Browsing by Subject "enzyme active site"
Now showing items 1-15 of 15
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The 1.76 Å resolution crystal structure of glycogen phosphorylase b complexed with glucose, and CP320626, a potential antidiabetic drug
(2002)CP320626, a potential antidiabetic drug, inhibits glycogen phosphorylase in synergism with glucose. To elucidate the structural basis of synergistic inhibition, we determined the structure of muscle glycogen phosphorylase ...
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Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase
(2001)Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to ...
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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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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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Fourier transform infrared (FTIR) and step-scan time-resolved FTIR spectroscopies reveal a unique active site in cytochrome caa3 oxidase from Thermus thermophilus
(2002)Fourier transform infrared (FTIR) and step-scan time-resolved FTIR difference spectra are reported for the [carbonmonoxy]cytochrome caa3 from Thermus thermophilus. A major C-O mode of heme a3 at 1958 cm-1 and two minor ...
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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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Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses
(2009)The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns ...
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Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses
(2009)The extensive polymorphisms among HIV-1 subtypes have been implicated in drug resistance development. Integrase inhibitors represent the latest addition to the treatment of HIV-1, and their efficacy and resistance patterns ...
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Nitric-oxide reductase: Structure and properties of the catalytic site from resonance Raman scattering
(2002)We have applied resonance Raman spectroscopy to investigate the properties of the dinuclear center of oxidized, reduced, and NO-bound nitric-oxide reductase from Paracoccus denitrificans. The spectra of the oxidized enzyme ...
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Photoselected electron transfer pathways in DNA photolyase
(2007)Cyclobutane dimer photolyases are proteins that bind to UV-damaged DNA containing cyclobutane pyrimidine dimer lesions. They repair these lesions by photo-induced electron transfer. The electron donor cofactor of a photolyase ...
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Resonance Raman detection of the Fe2+-C-N modes in heme-copper oxidases: A probe of the active site
(2004)Resonance Raman spectroscopy has been employed to investigate the reduced cyano complexes of cytochrome aa3 from bovine heart and Rhodobacter sphaeroides and of cytochrome bo3 from E. coli. In the aa 3-type oxidases, the ...
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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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Separation of the complexes formed between the regulatory and catalytic subunits of cyclic adenosine monophosphate-dependent protein kinase and topoisomerase I activity in preovulatory follicle-enriched immature rat ovaries
(1989)Our previous studies have shown that the regulatory subunits of the type II form of cAMP-dependent protein kinase (R‖) present in soluble extracts of immature rat ovaries elute from diethylaminoethyl-cellulose as three ...
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Simultaneous resonance Raman detection of the heme a3-Fe-CO and CuB-CO species in CO-bound ba3-cytochrome c oxidase from Thermus thermophilus: Evidence for a charge transfer CuB-CO transition
(2004)Understanding of the chemical nature of the dioxygen and nitric oxide moiety of ba3-cytochrome c oxidase from Thermus thermophilus is crucial for elucidation of its physiological function. In the present work, direct ...
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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 ...