Browsing by Subject "protein structure"

Article

Amphiphilic model conetworks based on cross-linked star copolymers of benzyl methacrylate and 2-(dimenthylamino)ethyl methacrylate: Synthesis, characterization, and DNA adsorption studies

Achilleos, Demetra S.; Georgiou, Theoni K.; Patrickios, Costas S. (2006)

Six amphiphilic model conetworks of a new structure, that of cross-linked "in-out" star copolymers, were synthesized by the group transfer polymerization (GTP) of the hydrophobic monomer benzyl methacrylate (BzMA) and the ...

Article

Architectural insight into inovirus-associated vectors (IAVs) and development of IAV-based vaccines inducing humoral and cellular responses: Implications in HIV-1 vaccines

Hassapis, K. A.; Stylianou, Dora C.; Kostrikis, Leontios G. (2014)

Inovirus-associated vectors (IAVs) are engineered, non-lytic, filamentous bacteriophages that are assembled primarily from thousands of copies of the major coat protein gp8 and just five copies of each of the four minor ...

Article

Computational sidechain placement and protein mutagenesis with implicit solvent models

Lopes, A.; Alexandrov, A.; Bathelt, C.; Archontis, Georgios Z.; Simonson, T. (2007)

Structure prediction and computational protein design should benefit from accurate solvent models. We have applied implicit solvent models to two problems that are central to this area. First, we performed sidechain placement ...

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

Detection of the His-heme Fe2+-NO species in the reduction of NO to N2O by ba3-oxidase from thermus thermophilus

Pinakoulaki, Eftychia; Ohta, T.; Soulimane, T.; Kitagawa, T.; Varotsis, Constantinos (2005)

Reaction pathways in the enzymatic formation and cleavage of the N-N and N-O bonds, respectively, are difficult to verify without the structure of the intermediates, but we now have such information on the heme a3 2+-NO ...

Article

High and low resolution theories of protein electron transfer

Skourtis, Spiros S.; Beratan, David N. (1997)

Protein-mediated electronic interactions facilitate biological electron transfer (ET) reactions. Theory and experiment are being used extensively to establish atomic-scale descriptions of these reactions. The last 20 years ...

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

Investigation of substituent effect of 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques

Afantitis, Antreas; Melagraki, G.; Sarimveis, H.; Koutentis, Panayiotis Andreas; Markopoulos, J.; Igglessi-Markopoulou, O. (2006)

A linear quantitative-structure activity relationship model is developed in this work using Multiple Linear Regression Analysis as applied to a series of 51 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides derivatives ...

Article

Nitric oxide activation and reduction by heme-copper oxidoreductases and nitric oxide reductase

Pinakoulaki, Eftychia; Varotsis, Constantinos (2008)

The understanding of the dynamics and conformational control involved in the interplay between structure and function of nitric oxide reductase (Nor) and heme-copper oxidoreductases in their function to convert nitric oxide ...

Article

Novel compstatin family peptides inhibit complement activation by drusen-like deposits in human retinal pigmented epithelial cell cultures

Gorham, R. D.; Forest, D. L.; Tamamis, Phanourios; López de Victoria, A.; Kraszni, M.; Kieslich, C. A.; Banna, C. D.; Bellows-Peterson, M. L.; Larive, C. K.; Floudas, C. A.; Archontis, Georgios Z.; Johnson, L. V.; Morikis, D. (2013)

We have used a novel human retinal pigmented epithelial (RPE) cell-based model that mimics drusen biogenesis and the pathobiology of age-related macular degeneration to evaluate the efficacy of newly designed peptide ...

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

Phenotypic heterogeneity in osteogenesis imperfecta: The mildly affected mother of a proband with a lethal variant has the same mutation substituting cysteine for α1-glycine 904 in a type I procollagen gene (COL1A1)

Constantinou-Deltas, Constantinos D.; Pack, M. A.; Young, S. B.; Prockop, D. J. (1990)

A proband with a lethal variant of osteogenesis imperfecta (OI) has been shown to have, in one allele in a gene for type I procollagen (COL1A1), a single base mutation that converted the codon for α1-glycine 904 to a codon ...

Article

Photosynthesis from the protein's perspective

Skourtis, Spiros S.; Beratan, David N. (2007)

Article

Processing of the FMRFamide Precursor Protein in the Snail Lymnaea stagnalis: Characterization and Neuronal Localization of a Novel Peptide, ‘SEEPLY’

Santama, Niovi; Wan Li, K.; Bright, K. E.; Yeoman, M.; Geraerts, W. P. M.; Benjamin, P. R.; Burke, J. F. (1993)

In the pulmonate snail Lymnaea stagnalis, FMRFamide‐like neuropeptides are encoded by a multi‐exon genomic locus which is subject to regulation at the level of mRNA splicing. We aim to understand the post‐translational ...

Article

Proton binding to proteins: A free-energy component analysis using a dielectric continuum model

Archontis, Georgios Z.; Simonson, T. (2005)

Proton binding plays a critical role in protein structure and function. We report pKa calculations for three aspartates in two proteins, using a linear response approach, as well as a "standard" Poisson-Boltzmann approach. ...

Article

The role of the cross-link His-Tyr in the functional properties of the binuclear center in cytochrome c oxidase

Pinakoulaki, Eftychia; Pfitzner, U.; Ludwig, B.; Varotsis, Constantinos (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 ...

Article

Self-assembly of phenylalanine oligopeptides: Insights from experiments and simulations

Tamamis, Phanourios; Adler-Abramovich, L.; Reches, M.; Marshall, K.; Sikorski, P.; Serpell, L.; Gazit, E.; Archontis, Georgios Z. (2009)

Studies of peptide-based nanostructures provide general insights into biomolecular self-assembly and can lead material engineering toward technological applications. The diphenylalanine peptide (FF) self-assembles into ...

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 ...