Bibliografie tematiche / Affinity-Based protein profiling

Letteratura scientifica selezionata sul tema "Affinity-Based protein profiling"

Autore: Grafiati

Pubblicato: 8 giugno 2024

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Articoli di riviste sul tema "Affinity-Based protein profiling":

Wirsing, Lisette, Kai Naumann e Thomas Vogt. "Arabidopsis methyltransferase fingerprints by affinity-based protein profiling". Analytical Biochemistry 408, n. 2 (gennaio 2011): 220–25. http://dx.doi.org/10.1016/j.ab.2010.09.029.

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Lafreniere, Matthew A., Geneviève F. Desrochers, Kedous Mekbib e John Paul Pezacki. "An affinity-based probe for methyltransferase enzymes based on sinefungin". Canadian Journal of Chemistry 95, n. 10 (ottobre 2017): 1059–63. http://dx.doi.org/10.1139/cjc-2017-0168.

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Abstract (sommario):

Epigenetics control numerous cellular processes such as gene transcription, signal transduction, and protein stabilization. An understanding of epigenetic mechanisms can lead to the development of therapeutic agents for various diseases. Herein, we report the design and synthesis of a sinefungin affinity-probe (BpyneSF) that targets methyltranferase enzymes and proteins involved in recognition of methylation. This probe contains a bioorthogonal alkyne residue for conjugation using the copper-catalyzed azide–alkyne cycloaddition and a photoactivatable crosslinker group for covalent attachment of the probe to its proteomic targets. We investigate the efficiency and selectivity of the probe to inhibit and label methyltransferase enzymes, and we demonstrate, through in-gel fluorescence, on-bead digestion, and tandem mass spectrometry, that BpyneSF can label methyltransferase SETD2 and reader proteins in vitro. These results establish the utility of BpyneSF as a tool for affinity-based protein profiling in complex biological environments.

Buneeva, Olga, Arthur Kopylov, Oksana Gnedenko, Marina Medvedeva, Alexander Veselovsky, Alexis Ivanov, Victor Zgoda e Alexei Medvedev. "Proteomic Profiling of Mouse Brain Pyruvate Kinase Binding Proteins: A Hint for Moonlighting Functions of PKM1?" International Journal of Molecular Sciences 24, n. 8 (21 aprile 2023): 7634. http://dx.doi.org/10.3390/ijms24087634.

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Affinity-based proteomic profiling is widely used for the identification of proteins involved in the formation of various interactomes. Since protein–protein interactions (PPIs) reflect the role of particular proteins in the cell, identification of interaction partners for a protein of interest can reveal its function. The latter is especially important for the characterization of multifunctional proteins, which can play different roles in the cell. Pyruvate kinase (PK), a classical glycolytic enzyme catalyzing the last step of glycolysis, exists in four isoforms: PKM1, PKM2, PKL, and PKR. The enzyme isoform expressed in actively dividing cells, PKM2, exhibits many moonlighting (noncanonical) functions. In contrast to PKM2, PKM1, predominantly expressed in adult differentiated tissues, lacks well-documented moonlighting functions. However, certain evidence exists that it can also perform some functions unrelated to glycolysis. In order to evaluate protein partners, bound to PKM1, in this study we have combined affinity-based separation of mouse brain proteins with mass spectrometry identification. The highly purified PKM1 and a 32-mer synthetic peptide (PK peptide), sharing high sequence homology with the interface contact region of all PK isoforms, were used as the affinity ligands. This proteomic profiling resulted in the identification of specific and common proteins bound to both affinity ligands. Quantitative affinity binding to the affinity ligands of selected identified proteins was validated using a surface plasmon resonance (SPR) biosensor. Bioinformatic analysis has shown that the identified proteins, bound to both full-length PKM1 and the PK peptide, form a protein network (interactome). Some of these interactions are relevant for the moonlighting functions of PKM1. The proteomic dataset is available via ProteomeXchange with the identifier PXD041321.

Jung, Se-Hui, Kangseung Lee, Deok-Hoon Kong, Woo Jin Kim, Young-Myeong Kim e Kwon-Soo Ha. "Integrative Proteomic Profiling of Protein Activity and Interactions Using Protein Arrays". Molecular & Cellular Proteomics 11, n. 11 (26 luglio 2012): 1167–76. http://dx.doi.org/10.1074/mcp.m112.016964.

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Abstract (sommario):

Proteomic studies based on abundance, activity, or interactions have been used to investigate protein functions in normal and pathological processes, but their combinatory approach has not been attempted. We present an integrative proteomic profiling method to measure protein activity and interaction using fluorescence-based protein arrays. We used an on-chip assay to simultaneously monitor the transamidating activity and binding affinity of transglutaminase 2 (TG2) for 16 TG2-related proteins. The results of this assay were compared with confidential scores provided by the STRING database to analyze the functional interactions of TG2 with these proteins. We further created a quantitative activity-interaction map of TG2 with these 16 proteins, categorizing them into seven groups based upon TG2 activity and interaction. This integrative proteomic profiling method can be applied to quantitative validation of previously known protein interactions, and in understanding the functions and regulation of target proteins in biological processes of interest.

Ma, Nan, Zhi-Min Zhang, Jun-Seok Lee, Ke Cheng, Ligen Lin, Dong-Mei Zhang, Piliang Hao, Ke Ding, Wen-Cai Ye e Zhengqiu Li. "Affinity-Based Protein Profiling Reveals Cellular Targets of Photoreactive Anticancer Inhibitors". ACS Chemical Biology 14, n. 12 (19 novembre 2019): 2546–52. http://dx.doi.org/10.1021/acschembio.9b00784.

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Chen, Xiong, Menglin Li, Manru Li, Dongmei Wang e Jinlan Zhang. "Harnessing affinity-based protein profiling to reveal a novel target of nintedanib". Chemical Communications 57, n. 25 (2021): 3139–42. http://dx.doi.org/10.1039/d1cc00354b.

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We identified tripeptidyl-peptidase 1 (TPP1) as one of the direct targets of nintedanib (NDNB) employing clickable photoaffinity probes, which provides insights into the functional meaning of the well-known IPF therapeutic drug.

Chou, Po-Hung, Shu-Hua Chen, Hsin-Kai Liao, Po-Chiao Lin, Gour-Rong Her, Alan Chuan-Ying Lai, Jenn-Han Chen, Chun-Cheng Lin e Yu-Ju Chen. "Nanoprobe-Based Affinity Mass Spectrometry for Selected Protein Profiling in Human Plasma". Analytical Chemistry 77, n. 18 (settembre 2005): 5990–97. http://dx.doi.org/10.1021/ac050655o.

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Lyu, Peng, Shengrong Li, Ying Han, Shengnan Shen, Zheling Feng, Piliang Hao, Zhengqiu Li e Ligen Lin. "Affinity-based protein profiling-driven discovery of myricanol as a Nampt activator". Bioorganic Chemistry 133 (aprile 2023): 106435. http://dx.doi.org/10.1016/j.bioorg.2023.106435.

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Cheng, Xiamin, Lin Li, Mahesh Uttamchandani e Shao Q. Yao. "A tuned affinity-based staurosporine probe for in situ profiling of protein kinases". Chemical Communications 50, n. 22 (2014): 2851. http://dx.doi.org/10.1039/c4cc00184b.

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Mezentsev, Yuri, Pavel Ershov, Evgeniy Yablokov, Leonid Kaluzhskiy, Konstantin Kupriyanov, Oksana Gnedenko e Alexis Ivanov. "Protein Interactome Profiling of Stable Molecular Complexes in Biomaterial Lysate". International Journal of Molecular Sciences 23, n. 24 (10 dicembre 2022): 15697. http://dx.doi.org/10.3390/ijms232415697.

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Abstract (sommario):

Most proteins function as part of various complexes, forming via stable and dynamic protein–protein interactions (PPIs). The profiling of PPIs expands the fundamental knowledge about the structures, functions, and regulation patterns of protein complexes and intracellular molecular machineries. Protein interactomics aims at solving three main tasks: (1) identification of protein partners and parts of complex intracellular structures; (2) analysis of PPIs parameters (affinity, molecular-recognition specificity, kinetic rate constants, and thermodynamic-parameters determination); (3) the study of the functional role of novel PPIs. The purpose of this work is to update the current state and prospects of multi-omics approaches to profiling of proteins involved in the formation of stable complexes. Methodological paradigm includes a development of protein-extraction and -separation techniques from tissues or cellular lysates and subsequent identification of proteins using mass-spectrometry analysis. In addition, some aspects of authors’ experimental platforms, based on high-performance size-exclusion chromatography, procedures of molecular fishing, and protein identification, as well as the possibilities of interactomic taxonomy of each protein, are discussed.

Più fonti

Tesi sul tema "Affinity-Based protein profiling":

Mahajan, Shikha. "Protein Profiling of Adenine Nucleoside and Nucleotide Analogs Binding Proteins Using N6-Biotinylated-8-azidoadenosine Analogs as Affinity Based Protein Profiling Probes". Scholar Commons, 2012. http://scholarcommons.usf.edu/etd/4139.

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Identification of differential expressions of proteins in proteomic profiles of biological samples shows great potential as a valuable technique for the early diagnosis of various diseases. An important challenge in modern protein profiling approaches is to reduce the complexity of the samples by limiting the number of proteins that need to be evaluated for distinction in the expression between normal and deceased cells. In this research, an affinity based approach for the enrichment of nucleotide and nucleoside binding proteins from a complex cell proteome has been developed. To achieve this goal, new N6-biotinylated-8-azido-adenosine probes (AdoRs) have been designed and synthesized to photolabel the nucleotide and nucleoside binding proteins. These probes contain a reactive group that forms a covalent bond with the target proteins, as well as a biotin tag for affinity enrichment using avidin chromatography. Further, a mass spectrometric protein profiling approach is employed to quantitatively identify small variations in expression of nucleoside and nucleotide binding proteins in samples of interest. Mouse neuroblastoma N18TG2 cell proteome has been used as a model system for the development of the LC-MS/MS based proteomic analysis of these affinity enriched protein fractions. Upon enrichment, the photolabeled proteome exhibited an approximately four-fold abundance of nucleoside and nucleotide binding proteins over nonlabeled proteome. The approach was extended to compare the proteomic profiles of nucleotide and nucleoside binding proteins in cancerous (Hey) and non-cancerous (T-80) human ovarian cell proteome. Certain proteins that were not detected in cell lysate were also identified in labeled proteome, thereby demonstrating the strength of our approach in enriching low abundant proteins. To substantiate the qualitative analysis, we have employed the Stable Isotope Labeling in Amino Acid Cell Culture (SILAC) for the quantitative study of the protein expression in cancerous and non-cancerous human ovarian cells. A modest panel of proteins with differential expressions in these cell lines was identified, a few of which have been correlated to various forms of cancer. Vimentin, stress induced phosphoprotein-1, and heat shock protein 90 that were identified to have altered expressions in these cell lines are among some of the proteins associated with ovarian cancer.

Yedji, Rodrigue. "Perturbateurs endocriniens de type phtalate et poisson zèbre Danio rerio : approche chémoprotéomique pour l'identification des cibles et recherche de signatures d'exposition". Electronic Thesis or Diss., Université de Lorraine, 2022. http://www.theses.fr/2022LORR0106.

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Abstract (sommario):

Les esters de phtalate constituent une famille de composés synthétiques très répandue du fait de leurs usages comme plastifiants. Ils entrent dans la composition de plusieurs produits plastiques tels que les emballages, les jouets, les produits cosmétiques, certains systèmes de toiture en plastique, ainsi que les matériaux de décoration de meubles. Les phtalates ne sont pas liés de manière covalente à la matrice des polymères et sont donc facilement rejetés dans l'environnement, entraînant par conséquent une exposition animale et humaine. En absence de produits de substitutions non-toxiques, les composés de type phtalate restent encore largement utilisés dans l'industrie en dépit de la classification de certains d'entre eux dans la catégorie des substances présumées toxiques par l'European Chemicals Agency (ECHA), en tant que perturbateurs endocriniens. De plus, ils sont cancérigènes et tératogènes. L'effet délétère des esters de phtalates sur les organismes est établi mais le caractère multiple des effets observés montre que les mécanismes d'action des phtalates ne sont que très partiellement élucidés. Nous avons utilisé deux approches de protéomique ciblée pour tenter d'éclairer nos connaissances sur les mécanismes d'actions des esters de phtalate. Pour cela, le dibutyl phtalate (DBP) a été utilisé comme phtalate modèle, et le poisson zèbre (D. rerio) comme organisme modèle. L'utilisation de la première approche de protéomique ciblée, le profilage protéique basé sur l'affinité (affinity-based protein profiling, AfBPP) a permis de montrer la perturbation fonctionnelle de protéines par le DBP avec des sondes photoactivables issues de la synthèse de types aryle azide. L'optimisation des conditions de fixation des sondes diazirine (Diazirine 2) devrait nous permettre de disposer d'une sonde pouvant être utilisée pour identifier les cibles protéiques du DBP dans le protéome du poisson zèbre. La deuxième approche, le profilage basé sur l'activité des enzymes (activity-based protein profiling, ABPP) a permis d'utiliser une sonde réactive spécifique des hydrolases à sérine (SHs) pour cartographier pour la première fois des SHs actives dans le protéome du poisson zèbre. L'identification des SHs dérégulées en présence de DBP chez les larves de poisson zèbre a également été rapportée dans cette étude. Nos résultats globaux indiquent que les approches de protéomiques ciblées telles que l'ABPP ou l'AfBPP peuvent être un atout pour comprendre les mécanismes d'action liés aux xénobiotiques en écotoxicologie
Phthalate esters are a family of synthetic compounds widely used as plasticisers. They are used in a number of plastic products such as packaging, toys, cosmetics, plastic roofing system and furniture decoration materials. Phthalates are not covalently bonded to the polymer matrix and are therefore easily released into the environment, resulting in animal and human exposure. In the absence of non-toxic substitutes, phthalate compounds are still widely used in industry, despite the classification of some of them by the European Chemicals Agency (ECHA) as suspected toxic substances and as endocrine disruptors. In addition, they are carcinogenic and teratogenic. The deleterious effect of phthalate esters on organisms is established, but the multiple nature of the effects observed shows that the mechanisms of action of phthalates are only partially elucidated. We used two targeted proteomics approaches to shed light on the mechanisms of action of phthalate esters. Dibutyl phthalate (DBP) was used as a model phthalate and zebrafish (D. rerio) as a model organism. Using the first targeted proteomics approach, affinity-based protein profiling (AfBPP), the functional disruption of proteins by DBP with photoaffinity probes from aryl azide synthesis was demonstrated. Optimisation of the binding conditions for diazirine probes (Diazirine 2) should provide us with a probe that can be used to identify DBP protein targets in the zebrafish proteome. The second approach, activity-based protein profiling (ABPP), used a reactive probe specific for serine hydrolases (SHs) to map active SHs in the zebrafish proteome for the first time. The identification of deregulated SHs in the presence of DBP in zebrafish larvae was also reported in this study. Overall, our results indicate that targeted proteomics approaches such as ABPP or AfBPP can be an asset for understanding xenobiotic-related mechanisms of action in ecotoxicology

Qundos, Ulrika. "Antibody based plasma protein profiling". Doctoral thesis, KTH, Proteomik och nanobioteknologi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-126270.

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This thesis is about protein profiling in serum and plasma using antibody suspension bead arrays for the analysis of biobanked samples and in the context of prostate cancer biomarker discovery. The influence of sample preparation methods on antibody based protein profiles were investigated (Papers I-III) and a prostate cancer candidate biomarker identified and verified (Papers III-V). Furthermore, a perspective on the research area affinity proteomics and its’ employment in biomarker discovery, for improved understanding and potentially improved disease diagnosis, is provided. Paper I presents the results of a comparative plasma and serum protein profiling study, with a targeted biomarker discovery approach in the context of metabolic syndrome. The study yielded a higher number of significant findings and a low experimental variability in blood samples prepared as plasma. Paper II investigated the effects from post-centrifugation delays at different temperatures prior sample storage of serum and plasma samples. Minor effects were found on the detected levels of more than 300 predicted or known plasma proteins. In Paper III, the detectability of proteins in plasma was explored by exposing samples to different pre-analytical heat treatments, prior target capture. Heat induced epitope retrieval was observed for approximately half of the targeted proteins, and resulted in the discovery of different candidate markers for prostate cancer. Several antibodies towards the prostate cancer candidate biomarker CNDP1 were generated, epitope mapped and evaluated in a bead based sandwich immunoassay, as presented in Papers IV and V. Furthermore, the developed sandwich immunoassay targeting multiple distinct CNDP1 epitopes in more than 1000 samples, confirmed the association of CNDP1 levels to aggres- sive prostate cancer and more specifically to prostate cancer patients with regional lymph node metastasis (Paper V). As an outcome of the present investigations and in parallel to studies within the Biobank profiling research group, valuable lessons from study design and multiplex antibody analysis of plasma within biomarker discovery to experimental, technical and biological verifications have been collected.

QC 20130821

Neiman, Maja. "Bead based protein profiling in blood". Doctoral thesis, KTH, Proteomik, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-117960.

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This thesis is about protein profiling in blood-derived samples using suspension bead ar- rays built with protein affinity reagents, and the evaluation of binding characteristics and potential disease relation of such profiles. A central aim of the presented work was to discover and verify disease associated protein profiles in blood-derived samples such as serum or plasma. This was based on immobiliz- ing antigens or antibodies on color-coded beads for a multiplexed analysis. This concept generally allow for a dual multiplexing because hundreds of samples can be screened for hundreds of proteins in a miniaturized and parallelized fashion. At first, protein antigens were used to study humoral immune responses in cattle suffering from a mycoplasma infec- tion (Paper I). Here, the most immunogenic of the applied antigens were identified based on reactivity profiles from the infected cattle, and were combined into an antigen cocktail to serve as a diagnostic assay in a standard ELISA set-up. Next, antibodies and their em- ployment in assays with directly labeled human samples was initiated. This procedure was applied in a study of kidney disorders where screening of plasma resulted in the discovery of a biomarker candidate, fibulin-1 (Paper II). In parallel to the disease related applica- tions, systematic evaluations of the protein profiles were conducted. Protein profiles from 2,300 antibodies were classified on the bases of binding properties in relation to sample heating and stringent washing (Paper III). With a particular focus on heat dependent de- tectability, a method was developed to visualize those proteins that were captured to the beads in an immunoassay by using Western blotting (Paper IV). In conclusion, this thesis presents examples of the possibilities of comparative plasma profiling enabled by protein bead arrays.

QC 20130208

Drobin, Kimi. "Antibody-based bead arrays for high-throughput protein profiling in human plasma and serum". Licentiate thesis, KTH, Proteinvetenskap, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-225980.

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Affinity-based proteomics utilizes affinity binders to detect target proteins in a large-scale manner. This thesis describes a high-throughput method, which enables the search for biomarker candidates in human plasma and serum. A highly multiplexed antibody-based suspension bead array is created by coupling antibodies generated in the Human Protein Atlas project to color-coded beads. The beads are combined for parallel analysis of up to 384 analytes in patient and control samples. This provides data to compare protein levels from the different groups. In paper I osteoporosis patients are compared to healthy individuals to find disease-linked proteins. An untargeted discovery screening was conducted using 4608 antibodies in 16 cases and 6 controls. This revealed 72 unique proteins, which appeared differentially abundant. A validation screening of 91 cases and 89 controls confirmed that the protein autocrine motility factor receptor (AMFR) is decreased in the osteoporosis patients. Paper II investigates the risk proteome of inflammatory bowel disease (IBD). Antibodies targeting 209 proteins corresponding to 163 IBD genetic risk loci were selected. To find proteins related to IBD or its subgroups, sera from 49 patients with Crohn’s disease, 51 with ulcerative colitis and 50 matched controls were analyzed. From these targeted assays, the known inflammation-related marker serum amyloid protein A (SAA) was shown to be elevated in the IBD cases. In addition, the protein laccase (multi-copper oxidoreductase) domain containing 1 (LACC1) was found to be decreased in the IBD subjects. In conclusion, assays using affinity-based bead arrays were developed and applied to screen human plasma and serum samples in two disease contexts. Untargeted and targeted screening strategies were applied to discover disease-associated proteins. Upon further validation, these potential biomarker candidates could be valuable in future disease studies.

QC 20180412

Rosa, Mira Anne dela Cruz dela, e 羅米拉. "Targeted Quantification and Glycosylation Profiling of Protein Biomarkers by Nanoprobe-based Affinity Mass Spectrometry". Thesis, 2016. http://ndltd.ncl.edu.tw/handle/84414137238466490842.

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博士
國立臺灣大學
化學研究所
104
Disease biomarker development is plagued by lack of acceptable analytical methods, difficulty and cost for method development, overwhelming need for validation on a large population and the poor performance of biomarkers under development. In this dissertation, we introduce alternative methods for protein biomarker discovery and validation that encompasses quantification and post-translational modification (PTM) profiling in non-invasive specimens. We first designed surfactant-coated monodisperse magnetic nanoprobes to improve detection sensitivity (MNP@IGEPAL). Following oriented antibody immobilization for increased specificity and immuno-activity, the MNP@IGEPAL were found to be superior in solvent dispersibility and enrichment efficiency compared to nanoprobes obtained by conventional co-precipitation method (MNPCP). We then coupled the MNP@IGEPAL-based enrichment to multiple reaction monitoring mass spectrometry (MRM-MS) for multiplexed quantification of alpha-fetoprotein (AFP) and golgi membrane protein 1 (GOLM1), which are low-abundant biomarkers in human serum. The method was found to be sensitive, have good analytical merits (average precision and accuracy of 15%) and wide dynamic range. This method was applied to qualify the biomarkers in serum of liver disease patients, where we found that AFP and GOLM1 had similar diagnostic accuracy for hepatocellular carcinoma (HCC), although AFP has a higher false negative rate (sensitivity = 22%). More importantly, we found complementarity between AFP and GOLM1, where GOLM1 was found to be elevated in 69% of patients with low AFP concentration (<20 ng/mL). To supplement disease diagnoses based on protein concentration, we designed a one-pot dual nanoprobe-based mass spectrometry method to simultaneously quantify the protein and profile its post-translational modification (PTM). Using AFP and another clinically-relevant protein, haptoglobin (Hp), we were able to quantify the protein and profile its glycoforms with superior speed and sensitivity and minimal amount of sample. In addition to obtaining individual biosignatures of AFP in HCC patients, we were able to identify a total of 59 glycoforms, 12 of which were identified on AFP for the first time. Ultimately, we were able to develop methods that can improve disease diagnosis, which can be applied to other cancers and diseases for large-scale biomarker triaging, qualification and PTM profiling.

Capitoli di libri sul tema "Affinity-Based protein profiling":

Birgersson, Elin, Jochen M. Schwenk e Burcu Ayoglu. "Bead-Based and Multiplexed Immunoassays for Protein Profiling via Sequential Affinity Capture". In Methods in Molecular Biology, 45–54. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7057-5_4.

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Atti di convegni sul tema "Affinity-Based protein profiling":

Warder, Scott E., Shaun M. McLoughlin, T. Matthew Hansen, Paul L. Richardson, Denise M. Wilcox, Sadiya N. Addo, Hua Tang et al. "Abstract 3059: Discovery of BET family proteins as cancer targets using phenotypic-based profiling and affinity capture mass spectrometry". In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-3059.

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