Browsing by Subject "protein conformation"

Now showing items 1-12 of 12

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. ...

Browsing by Subject "protein conformation"

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

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

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 ﻿

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 ﻿

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

Proteus and the design of ligand binding sites ﻿

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

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 ﻿

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 ﻿

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 ﻿

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

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

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

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

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

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

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

Proteus and the design of ligand binding sites

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

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

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

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

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

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