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Browsing by Subject "protein conformation"

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    • Article  

      The 1.76 Å resolution crystal structure of glycogen phosphorylase b complexed with glucose, and CP320626, a potential antidiabetic drug 

      Oikonomakos, Nikos G.; Zographos, Spyros E.; Skamnaki, Vicky T.; Archontis, Georgios Z. (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 ...

    • Article  

      C2, An Unusual Filamentous Bacterial Virus: Protein Sequence and Conformation, DNA Size and Conformation, and Nucleotide/Subunit Ratio 

      Kostrikis, Leontios G.; Reisberg, S. A.; Day, L. A.; Kim, H. -Y; Shin, S. (1995)
      Inovirus C2 is 1295 nm long and 6.8 nm in diameter, and its mass is 24 million Da. Its genome is a topologically circular, single-stranded DNA molecule of 8100 nucleotides. The DNA is packed in the virion as two antiparallel ...

    • Article  

      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 

      Alexacou, Kyra Melinda; Hayes, Joseph M.; Tiraidis, Costas; Zographos, Spyros E.; Leonidas, Demetres D.; Chrysina, Evangelia D.; Archontis, Georgios Z.; Oikonomakos, Nikos G.; Paul, J. V.; Varghese, B.; Loganathan, D. (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 ...

    • Article  

      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 

      Tamamis, Phanourios; Pierou, P.; Mytidou, C.; Floudas, C. A.; Morikis, D.; Archontis, Georgios Z. (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 ...

    • Article  

      Nitric-oxide reductase: Structure and properties of the catalytic site from resonance Raman scattering 

      Pinakoulaki, Eftychia; Gemeinhardt, S.; Saraste, M.; Varotsis, Constantinos (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 ...

    • Article  

      Proteus and the design of ligand binding sites 

      Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (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 ...

    • Article  

      Recognition of ribonuclease A by 3′-5′-pyrophosphate-linked dinucleotide inhibitors: A molecular dynamics/continuum electrostatics analysis 

      Polydoridis, Savvas; Leonidas, Demetres D.; Oikonomakos, Nikos G.; Archontis, Georgios Z. (2007)
      The proteins of the pancreatic ribonuclease A (RNase A) family catalyze the cleavage of the RNA polymer chain. The development of RNase inhibitors is of significant interest, as some of these compounds may have a therapeutic ...

    • Article  

      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 

      Pinakoulaki, Eftychia; Ohta, T.; Soulimane, T.; Kitagawa, T.; Varotsis, Constantinos (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 ...

    • Article  

      Substitution of cysteine for glycine-α1-691 in the proα1(I) chain of type I procollagen in a proband with lethal osteogenesis imperfecta destabilizes the triple helix at a site C-terminal to the substitution 

      Steinmann, B.; Westerhausen, A.; Constantinou-Deltas, Constantinos D.; Superti-Furga, A.; Prockop, D. J. (1991)
      Skin fibroblast from a proband with lethal osteogenesis imperfecta synthesized a type I procollagen containing a cysteine residue in the α1(I) helical domain. Assay of thermal stability of the triple helix by proteinase ...

    • Article  

      Substitutions for glycine α1-637 and glycine α2-694 of type I procollagen in lethal osteogenesis imperfecta: The conformational strain on the triple helix introduced by a glycine substitution can be transmitted along the helix 

      Tsuneyoshi, T.; Westerhausen, A.; Constantinou-Deltas, Constantinos D.; Prockop, D. J. (1991)
      Two substitutions for glycine in the triple-helical domain were found in type I procollagen synthesized by skin fibroblasts from two probands with lethal osteogenesis imperfecta. One was a substitution of valine for glycine ...

    • Article  

      Superhelices of poly[2-(acetoacetoxy)ethyl methacrylate] 

      Schlaad, H.; Krasia-Christoforou, T.; Antonietti, M. (2004)
      Poly[2-(acetoacetoxy) ethyl methacrylate] (PAEMA) homopolymers were found to self-assemble into hierarchical superstructures, that is, double-stranded helical tubes of either screw sense (scanning force microscopy). Both ...

    • Article  

      Two ligand-binding sites in the O2-sensing signal transducer HemAT: Implications for ligand recognition/discrimination and signaling 

      Pinakoulaki, Eftychia; Yoshimura, H.; Daskalakis, Vangelis; Yoshioka, S.; Aono, S.; Varotsis, Constantinos (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. ...

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