Browsing by Subject "Protein Conformation"

Article

Analysis of binding parameters of HIV-1 integrase inhibitors: Correlates of drug inhibition and resistance

Loizidou, Eriketi Z.; Zeinalipour-Yazdi, Constantinos D.; Christofides, Tasos C.; Kostrikis, Leontios G. (2009)

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine ...

Article

Analysis of binding parameters of HIV-1 integrase inhibitors: Correlates of drug inhibition and resistance

Loizidou, Eriketi Z.; Zeinalipour-Yazdi, Constantinos D.; Christofides, Tasos C.; Kostrikis, Leontios G. (2009)

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine ...

Article

Analysis of binding parameters of HIV-1 integrase inhibitors: Correlates of drug inhibition and resistance

Loizidou, Eriketi Z.; Zeinalipour-Yazdi, Constantinos D.; Christofides, Tasos C.; Kostrikis, Leontios G. (2009)

This study undertook an exploratory data analysis of the binding parameters of HIV-1 integrase inhibitors. The study group involved inhibitors in preclinical development from the diketo acid, pyrroloquinoline and naphthyridine ...

Article

Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase

Archontis, Georgios Z.; Simonson, T.; Karplus, M. (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 ...

Article

Computational design of novel fullerene analogues as potential HIV-1 PR inhibitors: Analysis of the binding interactions between fullerene inhibitors and HIV-1 PR residues using 3D QSAR, molecular docking and molecular dynamics simulations

Durdagi, S.; Mavromoustakos, Thomas M.; Chronakis, Nikos; Papadopoulos, Manthos G. (2008)

A series of experimentally reported as well as computationally designed monoadducts and bisadducts of [60]fullerene analogues have been used in order to analyze the binding interactions between fullerene based inhibitors ...

Article

Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase

Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (2011)

Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...

Article

Conformational analysis of compstatin analogues with molecular dynamics simulations in explicit water

Tamamis, Phanourios; Skourtis, Spiros S.; Morikis, D.; Lambris, J. D.; Archontis, Georgios Z. (2007)

The cyclic 13-residue peptide compstatin is a potential therapeutic agent against the unregulated activation of the complement system. A thorough knowledge of its structural and dynamical properties in solution may assist ...

Article

Dielectric relaxation in an enzyme active site: Molecular dynamics simulations interpreted with a macroscopic continuum model

Archontis, Georgios Z.; Simonson, T. (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, ...

Article

Enthalpic Contribution to Protein Stability: Insights from Atom-Based Calculations and Statistical Mechanics

Lazaridis, T.; Archontis, Georgios Z.; Karplus, M. (1995)

This chapter discusses published analyses of protein stability based on model compound data and outlines the assumptions that have been made. The enthalpy of protein folding is considered and a thermodynamic cycle is used ...

Article

Flavonoids as DNA topoisomerase antagonists and poisons: Structure-activity relationships

Constantinou, Andreas I.; Mehta, R.; Runyan, C.; Rao, K.; Vaughan, A.; Moon, R. (1995)

Selected flavonoids were tested for their ability to inhibit the catalytic activity of DNA topoisomerase (topo) I and II. Myricetin, quercetin, fisetin, and morin were found to inhibit both enzymes, while phloretin, ...

Article

Fourier transform infrared (FTIR) and step-scan time-resolved FTIR spectroscopies reveal a unique active site in cytochrome caa3 oxidase from Thermus thermophilus

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

Article

Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses

Loizidou, Eriketi Z.; Kousiappa, Ioanna; Zeinalipour-Yazdi, Constantinos D.; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (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 ...

Article

Implications of HIV-1 M group polymorphisms on integrase inhibitor efficacy and resistance: Genetic and structural in silico analyses

Loizidou, Eriketi Z.; Kousiappa, Ioanna; Zeinalipour-Yazdi, Constantinos D.; Van De Vijver, D. A. M. C.; Kostrikis, Leontios G. (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 ...

Article

Molecular optimization using computational multi-objective methods

Nicolaou, Christos A.; Brown, N.; Pattichis, Constantinos S. (2007)

Improving the profile of a molecule for the drug-discovery process requires the simultaneous optimization of numerous, often competing objectives. Traditionally, standard chemo-informatics methods ignored this problem and ...

Article

Nanoscopic cationic methacrylate star homopolymers: Synthesis by group transfer polymerization, characterization and evaluation as transfection reagents

Georgiou, Theoni K.; Vamvakaki, Maria; Patrickios, Costas S.; Yamasaki, E. N.; Phylactou, Leonidas A. (2004)

Seven star polymers with degrees of polymerization (DPs) of the arms from 10 to 100 and dimensions in the nanometer range were prepared using sequential group transfer polymerization of 2-(dimethylamino)-ethyl methacrylate ...

Article

The origin of the Fe IV = O intermediates in cytochrome aa 3 oxidase

Pinakoulaki, Eftychia; Daskalakis, Vangelis; Varotsis, Constantinos (2012)

The dioxygen reduction mechanism in cytochrome oxidases relies on proton control of the electron transfer events that drive the process. Proton delivery and proton channels in the protein that are relevant to substrate ...

Article

Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins

Curry, W. B.; Grabe, M. D.; Kurnikov, I. V.; Skourtis, Spiros S.; Beratan, David N.; Regan, J. J.; Aquino, A. J. A.; Beroza, P.; Onuchic, J. N. (1995)

The simplest views of long-range electron transfer utilize flat one-dimensional barrier tunneling models, neglecting structural details of the protein medium. The pathway model of protein electron transfer reintroduces ...

Article

Recognition and discrimination of gases by the oxygen-sensing signal transducer protein HemAT as revealed by FTIR spectroscopy

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

Article

A single base mutation that converts glycine 907 of the α2(I) chain of type I procollagen to aspartate in a lethal variant of osteogenesis imperfecta. The single amino acid substitution near the carboxyl terminus destabilizes the whole triple helix

Baldwin, C. T.; Constantinou-Deltas, Constantinos D.; Dumars, K. W.; Prockop, D. J. (1989)

Type I procollagen was examined in cultured skin fibroblasts from a patient with a lethal variant of osteogenesis imperfecta. About half of the pro-α chains were post-translationally overmodified and had a decreased thermal ...

Article

Species specificity of the complement inhibitor compstatin investigated by all-atom molecular dynamics simulations

Tamamis, Phanourios; Morikis, D.; Floudas, C. A.; Archontis, Georgios Z. (2010)

The development of compounds to regulate the activation of the complement system in non-primate species is of profound interest because it can provide models for human diseases. The peptide compstatin inhibits protein C3 ...