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Jeon CH, Ha TH. Covalent and Oriented Immobilization of Antibodies through Systematic Modification of Photoactivatable RNA Hybrid Aptamers. Bioconjug Chem 2022; 33:1527-1535. [DOI: 10.1021/acs.bioconjchem.2c00274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chang Hoon Jeon
- Core Research Facility & Analysis Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
| | - Tai Hwan Ha
- Core Research Facility & Analysis Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, South Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon 34113, South Korea
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2
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Delport A, Hewer R. The amyloid precursor protein: a converging point in Alzheimer's disease. Mol Neurobiol 2022; 59:4501-4516. [PMID: 35579846 DOI: 10.1007/s12035-022-02863-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 04/30/2022] [Indexed: 11/30/2022]
Abstract
The decades of evidence that showcase the role of amyloid precursor protein (APP), and its fragment amyloidβ (Aβ), in Alzheimer's disease (AD) pathogenesis are irrefutable. However, the absolute focus on the single APP metabolite Aβ as the cause for AD has resulted in APP and its other fragments that possess toxic propensity, to be overlooked as targets for treatment. The complexity of its processing and its association with systematic metabolism suggests that, if misregulated, APP has the potential to provoke an array of metabolic dysfunctions. This review discusses APP and several of its cleaved products with a particular focus on their toxicity and ability to disrupt healthy cellular function, in relation to AD development. We subsequently argue that the reduction of APP, which would result in a concurrent decrease in Aβ as well as all other toxic APP metabolites, would alleviate the toxic environment associated with AD and slow disease progression. A discussion of those drug-like compounds already identified to possess this capacity is also included.
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Affiliation(s)
- Alexandré Delport
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa.
| | - Raymond Hewer
- Discipline of Biochemistry, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, 3201, South Africa
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A Cross-Species Study of PI3K Protein-Protein Interactions Reveals the Direct Interaction of P85 and SHP2. Sci Rep 2016; 6:20471. [PMID: 26839216 PMCID: PMC4738311 DOI: 10.1038/srep20471] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/05/2016] [Indexed: 12/14/2022] Open
Abstract
Using a series of immunoprecipitation (IP) – tandem mass spectrometry (LC-MS/MS) experiments and reciprocal BLAST, we conducted a fly-human cross-species comparison of the phosphoinositide-3-kinase (PI3K) interactome in a drosophila S2R+ cell line and several NSCLC and human multiple myeloma cell lines to identify conserved interacting proteins to PI3K, a critical signaling regulator of the AKT pathway. Using H929 human cancer cells and drosophila S2R+ cells, our data revealed an unexpected direct binding of Corkscrew, the drosophila ortholog of the non-receptor protein tyrosine phosphatase type II (SHP2) to the Pi3k21B (p60) regulatory subunit of PI3K (p50/p85 human ortholog) but no association with Pi3k92e, the human ortholog of the p110 catalytic subunit. The p85-SHP2 association was validated in human cell lines, and formed a ternary regulatory complex with GRB2-associated-binding protein 2 (GAB2). Validation experiments with knockdown of GAB2 and Far-Western blots proved the direct interaction of SHP2 with p85, independent of adaptor proteins and transfected FLAG-p85 provided evidence that SHP2 binding on p85 occurred on the SH2 domains. A disruption of the SHP2-p85 complex took place after insulin/IGF1 stimulation or imatinib treatment, suggesting that the direct SHP2-p85 interaction was both independent of AKT activation and positively regulates the ERK signaling pathway.
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Hu L, Yang L, Lipchik AM, Geahlen RL, Parker LL, Tao WA. A quantitative proteomics-based competition binding assay to characterize pITAM-protein interactions. Anal Chem 2013; 85:5071-7. [PMID: 23611696 PMCID: PMC3715304 DOI: 10.1021/ac400359t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Characterization of ligand-protein binding is of crucial importance in drug discovery. Classical competition binding assays measure the binding of a labeled ligand in the presence of various concentrations of unlabeled ligand and typically use single purified proteins. Here, we introduce a high-throughput approach to study ligand-protein interactions by coupling competition binding assays with mass spectrometry-based quantitative proteomics. With the use of a phosphorylated immunoreceptor tyrosine-based activation motif (pITAM) peptide as a model, we characterized pITAM-interacting partners in human lymphocytes. The shapes of competition binding curves of various interacting partners constructed in a single set of quantitative proteomics experiments reflect relative affinities for the pITAM peptide. This strategy can provide an efficient approach to distinguish specific interacting partners, including two signaling kinases possessing tandem SH2 domains, SYK and ZAP-70, as well as other SH2 domain-containing proteins such as CSK and PI3K, from contaminants and to measure relative binding affinities of multiple proteins in a single experiment.
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Affiliation(s)
- Lianghai Hu
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
- College of Life Science, Jilin University, Changchun 130012, PR China
| | - Li Yang
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
| | - Andrew M. Lipchik
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
| | - Robert L. Geahlen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
- Purdue Center for Cancer Research, West Lafayette, IN, 47907
| | - Laurie L. Parker
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
- Purdue Center for Cancer Research, West Lafayette, IN, 47907
| | - W. Andy Tao
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907
- Purdue Center for Cancer Research, West Lafayette, IN, 47907
- Department of Chemistry, Purdue University, West Lafayette, IN 47907
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Chavez JD, Cilia M, Weisbrod CR, Ju HJ, Eng JK, Gray SM, Bruce JE. Cross-linking measurements of the Potato leafroll virus reveal protein interaction topologies required for virion stability, aphid transmission, and virus-plant interactions. J Proteome Res 2012; 11:2968-81. [PMID: 22390342 PMCID: PMC3402239 DOI: 10.1021/pr300041t] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein interactions are critical determinants of insect transmission for viruses in the family Luteoviridae. Two luteovirid structural proteins, the capsid protein (CP) and the readthrough protein (RTP), contain multiple functional domains that regulate virus transmission. There is no structural information available for these economically important viruses. We used Protein Interaction Reporter (PIR) technology, a strategy that uses chemical cross-linking and high resolution mass spectrometry, to discover topological features of the Potato leafroll virus (PLRV) CP and RTP that are required for the diverse biological functions of PLRV virions. Four cross-linked sites were repeatedly detected, one linking CP monomers, two within the RTP, and one linking the RTP and CP. Virus mutants with triple amino acid deletions immediately adjacent to or encompassing the cross-linked sites were defective in virion stability, RTP incorporation into the capsid, and aphid transmission. Plants infected with a new, infectious PLRV mutant lacking 26 amino acids encompassing a cross-linked site in the RTP exhibited a delay in the appearance of systemic infection symptoms. PIR technology provided the first structural insights into luteoviruses which are crucially lacking and are involved in vector-virus and plant-virus interactions. These are the first cross-linking measurements on any infectious, insect-transmitted virus.
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Affiliation(s)
- Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Michelle Cilia
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
| | - Chad R. Weisbrod
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Ho-Jong Ju
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
- Department of Agricultural Biology and Plant Medicinal Research Center, College of Agricultural & Life Sciences, Chonbuk National University, 664-14 Deokjin-Dong 1Ga Deokjin-Gu Jeonju Jeonbuk 561-756, South Korea
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Stewart M. Gray
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, 14853
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York 14853
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
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West R, Whitmon J, Williamson YM, Moura H, Nelson M, Melnick N, Tondella MLC, Schieltz D, Rees J, Woolfitt AR, Barr JR, Ades EW, Carlone GM, Sampson JS. A rapid method for capture and identification of immunogenic proteins in Bordetella pertussis enriched membranes fractions: a fast-track strategy applicable to other microorganisms. J Proteomics 2012; 75:1966-72. [PMID: 22245551 DOI: 10.1016/j.jprot.2011.12.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 12/12/2011] [Accepted: 12/23/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry (MS) coupled with 1-D and 2-D electrophoresis can be utilized to detect and identify immunogenic proteins, but these methods are laborious and time-consuming. We describe an alternative, simple, rapid gel-free strategy to identify multiple immunogenic proteins from Bordetella pertussis (Bp). It couples immunoprecipitation to nano liquid chromatography- tandem mass spectrometry (IP-nLC-MS/MS) and is significantly both time- and labor-saving. We developed a gel-free magnetic bead-based immunoprecipitation (IP) method using different NP-40/PBS concentrations in which solubilized proteins of Bp Tohama I membrane fractions were precipitated with polyclonal rabbit anti-Bp whole cell immune sera. Immune complexes were analyzed by MS and Scaffold analysis (>95% protein identification probability). Total immunoproteins identified were 50, 63 and 49 for 0.90%, 0.45% and 0.22% NP-40/PBS buffer concentrations respectively. Known Bp proteins identified included pertactin, serotype 2 fimbrial subunit and filamentous hemagglutinin. As proof of concept that this gel-free protein immunoprecipitation method enabled the capture of multiple immunogenic proteins, IP samples were also analyzed by SDS-PAGE and immunoblotting. Bypassing gels and subjecting immunoprecipitated proteins directly to MS is a simple and rapid antigen identification method with relatively high throughput. IP-nLC-MS/MS provides a novel alternative approach for current methods used for the identification of immunogenic proteins.
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Affiliation(s)
- Rolieria West
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
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Yang L, Vaitheesvaran B, Hartil K, Robinson AJ, Hoopmann MR, Eng JK, Kurland IJ, Bruce JE. The fasted/fed mouse metabolic acetylome: N6-acetylation differences suggest acetylation coordinates organ-specific fuel switching. J Proteome Res 2011; 10:4134-49. [PMID: 21728379 PMCID: PMC3204869 DOI: 10.1021/pr200313x] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The elucidation of extra-nuclear lysine acetylation has been of growing interest, as the cosubstrate for acetylation, acetyl CoA, is at a key metabolic intersection. Our hypothesis was that mitochondrial and cytoplasmic protein acetylation may be part of a fasted/re-fed feedback control system for the regulation of the metabolic network in fuel switching, where acetyl CoA would be provided by fatty acid oxidation, or glycolysis, respectively. To test this, we characterized the mitochondrial and cytoplasmic acetylome in various organs that have a high metabolic rate relative to their mass, and/or switch fuels, under fasted and re-fed conditions (brain, kidney, liver, skeletal muscle, heart muscle, white and brown adipose tissues). Using immunoprecipitation, coupled with LC-MS/MS label free quantification, we show there is a dramatic variation in global quantitative profiles of acetylated proteins from different organs. In total, 733 acetylated peptides from 337 proteins were identified and quantified, out of which 31 acetylated peptides from the metabolic proteins that may play organ-specific roles were analyzed in detail. Results suggest that fasted/re-fed acetylation changes coordinated by organ-specific (de)acetylases in insulin-sensitive versus -insensitive organs may underlie fuel use and switching. Characterization of the tissue-specific acetylome should increase understanding of metabolic conditions wherein normal fuel switching is disrupted, such as in Type II diabetes.
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Affiliation(s)
- Li Yang
- Department of Chemistry, Washington State University, Pullman, Washington, 99164
| | - Bhavapriya Vaitheesvaran
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine Diabetes Center, Bronx, New York, 10461
| | - Kirsten Hartil
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine Diabetes Center, Bronx, New York, 10461
| | - Alan J. Robinson
- Medical Research Council Mitochondrial Biology Unit, Cambridge, CB2 0XY, United Kingdom
| | - Michael R. Hoopmann
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
| | - Jimmy K. Eng
- University of Washington Proteomics Resource, Seattle, Washington, 98109
| | - Irwin J. Kurland
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Albert Einstein College of Medicine Diabetes Center, Bronx, New York, 10461
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98109
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Yang X, Turke AB, Qi J, Song Y, Rexer BN, Miller TW, Jänne PA, Arteaga CL, Cantley LC, Engelman JA, Asara JM. Using tandem mass spectrometry in targeted mode to identify activators of class IA PI3K in cancer. Cancer Res 2011; 71:5965-75. [PMID: 21775521 DOI: 10.1158/0008-5472.can-11-0445] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Phosphatiditylinositide-3-kinase (PI3K) is activated in some cancers by direct mutation, but it is activated more commonly in cancer by mutation of upstream acting receptor tyrosine kinases (TK). At present, there is no systematic method to determine which TK signaling cascades activate PI3K in certain cancers, despite the likely utility of such information to help guide selection of tyrosine kinase inhibitor (TKI) drug strategies for personalized therapy. Here, we present a quantitative liquid chromatography tandem mass spectrometry approach that identifies upstream activators of PI3K both in vitro and in vivo. Using non-small cell lung carcinoma to illustrate this approach, we show a correct identification of the mechanism of PI3K activation in several models, thereby identifying the most appropriate TKI to downregulate PI3K signaling. This approach also determined the molecular mechanisms and adaptors required for PI3K activation following inhibition of the mTOR kinase TORC1. We further validated the approach in breast cancer cells with mutational activation of PIK3CA, where tandem mass spectrometry detected and quantitatively measured the abundance of a helical domain mutant (E545K) of PIK3CA connected to PI3K activation. Overall, our findings establish a mass spectrometric approach to identify functional interactions that govern PI3K regulation in cancer cells. Using this technique to define the pathways that activate PI3K signaling in a given tumor could help inform clinical decision making by helping guide personalized therapeutic strategies for different patients.
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Affiliation(s)
- Xuemei Yang
- Beth Israel Deaconess Medical Center, Division of Signal Transduction, Boston, Massachusetts 02115, USA
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Bane TK, Timmons MS, Kauffman SJ, Catlin DH. Enrichment and immunoprecipitation of 22 kDa human growth hormone spiked into human urine. Drug Test Anal 2009; 1:441-6. [DOI: 10.1002/dta.101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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