Browsing by Subject "ligand binding"
Now showing items 1-15 of 15
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Crystallographic and computational studies on 4-phenyl-N-(β-D- glucopyranosyl)-1H-1,2, 3-triazole-1-acetamide, an inhibitor of glycogen phosphorylase: Comparison with α-D-glucose, N-acetyl-β-D- glucopyranosylamine and N-benzoyl-N′-β-D-glucopyranosyl urea binding
(2008)4-Phenyl-N-(β-D-glucopyranosyl)-1H-1,2,3-triazole-1-acetamide (glucosyltriazolylacetamide) has been studied in kinetic and crystallographic experiments with glycogen phosphorylase b (GPb), in an effort to utilize its ...
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Design of a modified mouse protein with ligand binding properties of its human analog by molecular dynamics simulations: The case of C3 inhibition by compstatin
(2011)The peptide compstatin and its derivatives inhibit the complement-component protein C3 in primate mammals and are potential therapeutic agents against the unregulated activation of complement in humans, but are inactive ...
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Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model
(2001)Dielectric relaxation plays an important role in many chemical processes in proteins, including acid-base titration, ligand binding, and charge transfer reactions. Its complexity makes experimental characterization difficult, ...
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Glycogen phosphorylase inhibitors: A free energy perturbation analysis of glucopyranose spirohydantoin analogues
(2005)GP catalyzes the phosphorylation of glycogen to Glc-1-P. Because of its fundamental role in the metabolism of glycogen, GP has been the target for a systematic structure-assisted design of inhibitory compounds, which could ...
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Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase
(2005)Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-β-D-glucopyranosylamine have been identified ...
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Model investigations for vanadium-protein interactions: Vanadium(III) compounds with dipeptides and their oxovanadium(IV) analogues
(2002)The reaction of VCl3 with 1,10-phenanthroline and a series of dipeptides (H2dip), having aliphatic as well as aromatic side chains, in methyl alcohol and in the presence of triethylamine affords vanadium(III) compounds of ...
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Probing nitrite coordination in horseradish peroxidase by resonance Raman spectroscopy: Detection of two binding sites
(2017)Nitrite is a powerful oxidant that affects the activity of peroxidases towards various substrates and leads to heme macrocycle modifications in members of the peroxidase family, such as the horseradish peroxidase (HRP). ...
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The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme copper binuclear center of cytochrome c oxidase
(2013)Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping ...
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Proteus and the design of ligand binding sites
(2016)This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...
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Recognition and discrimination of gases by the oxygen-sensing signal transducer protein HemAT as revealed by FTIR spectroscopy
(2006)The determination of ligand binding properties is a key step in our understanding of gas sensing and discrimination by gas sensory proteins. HemAT is a newly discovered signal transducer heme protein that recognizes O 2 ...
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Resonance Raman detection of a ferrous five-coordinate nitrosylheme b3 complex in cytochrome cbb3 oxidase from Pseudomonas stutzeri
(2002)Understanding the chemical nature of the nitric oxide (NO) moiety of nitrosylheme copper oxidases is crucial for elucidation of the NO activation process. In the present work, direct resonance Raman spectroscopic observation ...
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The role of the cross-link His-Tyr in the functional properties of the binuclear center in cytochrome c oxidase
(2002)Resonance Raman and Fourier transform infrared spectroscopies have been used to study the aa3-type cytochrome c oxidase and the Y280H mutant from Paracoccus denitrificans. The stability of the binuclear center in the absence ...
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Structure based inhibitor design targeting glycogen phosphorylase b. Virtual screening, synthesis, biochemical and biological assessment of novel N-acyl-β-d-glucopyranosylamines
(2014)Glycogen phosphorylase (GP) is a validated target for the development of new type 2 diabetes treatments. Exploiting the Zinc docking database, we report the in silico screening of 1888 N-acyl-β-d-glucopyranosylamines ...
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Time-Resolved Resonance Raman and Time-Resolved Step-Scan FTIR Studies of Nitric Oxide Reductase from Paracoccus denitrificans: Comparison of the Heme b3-FeB Site to That of the Heme-CuB in Oxidases
(2003)Time-resolved resonance Raman (TR3) and time-resolved step-scan (TRS2) FTIR spectroscopies have been used to probe the structural dynamics at the heme b3 proximal and distal sites after carbon monoxide photolysis from fully ...
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Two ligand-binding sites in the O2-sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling
(2006)We have identified a ligand (CO) accommodation cavity in the signal transducer sensor protein HemAT (heme-based aerotactic transducer) that allows us to gain single-molecule insights into the mechanism of gas sensor proteins. ...