Browsing by Subject "hydrogen bond"

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

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

Electron affinities of a homologous series of tertiary alkyl radicals and their C-H bond dissociation energies (BDEs)

Petrou, Panayiotis S.; Nicolaides, Athanassios V. (2009)

Heats of formation have been derived from G3(MP2)//B3LYP and G3MP2B3(+) atomization energies for tert-butyl radical (6R), cubyl radical, bicyclooctyl radical (1R), and tricyclo[3.3.n.03,7]alk-3(7)-yl (n=0-3, 2R-5R) radicals, ...

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

Equilibrium in soft-matter systems under the influence of competing forces

Zemb, T.; Leontidis, Epameinondas (2013)

Article

Intermolecular hydrogen bonding in chlorine dioxide photochemistry: A time-resolved resonance Raman study

Philpott, M. P.; Hayes, Sophia C.; Thomsen, C. L.; Reid, P. J. (2001)

The geminate-recombination and vibrational-relaxation dynamics of chlorine dioxide (OClO) dissolved in ethanol and 2,2,2-trifluoroethanol (TFE) are investigated using time-resolved resonance Raman spectroscopy. Stokes ...

Article

Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase

Watson, K. A.; Chrysina, Evangelia D.; Tsitsanou, K. E.; Zographos, Spyros E.; Archontis, Georgios Z.; Fleet, G. W. J.; Oikonomakos, Nikos G. (2005)

Glycogen phosphorylase (GP) is currently exploited as a target for inhibition of hepatic glycogenolysis under high glucose conditions. Spirohydantoin of glucopyranose and N-acetyl-β-D-glucopyranosylamine have been identified ...

Article

Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: The role of water molecules examined

Bischler, N.; Hayes, Joseph M.; Skamnaki, Vicky T.; Archontis, Georgios Z.; Lamprakis, Christos; Sarrou, Josephine; Skaltsounis, Alexios Leandros; Zographos, Spyros E.; Oikonomakos, Nikos G. (2011)

With an aim toward glycogenolysis control in Type 2 diabetes, we have investigated via kinetic experiments and computation the potential of indirubin (IC 50 > 50 μM), indirubin-3'-oxime (IC 50 = 144 nM), KT5720 (K i = 18.4 ...

Article

Long-range charge transport in single G-quadruplex DNA molecules

Livshits, G. I.; Stern, A.; Rotem, D.; Borovok, N.; Eidelshtein, G.; Migliore, A.; Penzo, E.; Wind, S. J.; Di Felice, R.; Skourtis, Spiros S.; Cuevas, J. C.; Gurevich, L.; Kotlyar, A. B.; Porath, D. (2014)

DNA and DNA-based polymers are of interest in molecular electronics because of their versatile and programmable structures. However, transport measurements have produced a range of seemingly contradictory results due to ...

Article

Manganese citrate chemistry: Syntheses, spectroscopic studies, and structural characterizations of novel mononuclear, water-soluble manganese citrate complexes

Matzapetakis, M.; Karligiano, N.; Bino, A.; Dakanali, M.; Raptopoulou, C. P.; Tangoulis, V.; Terzis, A.; Giapintzakis, John; Salifoglou, A. (2000)

The first two mononuclear manganese citrate complexes, (NH4)4[Mn(II)(C6H5O7)2] (1) and (NH4)5[Mn(III)(C6H4O7)2]·2H2O (2) were synthesized in aqueous solutions near physiological pH values. They were isolated in their pure ...

Article

Molecular Dynamics in Drug Design: New Generations of Compstatin Analogs

Tamamis, Phanourios; López de Victoria, A.; Gorham, R. D.; Bellows-Peterson, M. L.; Pierou, P.; Floudas, C. A.; Morikis, D.; Archontis, Georgios Z. (2012)

We report the computational and rational design of new generations of potential peptide-based inhibitors of the complement protein C3 from the compstatin family. The binding efficacy of the peptides is tested by extensive ...

Article

New antimony(III) halide complexes with dithiocarbamate ligands derived from thiuram degradation: The effect of the molecule's close contacts on in vitro cytotoxic activity

Urgut, O. S.; Ozturk, I. I.; Banti, Christina N.; Kourkoumelis, Nikolaos; Manoli, Maria; Tasiopoulos, Anastasios J.; Hadjikakou, Sotiris K. (2016)

Antimony(III) halide complexes of the formulae {[SbBr(Me2DTC)2]n} (1), {[SbI(Me2DTC)2]n} (2) and {[(Me2DTC)2Sb(μ2-I)Sb(Me2DTC)2]+.I3-} (3) (Me2DTC = dimethyldithiocarbomate) were synthesized from SbX3, (X = Br or I) and ...

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

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

Probing nitrite coordination in horseradish peroxidase by resonance Raman spectroscopy: Detection of two binding sites

Ioannou, Androulla; Pinakoulaki, Eftychia (2017)

Nitrite is a powerful oxidant that affects the activity of peroxidases towards various substrates and leads to heme macrocycle modifications in members of the peroxidase family, such as the horseradish peroxidase (HRP). ...

Article

The protein effect in the structure of two ferryl-oxo intermediates at the same oxidation level in the heme copper binuclear center of cytochrome c oxidase

Pinakoulaki, Eftychia; Daskalakis, Vangelis; Ohta, T.; Richter, O. -M H.; Budiman, K.; Kitagawa, T.; Ludwig, B.; Varotsis, Constantinos (2013)

Identification of the intermediates and determination of their structures in the reduction of dioxygen to water by cytochrome c oxidase (CcO) are particularly important to understanding both O2 activation and proton pumping ...

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

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

Resonance Raman detection of a ferrous five-coordinate nitrosylheme b3 complex in cytochrome cbb3 oxidase from Pseudomonas stutzeri

Pinakoulaki, Eftychia; Stavrakis, Stavros; Urbani, A.; Varotsis, Constantinos (2002)

Understanding the chemical nature of the nitric oxide (NO) moiety of nitrosylheme copper oxidases is crucial for elucidation of the NO activation process. In the present work, direct resonance Raman spectroscopic observation ...