Relevant bibliographies by topics / Ligand/enzyme interaction

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  1. Journal articles
  2. Dissertations / Theses
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  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Ligand/enzyme interaction'

Author: Grafiati
Published: 10 September 2022
Last updated: 18 September 2022

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Journal articles on the topic "Ligand/enzyme interaction"

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Kuznetsov, Aleksei, and Jaak Järv. "Ligand structure controlled allostery in cAMP-dependent protein kinase catalytic subunit." Open Life Sciences 4, no. 2 (June 1, 2009): 131–41. http://dx.doi.org/10.2478/s11535-009-0012-6.

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AbstractProtein kinase A (cAMP dependent protein kinase catalytic subunit, EC 2.7.11.11) binds simultaneously ATP and a phosphorylatable peptide. These structurally dissimilar allosteric ligands influence the binding effectiveness of each other. The same situation is observed with substrate congeners, which reversibly inhibit the enzyme. In this review these allosteric effects are quantified using the interaction factor, which compares binding effectiveness of ligands with the free enzyme and the pre-loaded enzyme complex containing another ligand. This analysis revealed that the allosteric effect depends upon structure of the interacting ligands, and the principle “better binding: stronger allostery” observed can be formalized in terms of linear free-energy relationships, which point to similar mechanism of the allosteric interaction between the enzyme-bound substrates and/or inhibitor molecules. On the other hand, the type of effect is governed by ligand binding effectiveness and can be inverted from positive allostery to negative allostery if we move from effectively binding ligands to badly binding compounds. Thus the outcome of the allostery in this monomeric enzyme is the same as defined by classical theories for multimeric enzymes: making the enzyme response more efficient if appropriate ligands bind.
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Merugu, Ramchander, Uttam Kumar Neerudu, Karunakar Dasa, and Kalpana V. Singh. "Molecular docking studies of deacetylbisacodyl with intestinal sucrase-maltase enzyme." International Journal of Advances in Scientific Research 2, no. 12 (January 1, 2017): 191. http://dx.doi.org/10.7439/ijasr.v2i12.3821.

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Molecular docking of sucrase-isomaltase with ligand deacetylbisacodyl when subjected to docking analysis using docking server, predicted in-silico result with a free energy of -3.36 Kcal/mol which was agreed well with physiological range for protein-ligand interaction, making bisacodyl probable potent anti-isomaltase molecule. According to docking server Inhibition constant is 5.98Mm. which predicts that the ligand is going to inhibits enzyme and result in a clinically relevant drug interaction with a substrate for the enzyme. Hydrogen bond with bond length 3.45is formed between Pro 64 (A) of target and of ligand, which is again indicative of the docking between target and ligand. Excellent electrostatic interactions of polar, hydrophobic, pi-pi and Van der walls are observed. The proteinligand interaction study showed 6 amino acid residues interaction with the ligand.
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Mulyati, Budi, and Riong Seulina Panjaitan. "Studi Penambatan Molekul Flavonoid Pada Reseptor α-Glukosidase menggunakan PLANTS." JURNAL KIMIA MULAWARMAN 18, no. 2 (May 30, 2021): 68. http://dx.doi.org/10.30872/jkm.v18i2.1004.

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ABSTRACT Plants that contain flavonoids are widely used in traditional medicine. Flavonoids can reduce blood glucose levels with their ability as anti-oxidants. The purpose of this study was to determine natural compounds from flavonoid derivatives that have good affinity and conformation and their interactions in inhibiting α-glucosidase (an enzyme that breaks down carbohydrates into glucose) and determine the sequence of ligands that interact more strongly with α protein / enzyme α-glucosidase. Molecular docking is a computational method that aims to imitate the interaction of a ligand molecule with the protein it targets in in-vitro tests. Molecular docking between flavonoids and α-glucosidase receptors was carried out using the PLANTS method to see its affinity. The flavonoids used as ligands were flavones, flavanols and chalcone with the results of the docking scores respectively, -65.41, -64.39 and -63.07 where the standard ligand used in this study was deoxynojirimycin (-77.12). In the active side of the α-Glucosidase enzyme that binds to flavonoid ligands is Gly 555, Glu 526 and Pro 556.
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BOUGIE, Isabelle, Amélie PARENT, and Martin BISAILLON. "Thermodynamics of ligand binding by the yeast mRNA-capping enzyme reveals different modes of binding." Biochemical Journal 384, no. 2 (November 23, 2004): 411–20. http://dx.doi.org/10.1042/bj20041112.

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RNA-capping enzymes are involved in the synthesis of the cap structure found at the 5′-end of eukaryotic mRNAs. The present study reports a detailed study on the thermodynamic parameters involved in the interaction of an RNA-capping enzyme with its ligands. Analysis of the interaction of the Saccharomyces cerevisiae RNA-capping enzyme (Ceg1) with GTP, RNA and manganese ions revealed significant differences between the binding forces that drive the interaction of the enzyme with its RNA and GTP substrates. Our thermodynamic analyses indicate that the initial association of GTP with the Ceg1 protein is driven by a favourable enthalpy change (ΔH=−80.9 kJ/mol), but is also clearly associated with an unfavourable entropy change (TΔS=−62.9 kJ/mol). However, the interaction between Ceg1 and RNA revealed a completely different mode of binding, where binding to RNA is clearly dominated by a favourable entropic effect (TΔS=20.5 kJ/mol), with a minor contribution from a favourable enthalpy change (ΔH=−5.3 kJ/mol). Fluorescence spectroscopy also allowed us to evaluate the initial binding of GTP to such an enzyme, thereby separating the GTP binding step from the concomitant metal-dependent hydrolysis of GTP that results in the formation of a covalent GMP–protein intermediate. In addition to the determination of the energetics of ligand binding, our study leads to a better understanding of the molecular basis of substrate recognition by RNA-capping enzymes.
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HOWES, Barry D., Nigel C. VEITCH, Andrew T. SMITH, Christopher G. WHITE, and Giulietta SMULEVICH. "Haem-linked interactions in horseradish peroxidase revealed by spectroscopic analysis of the Phe-221→Met mutant." Biochemical Journal 353, no. 2 (January 8, 2001): 181–91. http://dx.doi.org/10.1042/bj3530181.

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A gene encoding a Phe-221-to-Met substitution in the haem enzyme horseradish peroxidase has been constructed and expressed in Escherichia coli. In the wild-type enzyme the side chain of Phe-221 is tightly stacked against the imidazole ring of His-170, which provides the only axial ligand to the haem iron atom. The Phe-221 → Met enzyme is active, and forms characteristic complexes with typical peroxidase ligands (CO, cyanide, fluoride), and with benzhydroxamic acid. Significant differences between the mutant and wild-type enzymes can be detected spectroscopically. These include a change in the Fe(III) resting state of the enzyme to an unusual quantum mechanically mixed-spin haem species, a marked decrease in the pKa of the alkaline transition and a reduction in enzyme stability at alkaline pH for both Fe(III) and Fe(II) forms. The perturbation of the haem pocket in the mutant can be attributed to several factors, including the increased steric freedom and solvent accessibility of the His-170 ligand, as indicated by 1H-NMR data, and the loss of the πŐπ interaction between His-170 and Phe-221.
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Tharuni, Boya, T. Sathish, G. Nadana Raja Vadivu, and K. Vasumathi. "IN SILICO ANALYSIS OF DELTA 6 DESATURASE - A KEY ENZYME FOR OMEGA €“3/6€“ FATTY ACID PRODUCTION." International Journal of Advanced Research 9, no. 02 (February 28, 2021): 818–23. http://dx.doi.org/10.21474/ijar01/12519.

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Delta 6 desaturase is a key enzyme involved in the production of omega 3/6 fatty acids and it is the rate-limiting step. The study aims to characterize the delta 6 desaturase enzyme and to find the binding affinity of various ligand with the protein by docking. It is found that delta 6 desaturase enzyme sequence is very unique and has less similarity with the other desaturase protein. The structural analysis was performed by Ramachandran plot and SCOPe structure prediction. Modeller is used to determine the DOPE score of the selected enzyme. The lowest DOPE score protein is chosen to determine the binding affinity of ligand molecules. Three different ligands were selected and its interaction was determined by the PyRX - Autodock Vina. These studies will give a better idea of the interaction of various molecules, which help to deduce its function by further experimentation.
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Veniere, Sylvie, Christophe Ampe, Joël Vandekerckhove, and Anja Lambrechts. "The Interaction of Proline-Rich Ligands with Profilin Probed with an Enzyme-Linked Immunosorbent Assay." Journal of Biomolecular Screening 14, no. 4 (April 2009): 350–59. http://dx.doi.org/10.1177/1087057109332594.

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To detect interactions of different proline-rich ligands with profilins, the authors developed a simple analytical antibody-based screening method. Profilin I or profilin IIa was coated in microplates, and ligand binding was monitored via antibody detection. Using purified components, the authors show that the assay is very sensitive as nanomolar concentrations of recombinant profilin ligands can be used. They further apply this technique to detect interaction of profilin with various proline-rich partners, either endogenously present or ectopically expressed as tagged fusions, using lysates. With this assay, the authors identify Shootin1 as a novel profilin IIa partner. In addition, they demonstrate that this assay can be used for studying competition or ternary complex formation. In conclusion, they developed a sensitive, easy-to-use, and versatile method for the study of the interaction between profilin and different ligands. ( Journal of Biomolecular Screening 2009:350-359)
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SYGUSCH, Jurgen, and Danielle BEAUDRY. "Subunit interaction in mammalian aldolases." Biochemical Journal 323, no. 3 (May 1, 1997): 671–76. http://dx.doi.org/10.1042/bj3230671.

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Enzyme inactivation was utilized to study subunit interaction in the homotetrameric glycolytic enzyme, aldolase. Isoenzymes from rabbit liver and skeletal muscle were inactivated in the presence of Pi and d-glyceraldehyde-P to a maximum stoichiometry of one modification per aldolase subunit. Subunit modification increased net negative charge on each subunit surface and was used to resolve modified aldolase isoenzymes into various chromatographic species. A combination of anion-(Mono Q) and cation- (Mono S) exchange chromatography separated the modified aldolase homotetramers into three distinct enzyme populations: unchanged enzyme, fully modified enzyme corresponding to one ligand molecule incorporated per subunit and partially modified enzyme in which only one subunit out of four is modified. Both fully and partially modified species were devoid of catalytic activity. Activity loss through modification of a single subunit in both aldolase isoenzymes indicates tightly coupled communication between subunit active sites and suggests simple functional regulation of aldolases.
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Aziz, Fitri Kusvila, Cantika Nukitasari, Fauziyah Ardli Oktavianingrum, Lita Windy Aryati, and Broto Santoso. "Hasil In Silico Senyawa Z12501572, Z00321025, SCB5631028 dan SCB13970547 dibandingkan Turunan Zerumbon terhadap Human Liver Glycogen Phosphorylase (1l5Q) sebagai Antidiabetes." Jurnal Kimia VALENSI 2, no. 2 (November 30, 2016): 120–24. http://dx.doi.org/10.15408/jkv.v2i2.4170.

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Abstrak Human Liver Glycogen Phosphorylase (HLGP), suatu katalis glikogen yang mengontrol pelepasan glukosa-1-fosfat glikogen dari hati. Enzim ini mempunyai peran sentral dalam luaran glukosa hati sehingga menjadi target obat antidiabetik. Kajian docking dilakukan pada komputer dengan prosesor Intel Pentium, RAM 1 GB dan Windows 7. Ligan yang digunakan adalah senyawa obat (Z12501572, Z00321025, SCB5631028 dan SCB13970547), dataset pembanding aktif glycogen phosphorylase outer dimer site (PYGL-out) dan decoysdari www.dekois.com dan turunan zerumbon. Protein dipisahkan dari ligan nativ dan semua ligan beserta protein dikonversi menggunakan PyRx. Visualisasi interaksi ligan-protein dihasilkan dengan program Protein-Ligand Interaction Profiler (PLIP) dan PyMOL. Senyawa ZER11 memiliki binding energy terbaik, yaitu -7.11 kkal/mol (untuk metode LGA dan GA) dan -4.08 kkal/mol untuk metode SA. Nilai binding energy tersebut lebih rendah dari pada nilai untuk ligan native dan satu dari keempat senyawa obat, terlebih jika dibandingkan dengan bindingaffinity dari dataset dan decoys. Interaksi ligan-protein pada ketiga metode tersebut ditemukan sangat bervariasi. Hal berbeda terjadi untuk metode Vina, bindingenergy ZER11 (-9.9 kkal/mol) lebih baik dibandingkan dengan ligan native dan keempat senyawa obat. Senyawa ZER11 memiliki residu interaksi yang sama dengan ligan native pada TRP67 dan LYS191 untuk metode Vina. Kata kunci: PDBID-1L5Q, AutoDock, docking molekuler, vina, antidiabetes Abstract Human Liver Glycogen Phosphorylase (HLGP) can catalyze glycogen and control the release of glucose-1-phosphate of glycogen from the liver. This enzyme has a central role in output rule of liver glucose as it can be used as an antidiabetic drug targets. Docking studies were carried out on PC with Intel Pentium, 1 GB RAM, in environment of Windows 7. Ligands used are drug compounds (Z12501572, Z00321025, SCB5631028 and SCB13970547), the active dataset comparator wasglycogenphosphorylase outer dimer site (PYGL-out) and decoys from www.dekois.com andzerumbonederivates. Protein was separated from its native ligand and all ligands including the protein were converted to pdbqt using PyRx. The interaction of protein-ligand was visualized using software of PLIP and PyMOL. Compound of ZER11 had the best binding energy were -7.11 kcal/mol (LGA and GA) and -4.08 kcal/mol (SA). The binding energy value was lower than the ligand native and one of the four drug compounds, especially compared with the binding affinity of dataset and decoys. Vice versa, for Vina method, the value of ligand binding protein for ZER11 (-9.9 kcal/mol) was better than the ligand native and all of the fourth drugcompounds. Vina result showed that ZER11 had the same residual interaction as the ligand native, which are TRP67 and LYS191. Keyword: PDBID-1L5Q, AutoDock, molecular docking, vina, antidiabetic DOI: http://dx.doi.org/10.15408/jkv.v0i0.4170
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Vadivelu, Annapoorna. "Molecular docking studies of 1,3,4 -thiadiazoles as myeloperoxidase inhibitors." Journal of Pharmaceutical and Biological Sciences 9, no. 1 (July 15, 2021): 63–69. http://dx.doi.org/10.18231/j.jpbs.2021.008.

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Myeloperoxidase (MPO) is a heterodimeric, cationic and glycosylated haeme enzyme which gets released under increased oxidative stress producing neutrophil oxidant, hypochlorous acid having the capacity to modify various biomolecules by chlorination and/or oxidation of sulfhydryl groups in proteins causing their inactivation and promoting inflammatory tissue damage. Different levels of hypochlorus acid are used as a trait marker for prescribing the disorders e.g. atherosclerosis, rheumatoid arthritis, lung cancer, Immuno-reactivity. Mini library of 22500 2,5disubstituted 1,3,4 thiadiazoles were docked with Myeloperoxidase in order to identify the potent inhibitor against the enzyme. The chemical nature of the protein and ligands greatly influence the performance of docking process. Keeping this fact in view, critical evaluation of the performance was performed by GLIDE by HTVS, SP and XP. The ADME parameters by QIKPROP and protein-ligand binding free energies were calculated using the Prime/MM-GBSA module of Schrödinger.Both hydrogen bonding and hydrophobic interactions contributed significantly for its ligand binding and core influence the target site through prominent hydrophobic and charged interaction with the backbone and side chain residues in the target site that improves the affinity of the molecule. The compound selected as potent inhibitor is having minimum binding affinity, maximum GScore and minimum FlexX energy. The amino acids residues ASP98, ASP94, THR100 and GLU 102 in the MPO gene domain active site form hydrogen bonds with the ligand. Compounds 3350-5150 showed better interaction with haeme enzyme for further understanding of structures, reliability and Biomolecularactivityy in connection with oxidative stress induced disorders.
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Dissertations / Theses on the topic "Ligand/enzyme interaction"

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Hermansson, Anders. "Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-170722.

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Indications that existing parameter sets of extended Linear Interaction Energy (LIE) models are transferable between lipases from Rhizomucor Miehei and Thermomyces Lanigunosus in complex with a small set of vinyl esters are demonstrated. By calculat- ing energy terms that represents the cost of forming cavities filled by the ligand and the complex we can add them to a LIE model with en established parameter set. The levels of precision attained will be comparable to those of an optimal fit. It is also demonstrated that the Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods are in- applicable to the problem of calculating absolute binding energies, even when the largest source of variance has been reduced.
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Rodrigues, Fábio Henrique dos Santos 1986. "Derivados de quinazolinas na inibição da adenosina quinase." [s.n.], 2011. http://repositorio.unicamp.br/jspui/handle/REPOSIP/248424.

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Orientador: Ljubica Tasic
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química
Made available in DSpace on 2018-08-19T12:26:39Z (GMT). No. of bitstreams: 1 Rodrigues_FabioHenriquedosSantos_M.pdf: 24628982 bytes, checksum: f6b1490bc6bf2bf5497e5cad40a40daa (MD5) Previous issue date: 2011
Resumo: A Adenosina Quinase (ADK) é uma enzima importante (EC 2.7.1.20), cuja ação pode estar relacionada a diversas doenças, tais como inflamações, derrame, infarto, entre outras. Desse modo, a inibição de sua atividade é de grande importância, e desperta interesse científico. Na tentativa de inibir a ação da ADK, houve busca por compostos orgânicos cuja capacidade inibitória seja superior comparando-se com inibidores da ADK existentes. Desse modo, derivados de 4-anilinoquinazolinas mostraram-se alvos interessantes. Foi sintetizada uma série de 22 derivados de 8-metóxi-4-anilinoquinazolinas, substituídas nas posições 3'e 4'do anel anilínico. Os compostos sintetizados foram caracterizados e testados frente à ADK, de forma a verificar seu potencial inibitório, principalmente através da técnica de fluorescência de emissão. Da série de compostos, seis apresentaram-se promissores na inibição da ADK. Ensaios in silico também foram realizados, buscando-se uma melhor compreensão do mecanismo de inibição do sistema compostos/ADK
Abstract: The Adenosine Kinase (ADK) is an important enzyme (EC 2.7.1.20) that might be related to several diseases, such as inflammation, stroke and infarct, and many others. Therefore, its activity inhibition is of great importance, arising significant scientific interest. Aiming ADKs inhibition, a search for suitable organic species was realized, in such way that 4-anilinoquinazoline derivatives showed themselves interesting targets. A serie of 22 8-methoxy-4-anilinequinazoline derivatives, substituted on the aniline ring at 3'and 4'positions, was synthesized. The compounds were characterized and tested in in vitro ADKs inhibition, in order to verify their inhibitory potentials, mainly applying emission fluorescence technique. Six compounds of this serie presented promising properties in ADKs inhibition. In silico assays were also conducted, in order to better explain the inhibitory mechanism of the system compounds/ADK
Mestrado
Quimica Organica
Mestre em Química
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Anissimova, Marya. "Application du ligand pseudo-biospécifique (IDA-ME (II)) à l'étude de la relation structure/fonction des protéines natives et modifiées." Compiègne, 1999. http://www.theses.fr/1999COMP1228.

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L’étude de la structure des protéines présente un intérêt majeur en biochimie pour permettre de comprendre et d'interpréter leur fonctionnement. Dans ce travail, les relations structure/fonction d'enzymes natives et modifiées ont été étudiées par le biais de leurs interactions avec les ions métalliques immobilisés. Notre première exploitation des interactions métaux chélatés - protéines a été l'application de l'électrophorèse d'affinité sur gel avec les ions métalliques immobilisés (IMAGE) comme outil d'étude des changements dans la topographie des résidus histidine dans les ribonucléases microbiennes induits par mutagenèse dirigé, photo oxydation et interaction avec un inhibiteur. L'importance de His 102 dans la barnase et His 101 dans la binase pour l'activité catalytique et la reconnaissance de Cu (II) chélaté a été démontré par l'utilisation de ligand IDA-Cu(II). Dans la deuxième partie, la chromatographie et l'électrophorèse capillaire d'affinité avec les ions métalliques immobilisés (IMAC et IMACE) ont été utilisées afin d'identifier les changements dans la conformation active de l'α-chymotrypsine bovine pancréatique chimiquement glycosylée. Deux populations distinctes ont été obtenues après la glycosylation. Pour la partie majeure de protéine glycosylée, la diminution d'affinité pour IDA-Cu(II) correspondant à une perte d'activité enzymatique a été détectée en conditions d'IMAC et d'IMACE. En même temps, la glycosylation chimique a généré une autre forme active de chymotrypsine avec une plus forte affinité pour les ions Cu (II) immobilisés. Finalement, les systèmes IMA ont été appliqués à l'étude de différentes structures quaternaires de dimères natifs de BS-RNase et des oligomères artificiels de RNase A. L'augmentation de l'affinité pour les ions métalliques immobilisés après l'agrégation in vitro aussi bien qu'in vivo a été démontrée pour ces deux ribonucléases. Cette affinité provenant des résidus histidine de chaque sous-unité permet de supposer que les sites actifs (His 12, His 119, Lys 41) restent disponibles après l'agrégation et que leur action coopérative est un des facteurs déterminant les nouvelles propriétés enzymatiques de ces oligomères.
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Le, Thao Nhi. "Le frelon asiatique (Vespa velutina nigrithorax) : Stratégies d’études sur l’identification de nouvelles molécules actives pour la dermacosmétique." Thesis, Orléans, 2020. http://www.theses.fr/2020ORLE3143.

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La recherche de nouveaux composés pour prévenir ou atténuer le vieillissement de la peau est une priorité des recherches actuelles dans les cosmétiques. Dans ce contexte, le venin de frelon asiatique (Vespa velutina nigrithorax) a été étudié comme une source particulière de molécules potentiellement bioactives d’intérêt dermacosmétique. La première étude a tout d’abord porté sur la mise en œuvre d’un protocole fiable d’extraction et récupération du venin. Puis, la fraction peptidique et petites molécules a été sélectionnée afin d’évaluer, en comparaison avec le venin brut, la présence de molécules actives vis-à-vis d’une activité antioxydante, anti-microbienne (C. acnes) et inhibitrice enzymatique (tyrosinase, élastase, collagénase) in-tubo et in-cellulo. Ces études ont conduit à identifier par UHPLC-ESI-QTOF-HRMS/MS, dans le venin brut, une molécule responsable de l’activité anti-oxydante sur kératinocytes HaCaT. Dans une seconde étude, une approche peptidomique basée sur une méthode UHPLC-QTOF-HRMS et MS/MS suivie par un traitement statistique (PCA, PLS-DA) a été appliquée sur l’étude différentielle de profil peptidique du venin, en fonction de la période de collecte, des castes et du comportement. Ces derniers ont pour but d’évaluer l’influence de différents facteurs sur le patrimoine moléculaire de ces venins. Parallèlement, en troisième étude, une approche de criblage d’interaction Ligand/enzyme par spectrométrie de masse sur les enzymes élastase et tyrosinase immobilisées a été développée. Cette méthode a pour objectif de mettre en évidence la présence d’inhibiteurs ou de substrats dans des fractions plus ou moins complexes. On a montré que deux peptides présents dans le venin de frelon étaient capables d’interagir avec l’enzyme élastase en tant que substrat. La séquence peptidique de ces peptides a été partiellement obtenue par séquençage de novo
The search for new compounds to prevent or attenuate skin aging is a priority in current research in cosmetics. In this context, Asian Hornet venom (Vespa velutina nigrithorax) has been studied as a particular source of potentially bioactive molecules for dermacosmetic interest.The first study focused on the implementation of a reliable venom extraction and sampling protocol. Then, the peptide - small molecules fraction was selected to evaluate, in comparison with crude venom, the presence of active molecules with respect to antioxidant, anti-microbial (C. acnes) and enzyme inhibition (tyrosinase, elastase, collagenase) activity in-tubo and in-cellulo. These studies led to the identification in crude venom, by UHPLC-ESI-QTOF-HRMS/MS, of one molecule responsible for antioxidant activity on HaCaT keratinocytes.In a second study, a peptidomic approach based on UHPLC-ESI-QTOF-HRMS/MS followed by statistical processing (PCA, PLS-DA) was applied to the differential study of venom, according to the collection period, castes and behavior. The latter aims at evaluating the influence of these different factors on the venom molecular heritage. At the same time, in a third study, a ligand/enzyme interaction screening approach by mass spectrometry on solid-supported elastase enzymes was developed. The aim of this method is to detect the presence of inhibitors or substrates in more or less complex fractions. Two hornet venom peptides presenting in the hornet venom were identified to be capable of interacting with the enzyme elastase. Their peptide sequences were then partially obtained by de novo sequencing
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Zhou, Min. "Understanding non-covalent interactions : cooperativity in ligand binding and enzyme catalysis." Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615013.

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Ferey, Justine. "Développement d'outils analytiques basés sur la spectrométrie de masse pour le suivi d'interactions enzyme-ligand dans le domaine de la santé." Thesis, Orléans, 2017. http://www.theses.fr/2017ORLE2051/document.

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Les enzymes et leur diversité d’actions sont appréciées dans des domaines d’applications variés allant del’agroalimentaire à la thérapeutique. Ainsi, une attention toute particulière est portée à leur étude afin d’améliorer uneaction (contre le vieillissement de la peau, antivirale, anticancéreuse…) ou un procédé de synthèse. Ce projet derecherche s’inscrit dans une démarche de développement d’outils analytiques basés sur la spectrométrie de masse,permettant le suivi rapide et sensible d’interactions enzyme-ligand.Dans une première étude, l’approche TLC couplée à une détection par UV a été évaluée pour la déterminationde constantes enzymatiques de l’enzyme invertase. Cette approche couplée à un MALDI/TOF MS a permis d’identifierdes substrats spécifiques de l’invertase au sein d’extraits de plantes. Pour preuve de concept, l’interactioncellobiohydrolase II–ligand est présentée dans le cadre de l’identification d’inhibiteur par TLC-MALDI/TOF et TLCENALDIMS.En seconde étude, nos travaux ont porté sur la caractérisation directe de différentes enzymes kinases, puis auxsuivis des réactions de phosphorylation de nucléosides /tides endogènes. Ces études, basées sur des approches « offline» (Flow Injection Analysis, FIA) et « on-line » (Frontal Affinity Chromatography, FAC) couplées à unspectromètre de masse haute résolution, ont été réalisées au moyen de ces kinases libres et immobilisées. Dans le cadrede la recherche de nouveaux candidats médicamenteux antiviraux, le suivi d’une phosphorylation spécifique desmolécules de synthèse, au regard de souches humaine ou virale de kinase, a également été évalué par ces deuxméthodologies
Enzymes are very appreciated and useful in various application fields from agri-business to therapeutic due to theirdiversity of actions. Therefore, their action mechanisms are widely studied in order to enhance an action (anti-aging ofskin, antiviral, antitumorous) or a synthesis process. This research project is part of the approach to propose analyticaltools based on mass spectrometry, allowing rapid and sensitive follow-up of enzyme-ligand interactions.In a first study, the Thin-Layer Chromatography (TLC) approach coupled with UV detection was evaluated forthe determination of invertase kinetic constants. This approach coupled with a MALDI / TOF-MS led to theidentification of invertase substrates in plant extracts. As a proof of concept, the cellobiohydrolase II - ligand interactionwas presented in the framework of the identification of inhibitor by TLC-MALDI / TOF and TLC-ENALDI MS.In the second study, our work aimed at developing a direct method for the determination of kinetic parametersof kinases and following-up the phosphorylation reactions of endogenous nucleosides / tides. These studies, based on“off-line” (Flow Injection Analysis, FIA) and “on-line” (Frontal Affinity Chromatography, FAC) approaches coupledwith a high-resolution mass spectrometer, were carried out using free and immobilized kinases. In the context of thesearch for new antiviral drug candidates, a specific phosphorylation of synthetic molecules regards to human or viralkinase was also evaluated by these both approaches
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Yagnik, Asutosh Trilochan. "Molecular modelling applications in rational drug design and the study of enzyme-ligand interactions." Thesis, University of Exeter, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245931.

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Prasannan, Charulata Bhaskaran. "Modulation of restriction enzyme PvuII activity by metal ion cofactors." Diss., St. Louis, Mo. : University of Missouri--St. Louis, 2009. http://etd.umsl.edu/r4461.

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Geitmann, Matthis. "Biosensor Studies of Ligand Interactions with Structurally Flexible Enzymes : Applications for Antiviral Drug Development." Doctoral thesis, Uppsala universitet, Institutionen för naturvetenskaplig biokemi, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5797.

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The use of a surface plasmon biosensor fills a missing link in kinetic studies of enzymes, since it measures directly the interaction between biomolecules and allows determination of parameters that are determined only indirectly in activity assays. The present thesis deals with kinetic and dynamic aspects of ligand binding to two viral enzymes: the human cytomegalovirus (HCMV) protease and the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). The improved description of interactions presented herein will contribute to the discovery and development of antiviral drugs. The biosensor method provided new insights into the interaction between serine proteases and a peptide substrate, as well as substrate-induced conformational changes of the enzymes. The direct binding assay served as a tool for characterising the binding mechanism of HCMV protease inhibitors. Kinetic details of the interaction between HIV-1 RT and non-nucleoside reverse transcriptase inhibitors (NNRTIs) were unravelled. The recorded sensorgrams revealed several forms of complexity. A general binding model for the analysis was derived from the data, describing a two-state mechanism for the enzyme and a high- and a low-affinity interaction with the inhibitor. Interaction kinetic constants were determined for the clinically used NNRTIs and several investigational inhibitors. The established method was applied to investigate the mechanism of resistance against NNRTIs. Amino acid substitutions in the NNRTI-binding site resulted in both decreased association rates and increased dissociation rates for the inhibitors. The K103N and the L100I substitution also interfered with the formation of the binding site, thereby facilitating inhibitor binding and unbinding. Finally, thermodynamic analysis revealed that, despite the hydrophobic character of the interaction, NNRTI binding was mainly enthalpy-driven at equilibrium. Large entropy contributions in the association and dissociation indicated that binding is associated with a dynamic effect in the enzyme.
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Li, Quinn. "Elucidating enzyme catalytic power and protein-ligand dynamics of human glucokinase: the role of modern allostery." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6461.

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Glucokinase (GK) is an enzyme that catalyzes the ATP-dependent phosphorylation of glucose to form glucose-6-phosphate, and it is a tightly regulated checkpoint in glucose homeostasis. The monomeric enzyme possesses a highly exotic kinetic profile, with a sigmoidal dependence on glucose, which has been the source of vigorous investigation and debate in the last several decades. This unique regulatory behavior can be thought of as a remarkable glucose sensor, which may result in hyperglycemia when it is not active enough and hypoglycemia when it is too active. This interdisciplinary study, which draws on small angle X-ray scattering (SAXS) integrated with atomistic molecular dynamics simulations and experimental glucose binding thermodynamics, I reveal the critical regulation of the glucose sensor is due to a solvent controlled switch. Moreover, this solvent controlled switch manifests a regulatory mechanism of GK; a specific local conformational change that leads to an enzyme structure that has a much more favorable solvation energy than most of the protein ensemble. These findings have direct implications for the design of small molecule GK activators as anti- diabetes therapeutics as well as for understanding how proteins can be designed to have built-in regulatory functions via solvation energy dynamics.
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Books on the topic "Ligand/enzyme interaction"

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Kim, Sung-Kun (Sean), Dong-Woo Lee, and Ki Duk Park, eds. Interactions Between Small Molecule Ligands and Target Enzymes. Frontiers Media SA, 2021. http://dx.doi.org/10.3389/978-2-88966-685-0.

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Lambert, David G. Mechanisms and determinants of anaesthetic drug action. Edited by Michel M. R. F. Struys. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780199642045.003.0013.

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This chapter is broken into two main sections: a general description of the principles of ligand receptor interaction and a discussion of the main groups of ‘targets’; and explanation of some common pharmacological interactions in anaesthesia, critical care, and pain management. Agonists bind to and activate receptors while antagonists bind to receptors and block the effects of agonists. Antagonists can be competitive (most common) or non-competitive/irreversible. The main classes of drug target are enzymes, carriers, ion channels, and receptors with examples of anaesthetic relevance interacting with all classes. There are many examples in anaesthesia where multiple interacting drugs are co-administered—polypharmacology. To give an example: neuromuscular blockade. Rocuronium is a non-depolarizing neuromuscular blocker acting as a competitive antagonist at the nicotinic acetylcholine receptor. Rocuronium competes with endogenous acetylcholine to shift the concentration–response curve for contraction to the right. The degree of contractility is less for a given concentration of acetylcholine (agonist) in the presence of rocuronium. Using the same principle, the rightward shift can be compensated by increasing the amount of acetylcholine (as long as the amount of rocuronium presented to the receptor as an antagonist remains unchanged, its action can be overcome by increased agonist). Acetylcholine at the effect site is increased by acetylcholinesterase inhibition with neostigmine. One of the side-effects of neostigmine is that it acts as an indirect parasympathomimetic. In the cardiovascular system this would lead to muscarinic receptor-mediated bradycardia; these effects are routinely reversed by the competitive muscarinic antagonist glycopyrrolate.
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(Editor), Jonathan B. Chaires, and Michael J. Waring (Editor), eds. Drug-Nucleic Acid Interactions (Methods in Enzymology, Volume 340) (Methods in Enzymology). Academic Press, 2001.

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Book chapters on the topic "Ligand/enzyme interaction"

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Hussain, Rohanah, Charlotte S. Hughes, and Giuliano Siligardi. "Enzyme–Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism." In Methods in Molecular Biology, 87–118. New York, NY: Springer US, 2019. http://dx.doi.org/10.1007/978-1-0716-0163-1_6.

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Guillemer, Sabrina, Cécile Persillon, Jean-Michel Masson, and Gilles Ravot. "Cell-Free Protein-Based Enzyme Discovery and Protein–Ligand Interaction Study." In Methods in Molecular Biology, 131–47. Totowa, NJ: Humana Press, 2013. http://dx.doi.org/10.1007/978-1-62703-782-2_8.

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Hussain, Rohanah, Charlotte S. Hughes, and Giuliano Siligardi. "Correction To: Enzyme–Ligand Interaction Monitored by Synchrotron Radiation Circular Dichroism." In Methods in Molecular Biology, C1. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0163-1_19.

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Kopperschläger, G., J. Kirchberger, T. Kriegel, and M. Naumann. "Dye-Ligand Affinity Partitioning — A Powerful Method for Studying Enzyme-Dye Interaction." In Protein-Dye Interactions: Developments and Applications, 149–64. Dordrecht: Springer Netherlands, 1989. http://dx.doi.org/10.1007/978-94-009-1107-9_17.

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Bonomo, R. P., G. Impellizzeri, D. Mendola, G. Maccarrone, G. Pappalardo, A. Santoro, G. Tabbì, G. Vecchio, and E. Rizzarelli. "Functional Mimics of Cu, Zn- Superoxide Dismutase Enzymes." In Metal-Ligand Interactions, 41–63. Dordrecht: Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-010-0191-5_3.

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Cooper, Alan. "Microcalorimetry of Protein-Ligand Interactions." In The Enzyme Catalysis Process, 369–81. Boston, MA: Springer US, 1989. http://dx.doi.org/10.1007/978-1-4757-1607-8_25.

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Bennett, S. Paul, and Stephen E. Halford. "Mechanism and Specificity of two Restriction Enzymes, CauI and CauII, that Recognize Asymmetrical DNA Sequences." In DNA—Ligand Interactions, 239–50. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5383-6_17.

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Liang, Shuguang, Wei Xu, Kurumi Y. Horiuchi, Yuan Wang, and Haiching Ma. "Chemical Microarrays: A New Tool for Discovery Enzyme Inhibitors." In Ligand-Macromolecular Interactions in Drug Discovery, 149–60. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60761-244-5_9.

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Compadre, C. M., R. I. Sanchez, C. Bhuvaneswaran, R. L. Compadre, D. Plunkett, and S. G. Novick. "Analysis of enzyme-ligand interactions in organic solvents: A QSAR approach." In Trends in QSAR and Molecular Modelling 92, 112–15. Dordrecht: Springer Netherlands, 1993. http://dx.doi.org/10.1007/978-94-011-1472-1_15.

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Tirona, Rommel G. "Impact of Nuclear Receptors CAR, PXR, FXR, and VDR, and Their Ligands On Enzymes and Transporters." In Enzyme- and Transporter-Based Drug-Drug Interactions, 75–105. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-1-4419-0840-7_4.

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Conference papers on the topic "Ligand/enzyme interaction"

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Dzichenka, Yaraslau, Michail Shapira, Sergei Usanov, Marina Savić, Ljubica Grbović, Jovana Ajduković, and Suzana Jovanović-Šanta. "NOVEL LIGANDS OF HUMAN CYP7 ENZYMES – POSSIBLE MODULATORS OF CHOLESTEROL BLOOD LEVEL: COMPUTER SIMULATION STUDIES." In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac, 2021. http://dx.doi.org/10.46793/iccbi21.435d.

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Our in vitro studies showed that a couple of perspective steroidal derivatives showed previously biomedical potential via enzyme inhibition, receptor binding or antiproliferative effect against the cancer cells of reproductive tissues are able to bind to human CYP7 enzymes – key enzymes taking part in hydroxylation of cholesterol, 25-, 27-hydroxycholesterol and a number of steroidal hormones. In silico screening of binding affinity of the modified steroids toward CYP7 enzymes showed that interaction energy for the new ligands is comparable with consequent values, calculated for the ‘essential’ substrates of the enzymes – cholestenone (CYP7A1) and DHEA (CYP7B1). However, no correlation between binding energy and the affinity of the ligand was found. Novel ligands interact with conserved amino acids taking part in stabilization of natural substrates of CYP7 enzymes. A couple of structural features, governing ligand binding, were identified. Among which are planar structure of A-ring for CYP7A1 ligands, absence of many polar fragments in side-chain and presence of polar group at C3 position. Analysis of the docking results showed that CYP7B1 higher selectivity in comparison with CYP7A1 is connected by the structure of the cavity formed by α-helices I and B`. The data obtained will be used for the explanation of ligand specificity of human sterol- hydroxylases.
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Steiner, J., and D. Strickland. "INTERACTION OF PLASMIN WITH ALPHA-2 MACROGLOBULIN (α2 M): EFFECT OF ANTIFIBRINOLYTIC AGENTS." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644382.

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Harpel (Harpel, P.C. (1981) J. Clin. Invest 68, 46-55) reported that levels of α2M-plasmin complexes are elevated in patients receiving urokinase. He found that the distribution of plasmin between the two inhibitors, α2M and α2-plasmin inhibitor (α2PI) is dependent upon whether plasmin is added directly to plasma, or whether plasminogen in plasma is activated to plasmin by urokinase. In order to investigate possible mechanisms regulating the distribution of plasmin between these two inhibitors, a study was initiated to examine the effects of antifibrinolytic agents on the reaction of plasmin with α2M. The kinetics of the reaction were measured by monitoring conformational changes in the inhibitor resulting from exomplex formation. In order to minimize nonspecific proteolysis of the inhibitor by plasmin, the reaction was performed under conditions where the concentration of α2M was greater than that of the enzyme. The reaction between Lys77-plasmin and α2M followed second order kinetics with a rate constant of 1.8 X 105M-1 s-1. This rate was not affected 1 mM EACA or by 10 uM histidine rich glycoprotein (HRG). Further, it was found that the rate of Val442-plasmin was essentially the same as that found for Lys77-plasmin. Therefore, the binding of these ligands to the lysine binding sites of plasmin do not affect the association rate between plasmin and α2M. This is in contrast to the reaction of plasmin with α2-PI, where the binding of ligands to the lysine binding sites of plasmin reduce the rate of the reaction (Petersen & Clerrmensen (1981) Biochem. J. 199, 121-127). The kinetic constants measured predict that under conditions when the lysine binding sites of plasmin are occupied, α2M will effectively compete with α2PI in inhibiting plasmin. Further, these studies inplicate HRG as a molecule capable of regulating the distribution of plasmin between these two inhibitors.
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Riethorst, W., M. W. P. M. te Booy, T. Beugeling, A. Bantjes, J. Over, and W. G. van Aken. "THE ISOLATION OF COAGULATION FACTOR VIII FROM HUMAN BLOOD PLASMA BY AFFINITY CHROMATOGRAPHY." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644059.

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The need for high quality concentrates of coagulation factor VIII (FVIII:C) for treatment of haemophilia A is increasing. As the purity of FVIII:C obtained with existing large scale methods is poor and yields are low, another method for the isolation of FVIII is being developed primarily to avoid losses incurred during cryoprecipitation.Affinity gels were prepared by derivatizing Sepharose CL 4B with different positively charged ligand-spacer combinations. The adsorption of FVIII as well as the von Willebrand factor (VWF) from human blood plasma onto these gels was measured by a one-stage assay for FVIII:C, and enzyme immuno assays (ELISA) for FVIII:CAG and VWF:AG using monoclonal antibodies. The influences of pH, conductivity, ligand density, geltplasma ratio, and length and composition of the spacer as well as the adsorption kinetics were studied to obtain information about the types of interactions responsible for bonding of FVIII to the gels. A combination of at least electrostatic and hydrophobic interactions was concluded to play a role in most cases.At optimal conditions more than 90 % of FVIII could be adsorbed batch-wise from plasma at room temperature in less than one hour with a gel:plasma ratio of 1:20 (i.e. 2.5 g dried gel/1 plasma). In different runs 65-75 % of the FVIII:C applied was recovered by column-wise elution with a salt gradient. The eluate contained less than 0.34 % of the protein applied, which implies that FVIII was purified 190 times. Using fresh-frozen plasma (0.8 IU FVIII/ml) as a starting material for this one-step procedure the final specific activity was 2.3 IU/mg, which is significantly better than that obtained for FVIII isolated by cryoprecipitation. Furthermore, the F. VIII:C to VWF ratio in the eluate was approximately 1:1. The isolated FVIII:C was stable at room temperature and the supernatant plasma appears suitable for further fractionation. It is concluded that this method is worth scaling up and its use for purification of FVIII from other sources is anticipated.
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Timmons, Sheila, and Jack Hawiger. "REGULATION OF PLATELET RECEPTORS FOR FIBRINOGEN AND VON WILLEBRAND FACTOR BY PROTEIN KINASE." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644674.

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Positive and negative regulation of platelet receptors for adhesive proteins, fibrinogen (F) and von Willebrand Factor (vWF) determines whether binding of these ligands will or will not take place. We have shown previously that ADP stimulates and cyclic AMP inhibits binding of F and vWF to human platelets. Now we show that positive regulation of F and vWF binding to platelets via the glycoprotein 11b/1111a complex is dependent on platelet Protein Kinase C, a calcium- and phospholipid-dependent enzyme. A potent activator of Protein Kinase C, phorbol-12-myristoyl-13-acetate (PMA) induced saturable and specific binding of F and vWF which was inhibited by synthetic peptides, gamma chain .dodecapeptide (gamma 400-411) and RGDS. The phosphorylation of 47kDa protein (P47), a marker of Protein Kinase C activation in platelets, preceded binding of F and vWF induced with PMA as well as with ADP and thrombin. Sphingosine, an inhibitor of Protein Kinase C, blocked binding of F and vWF to platelets stimulated with PMA, ADP, and thrombin. Inhibition of binding was concentration-dependent and it was accompanied by inhibition of platelet aggregation. Thus, stimulation of Protein Kinase C is required for exposure of platelet receptors for adhesive proteins whereas inhibition of Protein Kinase C prevents receptorexposure. Protein Kinase C fulfills the role of an intraplatelet signal transducer, regulating receptors for adhesive proteins, and constitutes a target for pharmacologic modulation of the adhesive interactions of platelets.
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