; Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 Republic of Korea
| | - Kyung Jin Lee
- Molecular Synthetic Biology Laboratory; Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Republic of Korea
| | - Youngsam Kim
- Molecular Logic Gate Laboratory; Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 Republic of Korea
| | - Hee-Sung Park
- Molecular Synthetic Biology Laboratory; Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Republic of Korea
| | - David G. Churchill
- Molecular Logic Gate Laboratory; Department of Chemistry; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 305-701 Republic of Korea
- Center for Catalytic Hydrocarbon Functionalizations; Institute for Basic Science (IBS); Daejeon 305-701 Republic of Korea
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11
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Boyatzis AE, Bringans SD, Piggott MJ, Duong MN, Lipscombe RJ, Arthur PG. Limiting the Hydrolysis and Oxidation of Maleimide–Peptide Adducts Improves Detection of Protein Thiol Oxidation. J Proteome Res 2017; 16:2004-2015. [DOI: 10.1021/acs.jproteome.6b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Amber E. Boyatzis
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Matthew J. Piggott
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Marisa N. Duong
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
| | | | - Peter G. Arthur
- School
of Chemistry and Biochemistry, University of Western Australia, Crawley, Western Australia 6009, Australia
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12
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13
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Ullevig SL, Kim HS, Short JD, Tavakoli S, Weintraub ST, Downs K, Asmis R. Protein S-Glutathionylation Mediates Macrophage Responses to Metabolic Cues from the Extracellular Environment. Antioxid Redox Signal 2016; 25:836-851. [PMID: 26984580 PMCID: PMC5107721 DOI: 10.1089/ars.2015.6531] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS Protein S-glutathionylation, the formation of a mixed disulfide between glutathione and protein thiols, is an oxidative modification that has emerged as a new signaling paradigm, potentially linking oxidative stress to chronic inflammation associated with heart disease, diabetes, cancer, lung disease, and aging. Using a novel, highly sensitive, and selective proteomic approach to identify S-glutathionylated proteins, we tested the hypothesis that monocytes and macrophages sense changes in their microenvironment and respond to metabolic stress by altering their protein thiol S-glutathionylation status. RESULTS We identified over 130 S-glutathionylated proteins, which were associated with a variety of cellular functions, including metabolism, transcription and translation, protein folding, free radical scavenging, cell motility, and cell death. Over 90% of S-glutathionylated proteins identified in metabolically stressed THP-1 monocytes were also found in hydrogen peroxide (H2O2)-treated cells, suggesting that H2O2 mediates metabolic stress-induced protein S-glutathionylation in monocytes and macrophages. We validated our findings in mouse peritoneal macrophages isolated from both healthy and dyslipidemic atherosclerotic mice and found that 52% of the S-glutathionylated proteins found in THP-1 monocytes were also identified in vivo. Changes in macrophage protein S-glutathionylation induced by dyslipidemia were sexually dimorphic. INNOVATION We provide a novel mechanistic link between metabolic (and thiol oxidative) stress, macrophage dysfunction, and chronic inflammatory diseases associated with metabolic disorders. CONCLUSION Our data support the concept that changes in the extracellular metabolic microenvironment induce S-glutathionylation of proteins central to macrophage metabolism and a wide array of cellular signaling pathways and functions, which in turn initiate and promote functional and phenotypic changes in macrophages. Antioxid. Redox Signal. 25, 836-851.
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Affiliation(s)
- Sarah L Ullevig
- 1 Department of Kinesiology, Health, and Nutrition, University of Texas at San Antonio , San Antonio, Texas
| | - Hong Seok Kim
- 2 Department of Molecular Medicine, College of Medicine, Inha University , Incheon, Korea
| | - John D Short
- 3 Department of Pharmacology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Sina Tavakoli
- 4 Department of Radiology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Susan T Weintraub
- 5 Institutional Mass Spectrometry Core Laboratory, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,6 Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Kevin Downs
- 7 Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio , San Antonio, Texas
| | - Reto Asmis
- 4 Department of Radiology, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,6 Department of Biochemistry, University of Texas Health Science Center at San Antonio , San Antonio, Texas.,8 Department of Clinical Laboratory Sciences, University of Texas Health Science Center at San Antonio , San Antonio, Texas
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14
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Koo SJ, Spratt HM, Soman KV, Stafford S, Gupta S, Petersen JR, Zago MP, Kuyumcu-Martinez MN, Brasier AR, Wiktorowicz JE, Garg NJ. S-Nitrosylation Proteome Profile of Peripheral Blood Mononuclear Cells in Human Heart Failure. INTERNATIONAL JOURNAL OF PROTEOMICS 2016; 2016:1384523. [PMID: 27635260 PMCID: PMC5007369 DOI: 10.1155/2016/1384523] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/07/2016] [Accepted: 05/16/2016] [Indexed: 01/05/2023]
Abstract
Nitric oxide (NO) protects the heart against ischemic injury; however, NO- and superoxide-dependent S-nitrosylation (S-NO) of cysteines can affect function of target proteins and play a role in disease outcome. We employed 2D-GE with thiol-labeling FL-maleimide dye and MALDI-TOF MS/MS to capture the quantitative changes in abundance and S-NO proteome of HF patients (versus healthy controls, n = 30/group). We identified 93 differentially abundant (59-increased/34-decreased) and 111 S-NO-modified (63-increased/48-decreased) protein spots, respectively, in HF subjects (versus controls, fold-change | ≥1.5|, p ≤ 0.05). Ingenuity pathway analysis of proteome datasets suggested that the pathways involved in phagocytes' migration, free radical production, and cell death were activated and fatty acid metabolism was decreased in HF subjects. Multivariate adaptive regression splines modeling of datasets identified a panel of proteins that will provide >90% prediction success in classifying HF subjects. Proteomic profiling identified ATP-synthase, thrombospondin-1 (THBS1), and vinculin (VCL) as top differentially abundant and S-NO-modified proteins, and these proteins were verified by Western blotting and ELISA in different set of HF subjects. We conclude that differential abundance and S-NO modification of proteins serve as a mechanism in regulating cell viability and free radical production, and THBS1 and VCL evaluation will potentially be useful in the prediction of heart failure.
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Affiliation(s)
- Sue-jie Koo
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Heidi M. Spratt
- Department Preventive Medicine and Community Health, UTMB, Galveston, TX 77555, USA
- Institute for Translational Sciences, UTMB, Galveston, TX 77555, USA
| | - Kizhake V. Soman
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
| | - Susan Stafford
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
| | - Shivali Gupta
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555, USA
| | - John R. Petersen
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Maria P. Zago
- Instituto de Patología Experimental, CONICET-UNSa, 4400 Salta, Argentina
| | - Muge N. Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
| | - Allan R. Brasier
- Institute for Translational Sciences, UTMB, Galveston, TX 77555, USA
- Department of Internal Medicine-Endocrinology, UTMB, Galveston, TX 77555, USA
| | - John E. Wiktorowicz
- Institute for Translational Sciences, UTMB, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, Sealy Center of Molecular Medicine, UTMB, Galveston TX 77555, USA
- Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555, USA
| | - Nisha Jain Garg
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
- Department of Microbiology and Immunology, UTMB, Galveston, TX 77555, USA
- Institute for Human Infections and Immunity, UTMB, Galveston, TX 77555, USA
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15
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Garg NJ, Soman KV, Zago MP, Koo SJ, Spratt H, Stafford S, Blell ZN, Gupta S, Nuñez Burgos J, Barrientos N, Brasier AR, Wiktorowicz JE. Changes in Proteome Profile of Peripheral Blood Mononuclear Cells in Chronic Chagas Disease. PLoS Negl Trop Dis 2016; 10:e0004490. [PMID: 26919708 PMCID: PMC4769231 DOI: 10.1371/journal.pntd.0004490] [Citation(s) in RCA: 17] [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: 09/25/2015] [Accepted: 02/03/2016] [Indexed: 12/15/2022] Open
Abstract
Trypanosoma cruzi (Tc) infection causes chagasic cardiomyopathy; however, why 30-40% of the patients develop clinical disease is not known. To discover the pathomechanisms in disease progression, we obtained the proteome signature of peripheral blood mononuclear cells (PBMCs) of normal healthy controls (N/H, n = 30) and subjects that were seropositive for Tc-specific antibodies, but were clinically asymptomatic (C/A, n = 25) or clinically symptomatic (C/S, n = 28) with cardiac involvement and left ventricular dysfunction. Protein samples were labeled with BODIPY FL-maleimide (dynamic range: > 4 orders of magnitude, detection limit: 5 f-mol) and resolved by two-dimensional gel electrophoresis (2D-GE). After normalizing the gel images, protein spots that exhibited differential abundance in any of the two groups were analyzed by mass spectrometry, and searched against UniProt human database for protein identification. We found 213 and 199 protein spots (fold change: |≥ 1.5|, p< 0.05) were differentially abundant in C/A and C/S individuals, respectively, with respect to N/H controls. Ingenuity Pathway Analysis (IPA) of PBMCs proteome dataset identified an increase in disorganization of cytoskeletal assembly and recruitment/activation and migration of immune cells in all chagasic subjects, though the invasion capacity of cells was decreased in C/S individuals. IPA predicted with high probability a decline in cell survival and free radical scavenging capacity in C/S (but not C/A) subjects. The MYC/SP1 transcription factors that regulate hypoxia and oxidative/inflammatory stress were predicted to be key targets in the context of control of Chagas disease severity. Further, MARS-modeling identified a panel of proteins that had >93% prediction success in classifying infected individuals with no disease and those with cardiac involvement and LV dysfunction. In conclusion, we have identified molecular pathways and a panel of proteins that could aid in detecting seropositive individuals at risk of developing cardiomyopathy.
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Affiliation(s)
- Nisha Jain Garg
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
- Department of Pathology, UTMB, Galveston, Texas, United States of America
- Faculty of the Institute for Human Infections and Immunity, and Sealy Center for Vaccine Development, UTMB, Galveston, Texas, United States of America
| | - Kizhake V. Soman
- Department of Biochemistry and Molecular Biology, and the Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
| | - Maria P. Zago
- Instituto de Patología Experimental, CONICET-UNSa, Salta, Argentina
| | - Sue-Jie Koo
- Department of Pathology, UTMB, Galveston, Texas, United States of America
| | - Heidi Spratt
- Department of Preventive Medicine and Community Health, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
| | - Susan Stafford
- Department of Biochemistry and Molecular Biology, and the Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
| | - Zinzi N. Blell
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | - Shivali Gupta
- Department of Microbiology and Immunology, University of Texas Medical Branch (UTMB), Galveston, Texas, United States of America
| | | | | | - Allan R. Brasier
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
- Department of Internal Medicine, UTMB, Galveston, Texas, United States of America
| | - John E. Wiktorowicz
- Department of Biochemistry and Molecular Biology, and the Sealy Center for Molecular Medicine, UTMB, Galveston, Texas, United States of America
- Institute for Translational Sciences, UTMB, Galveston, Texas, United States of America
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16
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Wiktorowicz JE, Soman KV. Discovery of Candidate Biomarkers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:443-462. [PMID: 27975230 DOI: 10.1007/978-3-319-41448-5_21] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Properly performed, biomarker discovery can lead to effective candidates that can ultimately serve as predictors of disease, medical condition, define therapeutic parameters, and many other applications in medicine. Preferably, biomarkers comprise a panel of indicators, e.g. proteins and/or peptides that can be predictive or diagnostic of the medical condition of interest. Emphasis here is placed on "panel," as single candidates are rarely sufficient to provide the necessary sensitivity and specificity. To develop an effective panel that survives the development process described in Chap. 19 , proper experimental design and attention to important statistical parameters are critical to ensure success. Errors in discovery can lead to an inefficient use of expensive resources, as these may not be uncovered until the latter stages in biomarker development. Hence, accuracy, precision, and an estimate of the power of the proposed analyses are critical in the discovery of the panel of candidate biomarkers by proteomic methods, as is the selection of statistical approaches to refine and appropriately reduce the dataset for subsequent confirmatory assays.
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17
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Brasier AR, Zhao Y, Spratt HM, Wiktorowicz JE, Ju H, Wheat LJ, Baden L, Stafford S, Wu Z, Issa N, Caliendo AM, Denning DW, Soman K, Clancy CJ, Nguyen MH, Sugrue MW, Alexander BD, Wingard JR. Improved Detection of Invasive Pulmonary Aspergillosis Arising during Leukemia Treatment Using a Panel of Host Response Proteins and Fungal Antigens. PLoS One 2015; 10:e0143165. [PMID: 26581097 PMCID: PMC4651335 DOI: 10.1371/journal.pone.0143165] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 11/02/2015] [Indexed: 12/03/2022] Open
Abstract
Invasive pulmonary aspergillosis (IPA) is an opportunistic fungal infection in patients undergoing chemotherapy for hematological malignancy, hematopoietic stem cell transplant, or other forms of immunosuppression. In this group, Aspergillus infections account for the majority of deaths due to mold pathogens. Although early detection is associated with improved outcomes, current diagnostic regimens lack sensitivity and specificity. Patients undergoing chemotherapy, stem cell transplantation and lung transplantation were enrolled in a multi-site prospective observational trial. Proven and probable IPA cases and matched controls were subjected to discovery proteomics analyses using a biofluid analysis platform, fractionating plasma into reproducible protein and peptide pools. From 556 spots identified by 2D gel electrophoresis, 66 differentially expressed post-translationally modified plasma proteins were identified in the leukemic subgroup only. This protein group was rich in complement components, acute-phase reactants and coagulation factors. Low molecular weight peptides corresponding to abundant plasma proteins were identified. A candidate marker panel of host response (9 plasma proteins, 4 peptides), fungal polysaccharides (galactomannan), and cell wall components (β-D glucan) were selected by statistical filtering for patients with leukemia as a primary underlying diagnosis. Quantitative measurements were developed to qualify the differential expression of the candidate host response proteins using selective reaction monitoring mass spectrometry assays, and then applied to a separate cohort of 57 patients with leukemia. In this verification cohort, a machine learning ensemble-based algorithm, generalized pathseeker (GPS) produced a greater case classification accuracy than galactomannan (GM) or host proteins alone. In conclusion, Integration of host response proteins with GM improves the diagnostic detection of probable IPA in patients undergoing treatment for hematologic malignancy. Upon further validation, early detection of probable IPA in leukemia treatment will provide opportunities for earlier interventions and interventional clinical trials.
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Affiliation(s)
- Allan R. Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, United States of America
- Institute for Translational Sciences, UTMB, Galveston, TX, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States of America
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, United States of America
- Institute for Translational Sciences, UTMB, Galveston, TX, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States of America
| | - Heidi M. Spratt
- Institute for Translational Sciences, UTMB, Galveston, TX, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States of America
- Department of Preventive Medicine and Community Health, UTMB, Galveston, TX, United States of America
| | - John E. Wiktorowicz
- Institute for Translational Sciences, UTMB, Galveston, TX, United States of America
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States of America
- Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, United States of America
| | - Hyunsu Ju
- Institute for Translational Sciences, UTMB, Galveston, TX, United States of America
- Department of Preventive Medicine and Community Health, UTMB, Galveston, TX, United States of America
| | - L. Joseph Wheat
- MiraVista Laboratories, Indianapolis, IN, United States of America
| | - Lindsey Baden
- Harvard University, Boston, MA, United States of America
| | - Susan Stafford
- Biomolecular Resource Facility, UTMB, Galveston, TX, United States of America
| | - Zheng Wu
- Biomolecular Resource Facility, UTMB, Galveston, TX, United States of America
| | - Nicolas Issa
- Harvard University, Boston, MA, United States of America
| | | | | | - Kizhake Soman
- Sealy Center for Molecular Medicine, UTMB, Galveston, TX, United States of America
- Department of Biochemistry and Molecular Biology, UTMB, Galveston, TX, United States of America
| | | | - M. Hong Nguyen
- University of Florida, Gainesville, FLA, United States of America
| | | | | | - John R. Wingard
- University of Florida, Gainesville, FLA, United States of America
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18
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Brasier AR, Zhao Y, Wiktorowicz JE, Spratt HM, Nascimento EJM, Cordeiro MT, Soman KV, Ju H, Recinos A, Stafford S, Wu Z, Marques ETA, Vasilakis N. Molecular classification of outcomes from dengue virus -3 infections. J Clin Virol 2015; 64:97-106. [PMID: 25728087 DOI: 10.1016/j.jcv.2015.01.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 01/13/2015] [Accepted: 01/16/2015] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Dengue virus (DENV) infection is a significant risk to over a third of the human population that causes a wide spectrum of illness, ranging from sub-clinical disease to intermediate syndrome of vascular complications called dengue fever complicated (DFC) and severe, dengue hemorrhagic fever (DHF). Methods for discriminating outcomes will impact clinical trials and understanding disease pathophysiology. STUDY DESIGN We integrated a proteomics discovery pipeline with a heuristics approach to develop a molecular classifier to identify an intermediate phenotype of DENV-3 infectious outcome. RESULTS 121 differentially expressed proteins were identified in plasma from DHF vs dengue fever (DF), and informative candidates were selected using nonparametric statistics. These were combined with markers that measure complement activation, acute phase response, cellular leak, granulocyte differentiation and viral load. From this, we applied quantitative proteomics to select a 15 member panel of proteins that accurately predicted DF, DHF, and DFC using a random forest classifier. The classifier primarily relied on acute phase (A2M), complement (CFD), platelet counts and cellular leak (TPM4) to produce an 86% accuracy of prediction with an area under the receiver operating curve of >0.9 for DHF and DFC vs DF. CONCLUSIONS Integrating discovery and heuristic approaches to sample distinct pathophysiological processes is a powerful approach in infectious disease. Early detection of intermediate outcomes of DENV-3 will speed clinical trials evaluating vaccines or drug interventions.
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Affiliation(s)
- Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States.
| | - Yingxin Zhao
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States; Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States
| | - John E Wiktorowicz
- Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States; Department of Biochemistry and Molecular Biology, UTMB, United States
| | - Heidi M Spratt
- Sealy Center for Molecular Medicine, UTMB, United States; Institute for Translational Sciences, UTMB, United States; Department Preventive Medicine and Community Health, UTMB, United States
| | - Eduardo J M Nascimento
- Department of Infectious Diseases and Microbiology and Immunology, University of Pittsburgh, United States
| | - Marli T Cordeiro
- Laboratorio de Virologia e Terapie Experimental do Centro de Pesquisas Aggeu Magalhaes-CPqAM, Fiocruz, Recife, Pernambuco, Brazil
| | - Kizhake V Soman
- Sealy Center for Molecular Medicine, UTMB, United States; Department of Biochemistry and Molecular Biology, UTMB, United States
| | - Hyunsu Ju
- Department Preventive Medicine and Community Health, UTMB, United States
| | - Adrian Recinos
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, United States
| | | | - Zheng Wu
- Biomolecular Resource Facility, UTMB, United States
| | - Ernesto T A Marques
- Laboratorio de Virologia e Terapie Experimental do Centro de Pesquisas Aggeu Magalhaes-CPqAM, Fiocruz, Recife, Pernambuco, Brazil; Department of Infectious Diseases and Microbiology and Immunology, University of Pittsburgh, United States
| | - Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, United States; Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, United States; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, United States
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19
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Wiktorowicz JE, Jamaluddin M. Proteomic analysis of the asthmatic airway. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 795:221-32. [PMID: 24162912 DOI: 10.1007/978-1-4614-8603-9_14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Proteomic investigations in general utilize varied technologies for sample preparation, separations, quantification, protein identification, and biological rationalization. Their applications range from pure discovery and mechanistic studies to biomarker discovery/verification/validation. In each specific case, the analytical strategy to be implemented is tailored to the type of sample that serves as the target of the investigations. Proteomic investigations take into consideration sample complexity, the cellular heterogeneity (particularly from tissues), the potential dynamic range of the protein and peptide abundance within the sample, the likelihood of posttranslational modifications (PTM), and other important factors that might influence the final output of the study. We describe the sample types typically used for proteomic investigations into the biology of asthma and review the most recent related publications with special attention to those that deal with the unique airway samples such as bronchoalveolar lavage fluids (BALF), epithelial lining fluid and cells (ELF), induced sputum (IS), and exhaled breath condensate (EBC). Finally, we describe the newest proteomics approaches to sample preparation of the unique airway samples, BALF and IS.
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Affiliation(s)
- John E Wiktorowicz
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, 2.208A Basic Science Bldg, 301 University Blvd, Galveston, TX, 77555-0635, USA,
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20
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Guptarak J, Wiktorowicz JE, Sadygov RG, Zivadinovic D, Paulucci-Holthauzen AA, Vergara L, Nesic O. The cancer drug tamoxifen: a potential therapeutic treatment for spinal cord injury. J Neurotrauma 2013; 31:268-83. [PMID: 24004276 DOI: 10.1089/neu.2013.3108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Tamoxifen (TMX) is a selective estrogen receptor modulator that can mimic the neuroprotective effects of estrogen but lacks its systemic adverse effects. We found that TMX (1 mg/day) significantly improved the motor recovery of partially paralyzed hind limbs of male adult rats with thoracic spinal cord injury (SCI), thus indicating a translational potential for this cancer medication given its clinical safety and applicability and the lack of currently available treatments for SCI. To shed light on the mechanisms underlying the beneficial effects of TMX for SCI, we used proteomic analyses, Western blots and histological assays, which showed that TMX treatment spared mature oligodendrocytes/increased myelin levels and altered reactive astrocytes, including the upregulation of the water channels aquaporin 4 (AQP4), a novel finding. AQP4 increases in TMX-treated SCI rats were associated with smaller fluid-filled cavities with borders consisting of densely packed AQP4-expressing astrocytes that closely resemble the organization of normal glia limitans externa (in contrast to large cavities in control SCI rats that lacked glia limitans-like borders and contained reactive glial cells). Based on our findings, we propose that TMX is a promising candidate for the therapeutic treatment of SCI and a possible intervention for other neuropathological conditions associated with demyelination and AQP4 dysfunction.
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Affiliation(s)
- Jutatip Guptarak
- 1 Department of Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas
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21
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Ullevig S, Kim HS, Asmis R. S-glutathionylation in monocyte and macrophage (dys)function. Int J Mol Sci 2013; 14:15212-32. [PMID: 23887649 PMCID: PMC3759857 DOI: 10.3390/ijms140815212] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 06/15/2013] [Accepted: 06/18/2013] [Indexed: 12/31/2022] Open
Abstract
Atherosclerosis is a chronic inflammatory disease involving the accumulation of monocytes and macrophages in the vascular wall. Monocytes and macrophages play a central role in the initiation and progression of atherosclerotic lesion development. Oxidative stress, which occurs when reactive oxygen species (ROS) overwhelm cellular antioxidant systems, contributes to the pathophysiology of many chronic inflammatory diseases, including atherosclerosis. Major targets of ROS are reactive thiols on cysteine residues in proteins, which when oxidized can alter cellular processes, including signaling pathways, metabolic pathways, transcription, and translation. Protein-S-glutathionylation is the process of mixed disulfide formation between glutathione (GSH) and protein thiols. Until recently, protein-S-glutathionylation was associated with increased cellular oxidative stress, but S-glutathionylation of key protein targets has now emerged as a physiologically important redox signaling mechanism, which when dysregulated contributes to a variety of disease processes. In this review, we will explore the role of thiol oxidative stress and protein-S-glutathionylation in monocyte and macrophage dysfunction as a mechanistic link between oxidative stress associated with metabolic disorders and chronic inflammatory diseases, including atherosclerosis.
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Affiliation(s)
- Sarah Ullevig
- Department of Biochemistry, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; E-Mail:
| | - Hong Seok Kim
- Department of Clinical Laboratory Sciences, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; E-Mail:
| | - Reto Asmis
- Department of Biochemistry, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; E-Mail:
- Department of Clinical Laboratory Sciences, University of Texas Health Science Center San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-210-567-3411; Fax: +1-210-567-3719
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22
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Brasier AR, Garcia J, Wiktorowicz JE, Spratt HM, Comach G, Ju H, Recinos A, Soman K, Forshey BM, Halsey ES, Blair PJ, Rocha C, Bazan I, Victor SS, Wu Z, Stafford S, Watts D, Morrison AC, Scott TW, Kochel TJ. Discovery proteomics and nonparametric modeling pipeline in the development of a candidate biomarker panel for dengue hemorrhagic fever. Clin Transl Sci 2012; 5:8-20. [PMID: 22376251 PMCID: PMC3590808 DOI: 10.1111/j.1752-8062.2011.00377.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Secondary dengue viral infection can produce capillary leakage associated with increased mortality known as dengue hemorrhagic fever (DHF). Because the mortality of DHF can be reduced by early detection and intensive support, improved methods for its detection are needed. We applied multidimensional protein profiling to predict outcomes in a prospective dengue surveillance study in South America. Plasma samples taken from initial clinical presentation of acute dengue infection were subjected to proteomics analyses using ELISA and a recently developed biofluid analysis platform. Demographics, clinical laboratory measurements, nine cytokines, and 419 plasma proteins collected at the time of initial presentation were compared between the DF and DHF outcomes. Here, the subject's gender, clinical parameters, two cytokines, and 42 proteins discriminated between the outcomes. These factors were reduced by multivariate adaptive regression splines (MARS) that a highly accurate classification model based on eight discriminant features with an area under the receiver operator curve (AUC) of 0.999. Model analysis indicated that the feature-outcome relationship were nonlinear. Although this DHF risk model will need validation in a larger cohort, we conclude that approaches to develop predictive biomarker models for disease outcome will need to incorporate nonparametric modeling approaches.
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Affiliation(s)
- Allan R Brasier
- Department of Internal Medicine, University of Texas Medical Branch (UTMB), Galveston, Texas, USA.
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23
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Thiol redox proteomics seen with fluorescent eyes: The detection of cysteine oxidative modifications by fluorescence derivatization and 2-DE. J Proteomics 2011; 75:329-38. [DOI: 10.1016/j.jprot.2011.09.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 09/15/2011] [Accepted: 09/19/2011] [Indexed: 12/11/2022]
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24
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Wiktorowicz JE, Stafford S, Rea H, Urvil P, Soman K, Kurosky A, Perez-Polo JR, Savidge TC. Quantification of cysteinyl S-nitrosylation by fluorescence in unbiased proteomic studies. Biochemistry 2011; 50:5601-14. [PMID: 21615140 PMCID: PMC3133729 DOI: 10.1021/bi200008b] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cysteinyl S-nitrosylation has emerged as an important post-translational modification affecting protein function in health and disease. Great emphasis has been placed on global, unbiased quantification of S-nitrosylated proteins because of physiologic and oxidative stimuli. However, current strategies have been hampered by sample loss and altered protein electrophoretic mobility. Here, we describe a novel quantitative approach that uses accurate, sensitive fluorescence modification of cysteine S-nitrosylation that leaves electrophoretic mobility unaffected (SNOFlo) and introduce unique concepts for measuring changes in S-nitrosylation status relative to protein abundance. Its efficacy in defining the functional S-nitrosoproteome is demonstrated in two diverse biological applications: an in vivo rat hypoxia-ischemia/reperfusion model and antimicrobial S-nitrosoglutathione-driven transnitrosylation of an enteric microbial pathogen. The suitability of this approach for investigating endogenous S-nitrosylation is further demonstrated using Ingenuity Pathways analysis that identified nervous system and cellular development networks as the top two networks. Functional analysis of differentially S-nitrosylated proteins indicated their involvement in apoptosis, branching morphogenesis of axons, cortical neurons, and sympathetic neurites, neurogenesis, and calcium signaling. Major abundance changes were also observed for fibrillar proteins known to be stress-responsive in neurons and glia. Thus, both examples demonstrate the technique's power in confirming the widespread involvement of S-nitrosylation in hypoxia-ischemia/reperfusion injury and in antimicrobial host responses.
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Affiliation(s)
- John E Wiktorowicz
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch , Galveston, Texas 77555, USA.
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25
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Gauci VJ, Wright EP, Coorssen JR. Quantitative proteomics: assessing the spectrum of in-gel protein detection methods. J Chem Biol 2011; 4:3-29. [PMID: 21686332 PMCID: PMC3022124 DOI: 10.1007/s12154-010-0043-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022] Open
Abstract
Proteomics research relies heavily on visualization methods for detection of proteins separated by polyacrylamide gel electrophoresis. Commonly used staining approaches involve colorimetric dyes such as Coomassie Brilliant Blue, fluorescent dyes including Sypro Ruby, newly developed reactive fluorophores, as well as a plethora of others. The most desired characteristic in selecting one stain over another is sensitivity, but this is far from the only important parameter. This review evaluates protein detection methods in terms of their quantitative attributes, including limit of detection (i.e., sensitivity), linear dynamic range, inter-protein variability, capacity for spot detection after 2D gel electrophoresis, and compatibility with subsequent mass spectrometric analyses. Unfortunately, many of these quantitative criteria are not routinely or consistently addressed by most of the studies published to date. We would urge more rigorous routine characterization of stains and detection methodologies as a critical approach to systematically improving these critically important tools for quantitative proteomics. In addition, substantial improvements in detection technology, particularly over the last decade or so, emphasize the need to consider renewed characterization of existing stains; the quantitative stains we need, or at least the chemistries required for their future development, may well already exist.
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Affiliation(s)
- Victoria J. Gauci
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Elise P. Wright
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
| | - Jens R. Coorssen
- Molecular Physiology, School of Medicine, and Molecular Medicine Research Group, University of Western Sydney, Campbelltown, NSW 1797 Australia
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26
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Egelandsdal B, Ren L, Gong Y, Greaser M, Richards M. Factors affecting solubilisation and oxidation of proteins during equine metmyoglobin-mediated lipid oxidation in extensively washed cod muscle. Food Chem 2010. [DOI: 10.1016/j.foodchem.2010.03.092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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27
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Role of peroxiredoxin 1 and peroxiredoxin 4 in protection of respiratory syncytial virus-induced cysteinyl oxidation of nuclear cytoskeletal proteins. J Virol 2010; 84:9533-45. [PMID: 20610706 DOI: 10.1128/jvi.01005-10] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The respiratory epithelium plays a central role in innate immunity by secreting networks of inflammatory mediators in response to respiratory syncytial virus (RSV) infection. Previous proteomic studies focusing on the host cellular response to RSV indicated the existence of a nuclear heat shock response and cytoplasmic depletion of antioxidant proteins in model type II-like airway epithelial cells. Here, we increased the depth of nuclear proteomic interrogation by using fluorescence difference labeling followed by liquid isoelectric focusing prefractionation/two-dimensional gel electrophoresis (2-DE) to identify an additional 41 proteins affected by RSV infection. Surprisingly, we found inducible oligomers and shifts in isoelectric points for peroxiredoxin 1 (Prdx-1), Prdx-3, and Prdx-4 isoforms without changes in their total abundance, indicating that Prdxs were being oxidized in response to RSV. To address the role of Prdx-1 and Prdx-4 in RSV infection, isoforms were selectively knocked down by small interfering RNA (siRNA) transfection. Cells lacking Prdx-1, Prdx-4, or both showed increased levels of reactive oxygen species formation and a higher level of protein carbonylation in response to RSV infection. Using a novel saturation fluorescence labeling 2-DE analysis, we showed that 15 unique proteins had enhanced oxidative modifications of at least >1.2-fold in the Prdx knockdowns in response to RSV, including annexin A2 and desmoplakin. Our results suggest that Prdx-1 and Prdx-4 are essential for preventing RSV-induced oxidative damage in a subset of nuclear intermediate filament and actin binding proteins in epithelial cells.
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Abstract
Schizophrenia is a debilitating condition associated with high morbidity and mortality. While currently available atypical antipsychotic agents have significantly advanced the treatment of schizophrenia, there is still a great unmet need for new, effective and better-tolerated therapies. Iloperidone, a D(2)/5-HT(2) receptor antagonist, has been recently approved by the US FDA for the acute treatment of schizophrenia in adults. Iloperidone has been shown to be effective in the treatment of schizophrenia in four short-term (4-6 weeks) and three long-term (52 weeks) studies with over 3000 patients exposed to treatment. Results also indicated a reassuring safety profile, particularly regarding extrapyramidal symptoms, akathisia and prolactin elevation, with a modest effect on weight gain and no medically important changes in cholesterol, triglycerides and glucose. As other antipsychotics, iloperidone has been shown to prolong the QTc interval. Since none of the current therapies work for every patient, a pharmacogenetic approach was used to identify genetic markers associated with increased response to iloperidone, suggesting a personalized therapeutic option for this drug. In addition, a long-term 4-week injectable formulation is being developed that may assist with patient compliance. Key development findings for iloperidone are presented here.
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Affiliation(s)
- Andrew J Cutler
- Courtesy Assistant Professor, Department of Psychiatry, University of Florida, and CEO and Medical Director, Florida Clinical Research Center, LLC, 3914 SR 64 E, Bradenton, FL 34208, USA.
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Hansen RE, Winther JR. An introduction to methods for analyzing thiols and disulfides: Reactions, reagents, and practical considerations. Anal Biochem 2009; 394:147-58. [DOI: 10.1016/j.ab.2009.07.051] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Revised: 07/31/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
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Ahrends R, Pieper S, Neumann B, Scheler C, Linscheid MW. Metal-Coded Affinity Tag Labeling: A Demonstration of Analytical Robustness and Suitability for Biological Applications. Anal Chem 2009; 81:2176-84. [DOI: 10.1021/ac802310c] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Robert Ahrends
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Stefan Pieper
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Boris Neumann
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Christian Scheler
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
| | - Michael W. Linscheid
- Department of Chemistry, Humboldt-Universitaet zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany, Proteome Factory AG, Dorotheenstrasse 94, 10117 Berlin, Germany, and CCR/Institute of Pharmacology and Toxicology, Charité University Medicine, Hessische Strasse 3-4, 10115 Berlin, Germany
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