Relevant bibliographies by topics / Affinity labeling

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Affinity labeling'

Author: Grafiati
Published: 4 June 2021
Last updated: 25 February 2023

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Journal articles on the topic "Affinity labeling"

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Ji, Tae H., and Inhae Ji. "Macromolecular affinity labeling." In Vitro Cellular & Developmental Biology 25, no. 8 (August 1989): 676–78. http://dx.doi.org/10.1007/bf02623719.

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Martini, C., and A. Lucacchini. "Affinity Labeling of Adenosine A1Binding Sites." Journal of Neurochemistry 49, no. 3 (September 1987): 681–84. http://dx.doi.org/10.1111/j.1471-4159.1987.tb00947.x.

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SWEET, FREDERICK, and GARY L. MURDOCK. "Affinity Labeling of Hormone-Specific Proteins*." Endocrine Reviews 8, no. 2 (May 1987): 154–84. http://dx.doi.org/10.1210/edrv-8-2-154.

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Shi, Yi Qun, Setsuo Furuyoshi, Ivo Hubacek, and Robert R. Rando. "Affinity labeling of lecithin retinol acyltransferase." Biochemistry 32, no. 12 (March 1993): 3077–80. http://dx.doi.org/10.1021/bi00063a019.

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Li, Hong-yu, Ying Liu, Kan Fang, and Koji Nakanishi. "A simple photo-affinity labeling protocol." Chemical Communications, no. 4 (1999): 365–66. http://dx.doi.org/10.1039/a809507h.

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SYVERTSEN, Christian, and John S. McKINLEY-McKEE. "Affinity Labeling of Liver Alcohol Dehydrogenase." European Journal of Biochemistry 117, no. 1 (March 3, 2005): 165–70. http://dx.doi.org/10.1111/j.1432-1033.1981.tb06316.x.

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Vinkenborg, Jan L., Günter Mayer, and Michael Famulok. "Aptamer-Based Affinity Labeling of Proteins." Angewandte Chemie International Edition 51, no. 36 (August 2, 2012): 9176–80. http://dx.doi.org/10.1002/anie.201204174.

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Takaoka, Yousuke, Yuuki Nukadzuka, and Minoru Ueda. "Reactive group-embedded affinity labeling reagent for efficient intracellular protein labeling." Bioorganic & Medicinal Chemistry 25, no. 11 (June 2017): 2888–94. http://dx.doi.org/10.1016/j.bmc.2017.02.059.

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Nakanishi, Shuichi, Hiroyuki Tanaka, Kazuhito Hioki, Kohei Yamada, and Munetaka Kunishima. "Labeling study of avidin by modular method for affinity labeling (MoAL)." Bioorganic & Medicinal Chemistry Letters 20, no. 23 (December 2010): 7050–53. http://dx.doi.org/10.1016/j.bmcl.2010.09.109.

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Rivera-Monroy, Zuly, Guenther K. Bonn, and András Guttman. "Fluorescent isotope-coded affinity tag 2: Peptide labeling and affinity capture." ELECTROPHORESIS 30, no. 7 (April 2009): 1111–18. http://dx.doi.org/10.1002/elps.200800830.

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Dissertations / Theses on the topic "Affinity labeling"

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Kuzmich, Oleksandra. "Metal Labeling for Low Affinity Binding Biomolecules." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/18862.

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Unter den Techniken der chemischen Proteomik hat Capture Compound – Massenspektrometrie (CCMS) den Vorteil, Interaktionen von Molekülen mit geringer Affinität zueinander effektiv untersuchen zu können. CCMS beruht auf kleinen molekularen Sonden (Capture Compounds, CCs), die aus drei funktionalen Bestandteilen bestehen: die Selektivitätsfunktion, ist ein kleines Molekül, das mit einem Zielprotein eine schwache Wechselwirkung eingeht. Die zweite Funktionalität erlaubt kovalente Anhaftung der molekularen Sonde an Proteine. Der dritte Anteil erlaubt Detektion mit sehr guten Sensitivität; allerdings ist die Quantifizierung weiterhin ein Schwachpunkt dieser Technik. Ziel dieses Projektes ist, eine in CCMS verwendbare Quantifizierungsmethode zu entwickeln. Heutzutage gibt es zahlreiche MS-basierte Quantifizierungsstrategien; unsere beruht auf der Einführung von Lanthanoid-haltigen Labels – Metal Coded Affinity Tagging (MeCAT). In dieser Arbeit wurde erstmalig die erfolgreiche Verwendung mit Metall- Markern chemoproteomischer Sonden (CCs) zur Detektion und absoluten Quantifizierung von Zielproteinen mit schwacher Wechselwirkung etabliert. Mit den Experimenten an isolierten Enzymen und an lebenden Zellen wurde nachgewiesen, dass Metall-Marker keinen negativen Einfluss auf andere funktionelle Teile chemoproteomischer Sonden haben. CCs, die mit Lanthanoid-Chelaten funktionalisiert sind, zeigen ähnliche Affinität zu ihren Zielproteinen wie die Referenz-Sonden. Zudem erlauben Metall-Marker, die für diese Art molekularer Sonden verwendet werden, die Entwicklung einer element-basierten Technik zur Bilderzeugung. Der herausragende Vorteil der Metall-funktionalisierten CCs kombiniert mit ICP-MS ist, dass diese eine absolute Quantifizierung der Ausbeute der Quervernetzungen ermöglichen.
Capture compound mass spectrometry (CCMS) is a chemical proteomics technique that has the advantage of addressing low abundant target proteins in lysates as well as in living cells. The CCMS is based on small molecule probes (capture compounds) that consist of three functionalities: a small molecule (quite often it is a drug), which interacts with the target protein; the moiety that allows covalent attachment of the molecular probe to the protein; the one that allows detection. The detection moiety utilized for CCMS can offer high sensitivity; however, the challenge of absolute quantification is still a bottleneck of this technique. Metal Coded Affinity Tagging (MeCAT) is a quantitative approach based on the chemical labeling with lanthanide; it allows obtaining both the structural and quantitative information. In this work for the first time the successful utilization of chemoproteomic probes functionalized with a metal tag for the detection and absolute quantification of target proteins was established. With the experiments both on isolated enzymes and living cells it was determined that MeCAT does not negatively influence other functional parts of the probes; therefore, capture compounds functionalized with lanthanide chelates demonstrate similar affinity to the target as the reference probes. Moreover, metal tags utilized for this type of molecular probes can offer a promising elemental imaging technique. However, to achieve the sufficient resolution multiple metal tags per molecular probe are needed. The striking advantage of the approach of utilization metal functionalized capture compound combined with ICP-MS detection is that it allows absolute quantification of crosslink yield, what cannot be performed with other detection methods applied for this technology.
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Attiya, Said. "Antibody labeling methods for automated affinity electrophoresis on microchips." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0010/NQ59926.pdf.

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Seebregts, Christopher J. "Photoaffinity labeling the nucleotide sites of the sarcoplasmic reticulum Ca²⁺-ATPase." Doctoral thesis, University of Cape Town, 1989. http://hdl.handle.net/11427/27167.

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We have synthesized a new class of photoaffinity analogs, 2',3'-O-(2,4,6-trinitrophenyl)-8-azido-ATP, -ADP and -AMP (TNP- 8N₃ATP, -ADP and -AMP), and their radiolabeled derivatives, and characterized their interaction with the sarcoplasmic reticulum Ca²⁺-ATPase. The TNP-8N₃-nucleotides were synthesized from ATP in three steps involving bromination in the 8-position of the adenine ring followed by displacement with an azido group and then trinitrophenylation of the resulting 8N₃-nucleotide with TNBS. Inclusion of the oxidizing agent, DTNB, in the final reaction was found to be necessary to prevent reduction of the azido group by the released sulfite anion and also elevated the yield of trinitrophenylation to about 80%. Purity was determined spectrophotometrically, as well as by anion exchange TLC and reversed phase HPLC. In the dark, the compounds were found to display most of the features of the parent TNP-nucleotides and interacted with the Ca²⁺-ATPase in a similar way. When activated by illumination, the probes were specifically incorporated into SR vesicles with high efficiency at alkaline pH. The site of labeling was identified as being on the A₁ tryptic fragment.
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Perols, Anna. "Site-specific labeling of affinity molecules for in vitro and in vivo studies." Doctoral thesis, KTH, Proteinteknologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-152349.

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The thesis is focused on site-specific labeling of affinity molecules for different applications where two types of binding proteins, Affibody molecules and antibodies, have been used. For the purpose of improving the properties of Affibody molecules for in vivo imaging, novel bi-functional chelators for radiolabeling using the radionuclide 111In were evaluated. In a first study, two chelators denoted NOTA and DOTA, respectively, were separately conjugated via maleimide chemistry to a C-terminal cysteine residue in a HER2-binding Affibody molecule (ZHER2:2395). In vivo evaluation using mice with prostate carcinoma cell line xenografts showed that the 111In-NOTA-MMA-ZHER2:2395 tracer exhibited faster clearance from blood than the 111In-DOTA-MMA-ZHER2:2395 counterpart,resulting in improved tumor-to-organ ratios. In a second study the in vivo imaging properties of a third tracer, 111In-NODAGA-MMA-ZHER2:2395, was investigated in tumor-bearing mice. While the tumor uptake was lower than seen for the 111In-DOTA-MMA-ZHER2:2395 tracer, a low uptake in non-targeted organs and a fast clearance from blood resulted in higher tumor-to-organ ratios for 111In-NODAGA-MMA-ZHER2:2395 compared to the DOTA variant. In a following study, a synthetically produced HER2-targeting affibody variant, denoted ZHER2:S1, was used where NODAGA, NOTA and DOTA chelators instead were conjugated via an amide bond to the N-terminus. In vivo evaluation in mice showed an unfavorable uptake in liver for 111In-NOTA-ZHER2:S1, resulting in a discontinuation. The study showed faster clearance of 111In-NODAGA-ZHER2:S1 from blood, but also an increased uptake in bone in comparison to 111In-DOTA-ZHER2:S1. As bone is a common metastatic site in prostate cancer, the favorable tumor-to-bone ratio for 111In-DOTA-ZHER2:S1 suggests it as the tracer of choice for prostate cancer. Further, the DOTA chelator was also evaluated as conjugated to either N- or C-terminus or to the back of helix 3 via an amide bond, where the in vivo evaluation showed that that C-terminal conjugation resulted in the highest contrast. Site specificity is also of great importance for labeling antibodies, as conjugation in the antigen-binding regions might influence the affinity. A method for site-specific labeling of antibodies using an IgG-binding domain that becomes covalently attached to the Fc-region of an antibody by photoconjugation was optimized. By investigation of positions most suitable for incorporation of the photoreactive probe, the conjugation efficiencies were increased for antibody subclasses important for both diagnostic and therapeutic applications. In addition, optimized variants were used in combination with an incorporated click-reactive handle for selective labeling of the antibody with a detection molecule.

QC 20140929

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Lui, James Kwok Ching. "A fluorescent labelling technique to detect changes in the thiol redox state of proteins following mild oxidative stress." University of Western Australia. School of Biomedical, Biomolecular and Chemical Sciences, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0056.

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There is increasing evidence that hydrogen peroxide (H2O2) can act as a signalling molecule capable of modulating a variety of biochemical and genetic systems. Using Jurkat T-lymphocytes, this study initially investigated the involvement of H2O2 in the activation of a specific signalling protein extracellular signal-regulated protein kinase (ERK). It was found that as a result of H2O2 treatment, mitochondrial complex activities decreased which led to subsequent increase of mitochondrial reactive oxygen species (ROS) production. The increase of ROS resulted in higher cellular H2O2 as well as increased ERK activation. This study demonstrated that in an oxidative stress setting, H2O2 production from the mitochondria was an essential component in maintaining the activation of a signalling protein. One way in which H2O2 could influence protein function is by the oxidation of susceptible thiol groups of cysteine residues. To further understand the variety of signalling pathways that H2O2 may be involved in, an improved proteomics technique was developed to globally identify proteins with susceptible thiol groups. The
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Tran, Hang T. "Photocleavable Linker for Protein Affinity Labeling to Identify the Binding Target of KCN-1." Digital Archive @ GSU, 2010. http://digitalarchive.gsu.edu/chemistry_theses/35.

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KCN-1 is known to reduce tumor growth 6-fold in mice implanted with LN229 glioma cells. Although this inhibitor is effective, the mechanism of action for KCN-1 is not well understood. Based on preliminary studies, KCN-1 reduces tumor growth by disrupting the HIF 1 (hypoxia-induced factor-1) pathway. The binding target of KCN-1 needs to be investigated in order to develop KCN-1 or its analogs for therapeutic applications. In this research, a molecule was designed and synthesized for the identification of the binding target of KCN-1. Specifically, this molecule contains the inhibitor (KCN-1), a photocleavable linker, beads, and the affinity label (L DOPA). When UV light shines on the linker, the trans-alkene isomerizes to cis-alkene and undergoes intramolecular ring-closing reaction, which helps cleave the immobilized bead from the linker. The immobilized bead is used to separate the binding fragment attached to the photocleavable linker from the solution after enzyme digestion. The affinity label (L-DOPA) reacts with a nucleophile from the binding target and creates a covalent bond. If the design is successful, this method is able to analyze the mass of the peptide sequence and determine the binding target of KCN-1.
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Song, Zhi-Ning. "Development of novel affinity-guided catalysts for specific labeling of endogenous proteins in living systems." Kyoto University, 2017. http://hdl.handle.net/2433/228238.

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Kuzmich, Oleksandra [Verfasser], Michael [Gutachter] Linscheid, Hubert [Gutachter] Köster, and Michael [Gutachter] Weller. "Metal Labeling for Low Affinity Binding Biomolecules / Oleksandra Kuzmich ; Gutachter: Michael Linscheid, Hubert Köster, Michael Weller." Berlin : Humboldt-Universität zu Berlin, 2018. http://d-nb.info/1185579265/34.

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Bagchi, Pritha. "Expanding the metallomics toolbox: Development of chemical and biological methods in understanding copper biochemistry." Diss., Georgia Institute of Technology, 2013. http://hdl.handle.net/1853/52160.

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Copper is an essential trace element and required for various biological processes, but free copper is toxic. Therefore, copper is tightly regulated in living cells and disruptions in this homeostatic machinery are implicated in numerous diseases. The current understanding of copper homeostasis is substantial but incomplete, particularly in regard to storage and exchange at the subcellular level. Intracellular copper is primarily present in the monovalent oxidation state. Therefore, copper(I) selective fluorescent probes can be utilized for imaging exchangeable copper ions in live cells, but these probes are often lipophilic and hence poorly water soluble. To address this problem, water-soluble fluorescent probes with greatly improved contrast ratio and fluorescence quantum yield are characterized in this work. This work also describes a novel application of water-soluble fluorescent probes, in-gel detection of copper proteins with solvent accessible Cu(I) sites under non-denaturing conditions. Knowledge of copper(I) stability constants of proteins is important to elucidate the mechanisms of cellular copper homeostasis. Due to the high affinity of most Cu(I)-binding proteins, the stability constants cannot be determined directly by titration of the apo-protein with Cu(I). Therefore, accurate determination of Cu(I) stability constants of proteins critically depends on the Cu(I) affinity standards. However, the previously reported binding affinity values of the frequently used Cu(I) affinity standards are largely inconsistent impeding reliable data acquisition for the Cu(I) stability constants of proteins. To solve this problem, a set of water-soluble ligands are developed in this work that form colorless, air-stable copper(I)-complexes with 1:1 stoichiometry. These ligands can be applied as copper(I) buffering agents and affinity standards in order to study copper biochemistry. Copper(I) binding proteins are an integral part of the copper homeostatic machinery and they work in conjunction to regulate copper uptake, distribution, and excretion. However, available evidence indicates the existence of putative copper-binding proteins that are yet to be characterized. Therefore, several proteomics-based methods are developed in this work by employing the strategy to label Cu(I)-binding cysteines in a copper-dependent manner which lays the foundation for the identification of new copper proteins from cellular extracts.
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Barnett, Derek W. "PART 1. SYNTHESIS OF STABLE-ISOTOPE LABELED AMINO ACIDS PART 2. SYNTHESIS OF MECHANISTIC PROBES OF RETINOID ACTION." The Ohio State University, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=osu1038951598.

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Books on the topic "Affinity labeling"

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Viktorovich, Vlasov Valentin, ed. Affinity modification of biopolymers. Boca Raton, Fla: CRC Press, 1989.

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H, Gronemeyer, ed. Affinity labelling and cloning of steroid and thyroid hormone receptors. Weinheim, Federal Republic of Germany: VCH, 1988.

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Protein affinity tags: Methods and protocols. New York: Humana Press, 2014.

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1940-, Creighton Thomas E., ed. Protein function: A practical approach. Oxford: IRL Press, 1989.

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Lajambe, Roxanne. Affinity labelling of functionally active caspases in Sp2/0-Ag14 cells during l-glutamine deprivation. Sudbury, Ont: Laurentian University, 2004.

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1949-, Müller S. C., ed. Synthetic peptides as antigens. Amsterdam: Elsevier, 1999.

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1962-, Meier T., and Fahrenholz F, eds. A laboratory guide to biotin-labeling in biomolecule analysis. Basel: Birkhäuser Verlag, 1996.

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Maeda, Dean Yoshimasa. Synthesis and evaluation of affinity labels based on peptide antagonists for delta opioid receptors. 1997.

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Leelasvatanakij, Leena. Synthetic strategies for the preparation of affinity label dynorphin A(1-11)NH₂ analogues. 1996.

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Warth, Rainer K. Large subunit of vaccinia cirus ribonucleotide reductase: Affinity chromatography-based purification and photoaffinity labeling. 1993.

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Book chapters on the topic "Affinity labeling"

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Patchornik, A., K. Jacobson, and M. P. Strub. "Photo Reversible Affinity Labeling." In Design and Synthesis of Organic Molecules Based on Molecular Recognition, 235–41. Berlin, Heidelberg: Springer Berlin Heidelberg, 1986. http://dx.doi.org/10.1007/978-3-642-70926-5_20.

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Tamura, Tomonori, and Itaru Hamachi. "Labeling Proteins by Affinity-Guided DMAP Chemistry." In Site-Specific Protein Labeling, 229–42. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2272-7_16.

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Landgraf, Peter, Elmer R. Antileo, Erin M. Schuman, and Daniela C. Dieterich. "BONCAT: Metabolic Labeling, Click Chemistry, and Affinity Purification of Newly Synthesized Proteomes." In Site-Specific Protein Labeling, 199–215. New York, NY: Springer New York, 2014. http://dx.doi.org/10.1007/978-1-4939-2272-7_14.

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Miziorko, Henry M., and Christine A. Brodt. "Affinity Labeling of Phosphoribulokinase by Adenosine Polyphosphopyridoxals." In Current Research in Photosynthesis, 2881–84. Dordrecht: Springer Netherlands, 1990. http://dx.doi.org/10.1007/978-94-009-0511-5_651.

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Hughes, David A. "Applications of Affinity Labeling in Biomedical Sciences." In Immunocytochemistry and In Situ Hybridization in the Biomedical Sciences, 223–53. Boston, MA: Birkhäuser Boston, 2001. http://dx.doi.org/10.1007/978-1-4612-0139-7_11.

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Fabry, M., and D. Brandenburg. "Photoreactive Biotinylated Peptide Ligands for Affinity Labeling." In A Laboratory Guide to Biotin-Labeling in Biomolecule Analysis, 65–81. Basel: Birkhäuser Basel, 1996. http://dx.doi.org/10.1007/978-3-0348-7349-9_4.

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Kodama, Hiroaki, Teruo Yasunaga, Michio Kondo, Rei Matsueda, and Yasuyuki Shimohigashi. "Discriminative affinity labeling of δ- and μ-opioid receptors." In Peptides 1990, 635–36. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3034-9_263.

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Thiele, Christoph, and Falk Fahrenholz. "Synthesis of Photocleavable Biotinylated Ligands and Application for Affinity Chromatography." In A Laboratory Guide to Biotin-Labeling in Biomolecule Analysis, 31–44. Basel: Birkhäuser Basel, 1996. http://dx.doi.org/10.1007/978-3-0348-7349-9_2.

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Colman, Roberta F. "Affinity Labeling of Nucleotide Binding Sites of Enzymes and Platelets." In Advances in Experimental Medicine and Biology, 257–63. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4615-3806-6_26.

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Donner, David B., Kazuyo Yamada, Kenneth E. Lipson, and Andrea Dorato. "Structural Studies of the Growth Hormone Receptor by Affinity Labeling." In Human Growth Hormone, 463–73. Boston, MA: Springer US, 1986. http://dx.doi.org/10.1007/978-1-4615-7201-5_37.

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Conference papers on the topic "Affinity labeling"

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Das, Nilaksh, Sanya Chaba, Renzhi Wu, Sakshi Gandhi, Duen Horng Chau, and Xu Chu. "GOGGLES: Automatic Image Labeling with Affinity Coding." In SIGMOD/PODS '20: International Conference on Management of Data. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3318464.3380592.

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Surber, Bruce, Shomir Ghosh, Anne-Laure Grillot, Jyoti Patel, Charlotte Woodall, Yuanwei Chen, Lin Yi, Irini Zanze, and Ye Yao. "Uniform Tritium Labeling of Combinatorial Libraries for Affinity Selection Screening." In Proceedings of the 3rd International Conference on Isotopes. WORLD SCIENTIFIC, 2000. http://dx.doi.org/10.1142/9789812793867_0109.

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Jefferson, J. R., J. T. Harmon, and G. A. Jamieson. "ADP-BINDING SITES IN PLATELETS: CHARACTERIZATION BY PHOTOAFFINITY LABELING AND BINDING STUDIES WITH FIXED PLATELETS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644463.

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Attempts to photoaffinity label platelet ADP receptors with 2-azidoADP have not been successful possibly due to the absence of a spacer arm between the nucleotide and the photolabile group. We have synthesized a probe having a long spacer arm by coupling 2-(3-aminopropylthio)-ADP to succinimidyl 4-3H-azidobenzoate. Labeling competable by ADP could not demonstrated with intact platelets. With isolated platelet membranes, three bands (Mr 140,000, 110,000 and 46,000) were labeled that were not competed by ADP while three other bands (Mr 188,000, 92,000 and 51,000) were competable by 100 uM ADP.Another problem in characterizing ADP receptors has been complications due to ADP metabolism and secretion from the dense granules. To avoid this problem we have measured the binding of ADP and analogues to formalin-fixed platelets. ADP bound to two sites (Kl, 0.35 ± 0.04 uM; R1, 160,000 ± 20,000 sites/platelet; K2 7.9 ± 2.0 uM; R2, 400,000 ± 40,000 sites/platelet) with low non-specific binding: these values are in agreement with ADP concentrations required for activation. Affinity at the high affinity site was in the sequence ADP(0.35 uM)=ATP(0.4 uM)›2-MeS.ADP(6.8 uM)› GDP(49 uM) › AMP(360 uM); adenosine did not compete. Binding at the high affinity site was blocked by pMBS (EC50 250 uM) and 5-fluoro-sulfonylbenzoyladenosine (EC50 1 mM). This is the first report of photoaffinity labeling of putative ADP receptors. Our experiments with fixed platelets suggest that they may be useful in testing agonists, antagonists and inhibitors in the absence of complications due to secretion and metabolism.
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Bandi, Adithya, Karuna Joshi, and Varish Mulwad. "Affinity Propagation Initialisation Based Proximity Clustering For Labeling in Natural Language Based Big Data Systems." In 2020 IEEE 6th Intl Conference on Big Data Security on Cloud (BigDataSecurity), IEEE Intl Conference on High Performance and Smart Computing, (HPSC) and IEEE Intl Conference on Intelligent Data and Security (IDS). IEEE, 2020. http://dx.doi.org/10.1109/bigdatasecurity-hpsc-ids49724.2020.00012.

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Chir, Jiunly, Steven Withers, Chin-Feng Wan, and Yaw-Kuen Li. "IDENTIFICATION OF THE ESSENTIAL GROUPS OF A FAMILY 3 BETA-GLUCOSIDASE BY AFFINITY LABELING AND TANDEM MASS SPECTROMETRIC ANALYSIS." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.746.

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Hannan, Tanveer, Rajat Koner, Jonathan Kobold, and Matthias Schubert. "Box Supervised Video Segmentation Proposal Network." In 24th Irish Machine Vision and Image Processing Conference. Irish Pattern Recognition and Classification Society, 2022. http://dx.doi.org/10.56541/azwk8552.

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Bounding box supervision provides a balanced compromise between labeling effort and result quality for image segmentation. However, there exists no such work explicitly tailored for videos. Applying the image segmentation methods directly to videos produces sub-optimal solutions because they do not exploit the temporal information. In this work, we propose a box-supervised video segmentation proposal network. We take advantage of intrinsic video properties by introducing a novel box-guided motion calculation pipeline and a motion-aware affinity loss. As the motion is utilized only during training, the run-time remains fixed during inference time. We evaluate our model on Video Object Segmentation (VOS) challenge. The method outperforms the state-of-the-art self-supervised methods by 16.4% and 6.9% J&F score, and the majority of fully supervised ones on the DAVIS and Youtube-VOS dataset. Code is available at https://github.com/Tanveer81/BoxVOS.git.
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Kirby, Edward P., Mary Ann Mascelli, Carol Silverman, and Daniel W. Karl. "LOCALIZATION OF THE PLATELET-BINDING AND HEPARIN-BINDING DOMAINS OF BOVINE VON WILLEBRAND FACTOR." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644097.

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Bovine von Willebrand Factor (vWF) binds directly to human platelets and also to heparin-agarose. Cleavage of vWF with Protease I, a metalloenzyme isolated from the venom of the western diamondback rattlesnake, produces two major fragments with apparent Mr of 250 kD and 200 kD. The 200 kD fragment competes with native vWF for binding to the GPIb-associated vWF receptor on formalin-fixed human platelets and has weak platelet-agglutinating activity. It is composed of three polypeptide chains of apparent Mr of 97 kD, 61 kD, and 35 kD. Monoclonal antibodies #2 and H-9, which inhibit binding of vWF to a GPIb-associated receptor of platelets, recognize the 200 kD fragment.Modification of vWF with ^5x-la.beled. Bolton-Hunter reagent (I*-BHR) causes inhibition of platelet-agglutinating activity at very low levels of incorporation. Modification of less than 2% of the amino groups in vWF causes 50% loss of platelet agglutinating activity and a decreased affinity of vWF for binding to platelets. Labeling with I*-BHR does not block binding to heparin-agarose, even when 5-10% of the amino groups are modified. Differential labeling at pH 7.0 and pH 8.5, followed by proteolytic fragmentation with Protease I, suggests that it is the modification of amino groups on the 200 kD fragment which is responsible fpr the decrease in platelet binding activity. Modification of the 97 kD peptide chain is best correlated with this loss of platelet binding activity.Heparin inhibits the agglutination of human platelets by bovine vWF. The 200 kD fragment of vWF binds both to platelets and to heparin-agarose. These observations suggest that the heparin-binding and platelet-binding domains of vWF, although distinct from one another, reside in the same region of the vWF molecule. The platelet-binding domain contains a small number of very reactive amino groups which are required for vWF binding to human platelets.These studies were supported by a grant from the National Institutes of Health (#HL27993).
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8

Apap-Bologna, Angela, Ailsa Webster, Fiona Raitt, and Graham Kemp. "THE DYNAMIC STRUCTURE OF FIBRINOGEN PROBED BY SURFACE LABELLING AND CHEMICAL CROSS-LINKING." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642886.

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There is much controversy regarding the conformation of fibrinogen. Several models have been proposed ranging from an almost linear trinodular arrangement to a globular conformation. Consequently, it has been suggested that fibrinogen has a flexible structure where the actual conformation is influenced by its environment - one major factor being calcium concentration. Although the importance of tightly bound calcium ions (Kd ∼ luM) to fibrinogen structure is well established, the role of the larger number of low affinity sites (Kd∼lmM) is still a matter of debate.We have utilised the techniques of radio-active photoaffinity surface labelling and chemical cross-linking to probe the molecule's conformation under different conditions. Studies were carried out in an attempt to provide information on: (1) The relative locations of the major domains within the fibrinogen molecule (2) The regions of the chains which are exposed on the surface (3) The dependence of the conformation on the solvent composition with particular reference to the effect of calcium concentration. Our results indicate that the central, or E domain of the molecule is partially buried and that the conformation of fibrinogen is certainly influenced by changes in solvent composition. Increasing calcium concentration in the millimolar range results in an increase in the proportion of intermolecular cross-linking, mainly through the [A]α chains. There have been several reports that the C-terminal regions of the [A]α chains are in close association, forming a fourth domain within the molecule. Our results suggest that calcium ions promote the dissociation of this domain.
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9

Kruithof, E. KO, W. D. Schleuning, and F. Bachman. "PLASMINOGEN ACTIVATOR INHIBITOR BIOCHEMICAL AND CLINICAL ASPECTS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644764.

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Plasminogen activator (PAs) are enzymes that convert the zymogen plasminogen into the trypsin-like protease plasmin, which degrades extracellular matrix proteins and fibrin in the course of fibrinolysis, embryogenesis, tissue remodeling and in tumor metastasis. Plasminogen activator inhibitors (PAIs) are important modulators of PA activity. Several proteins have been identified which inhibit at fast rates urokinase (u-PA) and tissue-type PA (t-PA). In the order of inhibition rate constants these are: a) PAI-1, present in human plasma and platelet extracts and purified from human endothelial cell, fibrosarcoma cell and melanoma cell conditioned media; b) PAI-2, first identified in extracts of human placenta and later also in extracts and conditioned media of human granulocytes and monocytes; and c) protease nexin, a broad specificity protease inhibitor that was first identified and purified from human fibroblasts. We have chosen to use phorbol myristate acetate (30 ng/ml) stimulated histiocytic lymphoma cells (U-937) for the purification of PAI-2. The concentration of PAI-2 in the conditioned media after three days culture in the absence of fetal calf serum is 5 mg/1 and PAI-2 represents 3% of total protein. PAI-2 was purified by a two step procedure consisting of isoelectric focusing and affinity chromatography on Cibacron-Blue agarose. Two forms of PAI-2 were identified: a 47 kDa, nonglycosylated, pi 5.0 form and a 60 kDa glycosylated, pi 4.4 form. Immunctolot analysis and in vivo protein labeling studies under culture conditions that assure 100% viability of the cells showed that the glycosylated Torn is secreted, whereas the 47 kDa, nonglycosylated form remains intracellular. The glycosylation does not affect the activity of the inhibitors since both forms of PAI-2 react with the same rate with u-PA. PAI-2 is a fast inhibitor of u-PA (kl=9×l05M−1s−1) and two-chain t-PA (kl=2×l05) and a rather slow inhibitor of one chain t-PA (kl=l×l02) and of plasmin (kl×l02), but does not inhibit glandular and plasma kallikrein or thrombin. The inhibition spectrum and the kinetics of inhibition clearly distinguish PAI-2 from PAI-1 (kl of reaction with u-PA and two and one chain t-PA above 107) and from protease nexin, that is an efficient inhibitor also of thrombin and plasmin.We have cloned a 1880 Ip fragment of PAI-2 cDNA and determined its nucleotide sequence. The derived acid sequence reveals that PAI-2 is like PAI-1 and protease nexin a member of the serpin family of proteins and contains arginine at its putative active site. In an attenpt to identify parts of the inhibitor proteins that are responsible for conferring PA specificity to PAI-1 and PAI-2 we have compared the primary structures of PAI-1 and PAI-2 with each other and with antithrombin III (AT III). Surprisingly, PAI-2 exhibits no homology with PAI-1 in the region close to the active site except for the active site arginine, whereas, in that region, AT III showed three and seven conserved aminoacids when compared to PAI-1 and PAI-2, respectively. This finding suggests that other regions than those close to the active site contribute to the specificity of PAIs.Plasma concentrations of PAI-2 were measured by a specific radioimmunoassay in over 50 healthy individuals, PAI-2 levels were below detection limit (15 ng/ml) in half of the saitples. Maximal concentrations encountered were in the 30 ng/ml range. PAI-2 measurements in over 300 hospitalized patients demonstrated significantly elevated PAI-2 concentrations only in pregnant women. Measurements in various stages of pregnancy showed a steady increase of PAI-2 from below detection limit in nonpregnant women to values of 250 ng/ml at term and of PAI-1 frcm 25 ng/ml to 150 ng/ml. Unlike to PAI-1 concentrations that normalize rapidly after delivery, PAI-2 concentrations remain significantly elevated for several days.
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10

Taki, M., K. Sato, Y. Ikeda, M. Yamamoto, and K. Watanabe. "THE FUNCTIONAL DOMAIN OF PLATELET MEMBRANE GLYCOPROTEIN lb FOR VON WILLEBRAND FACTOR AND THROMBIN-BINDING." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643512.

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In this paper, we have examined the functional domain of platelet membrane glycoprotein lb (GPIb) by using elastase and a monoclonal antibody against GPIb which specific inhibits both von Willebrand factor (vWF) and thrombin interaction with platelets. Elastase was purified from human granulocytes by using affinity column chromatography according to the method of Okada et al.. A monoclonal antibody against platelet membrane GPIb (56-2) which inhibits both vWF and thrombin-binding to platelets was used for this study. Platelet surface glycoproteins were labelled with 3H by the method of Nurden et al.. Purified GPIb was obtained by a modification of the method of Coller et al. and labelled with 125I using chloramine-T method. Either 3H-labelled platelets or 125I-labelled GPIb was treated with elastase for various time periods. Elastase-treated l25I-GPIb was subjected to immunoaffinity chromatography using 56-2 antibody to determine the functional site of GPIb. Elastase inhibited platelet aggregation or 5-HT release by thrombin, ristocetin-induced platelet agglutination and vWF-binding to platelets in the presence of ristocetin in a dose- and time dependent manner. A fluorogram of SDS-PAGE of 3H-labelled platelets treated with elastase revealed that GPIb band was reduced gradually, and fragments with MW of 97, 70, 60, 47, 44, 37, 25 and 15 KD were released from the platelets. The 47 KD fragment was initially cleaved from the platelets, and subsequently other fragments were digested. Similar results were obtained when purified 125I-GPIb was digested by elastase. When the fragments from purified 125I-GPIb were reacted with 56-2 antibody, only three fragments with MW of 47, 44 and 25 KD were immunoisolated. The electrophoretic mobility of all these three bands was altered under reduced conditions, indicating that all these fragments contain disulfide bonds in their molecules. The 25 KD band showed a much fainter in 3H-labelling than in 125I-labelling.These results suggest that the functional domains of GPIb for both vWF and thrombin-binding may be located in a less glycosylated fragment with a MW of 25 KD on the distal portion of the GPIb molecule, which should contain at least one intramolecular disulfide bond.
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Reports on the topic "Affinity labeling"

1

Yang, KyoungLang, and Gunda I. Georg. Synthesis of Cryptophycin Affinity Labels and Tubulin Labeling. Fort Belvoir, VA: Defense Technical Information Center, May 2005. http://dx.doi.org/10.21236/ada443679.

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2

Yang, Kyounglang, and AGunda I. Georg. Synthesis of Cryptophycin Affinity Labels and Tubulin Labeling. Fort Belvoir, VA: Defense Technical Information Center, May 2004. http://dx.doi.org/10.21236/ada432471.

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3

Ramadas, Vidya. Synthesis of Cryptophycin Affinity Labels and Tubulin Labeling. Fort Belvoir, VA: Defense Technical Information Center, May 2003. http://dx.doi.org/10.21236/ada416994.

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4

Yang, KyoungLang, and Gunda I. Georg. Synthesis of Cryptophycin Affinity Labels and Tubulin Labeling. Fort Belvoir, VA: Defense Technical Information Center, May 2006. http://dx.doi.org/10.21236/ada474734.

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5

Pines, Mark, Arieh Bar, David A. Carrino, Arnold I. Caplan, and James A. Dennis. Extracellular Matrix Molecules of the Eggshell as Related to Eggshell Quality. United States Department of Agriculture, 1997. http://dx.doi.org/10.32747/1997.7575270.bard.

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The extracellular matrix of the mineralizing eggshell contains molecules hypothesized to be regulators biomineralization. To study eggshell matrix molecules, a bank of monoclonal antibodies was generated that bound demineralized eggshell matrix or localized to oviduct epithelium. Immunofluorescence staining revealed several staining patterns for antibodies that recognized secretory cells: staining for a majority of columnar lining cells, staining for a minor sub-set of columnar lining cells, intensified staining within epithelial crypts, and staining of the entire tubular gland. Western blotting with the antibody Epi2 on eggshell matrix showed binding to molecules with the apparent molecular weight of eggshell matrix dermatan sulfate proteoglycan (eggshell DSPG) (Carrino, et al., 1997). Immunoblots of cyanogen bromide-cleaved eggshell DSPG revealed broad band of reactivity that shifted to 25 kDa after chondroitinase digestion; indicating that the Epi2 binding site is located on a fragment which contains dermatan sulfate side chains. Immunogold labeling showed that Epi2 binds to secretory vesicles within the non-ciliated cells of the columnar epithelium, while the antibodies Tg1 and Tg2 bind to secretory vesicles of tubular gland cells. Immunogold labeling of demineralized shell matrix showed binding of Epi2, Tg1, and Tg2 to the matrix of the palisades layer, and showed little reactivity to other regions of the shell matrix. Quantification of the immunogold particles within the eggshell matrix revealed that antibodies Epi2 and Tg1 bind all calcified regions equally while antibody Tg2 has a greater affinity for the baseplate region of the calcium reserve assembly.
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6

Wisniewski, Michael, Samir Droby, John Norelli, Dov Prusky, and Vera Hershkovitz. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the identification of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2012. http://dx.doi.org/10.32747/2012.7597928.bard.

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Use of Lqh2 mutants (produced at TAU) and rNav1.2a mutants (produced at the US side) for identifying receptor site-3: Based on the fact that binding of scorpion alpha-toxins is voltage-dependent, which suggests toxin binding at the mobile voltage-sensing region, we analyzed which of the toxin bioactive domains (Core-domain or NC-domain) interacts with the DIV Gating-module of rNav1.2a. This analysis was based on the assumption that the dissociation of toxin mutants upon depolarization would vary from that of the unmodified toxin should the substitutions affect a site of interaction with the channel Gating-module. Using a series of toxin mutants (mutations at both domains) and two channel mutants that were shown to reduce the sensitivity to scorpion alpha-toxins, and by comparison of depolarization-driven dissociation of Lqh2 derivatives off their binding site at rNav1.2a mutant channels we found that the toxin Core-domain interacts with the Gating-module of DIV. Details of the experiments and results appear in Guret al (2011). Mapping receptor site 3 at Nav1.2a by extensive channel mutagenesis (Seattle): Since previous studies with photoaffinity labeling and antibody mapping implicated domains I and IV in scorpion alpha-toxin binding, Nav1.2 channel mutants containing substitutions at these extracellular regions were expressed and tested for receptor function by whole-cell voltage clamp. Of a large number of channel mutants, T1560A, F1610A, and E1613A in domain IV had ~5.9-, ~10.7-, and ~3.9-fold lower affinities for the scorpion toxin Lqh2, respectively, and mutant E1613R had 73-fold lower affinity. Toxin dissociation was accelerated by depolarization for both wild-type and mutants, and the rates of dissociation were also increased by mutations T1560A, F1610A and E1613A. In contrast, association rates for these three mutant channels at negative membrane potentials were not significantly changed and were not voltage-dependent. These results indicated that Thr1560 in the S1-S2 loop, Phe1610 in the S3 segment, and Glu1613 in the S3-S4 loop in domain IV participate in toxin binding. T393A in the SS2-S6 loop in domain I also showed a ~3.4-fold lower affinity for Lqh2, indicating that this extracellular loop may form a secondary component of the toxin binding site. Analysis with the Rosetta-Membrane algorithm revealed a three-dimensional model of Lqh2 binding to the voltage sensor in a resting state. In this model, amino acid residues in an extracellular cleft formed by the S1-S2 and S3-S4 loops in domain IV that are important for toxin binding interact with amino acid residues on two faces of the wedge-shaped Lqh2 molecule that are important for toxin action. The conserved gating charges in the S4 transmembrane segment are in an inward position and likely form ion pairs with negatively charged amino acid residues in the S2 and S3 segments (Wang et al 2011; Gurevitz 2012; Gurevitzet al 2013).
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Shomer, Ilan, Louise Wicker, Uzi Merin, and William L. Kerr. Interactions of Cloud Proteins, Pectins and Pectinesterases in Flocculation of Citrus Cloud. United States Department of Agriculture, February 2002. http://dx.doi.org/10.32747/2002.7580669.bard.

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The overall objective was to understand the cloud flocculation of citrus juice by characterization of the interactions between proteins and pectins, and to determine the role of PE isozymes in catalyzing this phenomenon. Specific objectives were to: 1. identify/characterize cloud-proteins in relation to their coagulable properties and affinity to pectins; 2. to determine structural changes of PME and other proteins induced by cation/pectin interactions; 3. localize cloud proteins, PME and bound protein/pectates in unheated and pasteurized juices; 4. to create "sensitized" pectins and determine their effect on clarification. The original objectives were not changed but the methods and approach were modified due to specific research requirements. Two i postulates were: 1. there is a specific interaction of cloud proteins with de-esterified regions of ! pectin and this contributes to cloud loss; 2. isozymes of pectin-methyl-esterase (PME) vary in efficiency to create sensitized pectins. The appearance of citrus fruit juice is an important quality factor and is determined by the color and turbidity that .are conferred by the suspended particles, i.e., by the cloud and its homogeneity. Under some circumstances the cloud tend to flocculate and the juice clarifies. The accepted approach to explain the clarification is based on pectin demethoxylation by PME that promotes formation of Ca-pectate. Therefore, the juice includes immediate heat-inactivation upon ~ squeezing. Protein coagulation also promotes cloud instability of citrus fruit extracts. However, the clarification mechanism is not fully understood. Information accumulated from several laboratories indicates that clarification is a more complex process than can be explained by a single mechanism. The increasing trend to consume natural-fresh juice emphasizing the importance of the knowledge to assure homogeneity of fresh juice. The research included complementary directions: Conditions that induce cloud-instability of natural- juice [IL]. Evaluate purification schemes of protein [USA]. Identifications of proteins, pectin and neutral sugars ([IL]; Structure of the cloud components using light and electron microscopy and immuno-labeling of PME, high-methoxyl-pectin (HMP) and low-methoxyl-pectin (LMP); Molecular weight of calcium sensitized pectins [US]; Evaluation of the products of PME activity [US]. Fractions and size distribution and cloud components [IL-US]. The optimal pH activity of PME is 7 and the flocculation pH of the cloud is 3-4. Thus, the c roles of PME, proteins and pectins in the cloud instability, were studied in pH ranges of 2- 7. The experiments led to establish firstly repeatable simulate conditions for cloud instability [IL]. Thermostable PME (TS-PE) known to induce cloud instability, but also thermolabile forms of PME (TL-PE) caused clarification, most likely due to the formation and dissolution of inactive :. PE-pectin complexes and displacement of a protective colloid from the cloud surface [US]. Furthermore, elimination of non-PME protein increases TS-PE activity, indicating that non-PME proteins moderate PME activity [US]. Other experiments Concomitantly with the study of the PME activity but promotes the association of cloud-proteins to pectin. Adjusting of the juice pH to f 7 retains the cloud stability and re-adjusting of the pH to 40% DE reacts to immuno-labeling in the cloud fragments, whereas
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