Search results for "conformation"
showing 10 items of 1414 documents
A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation
2015
International audience; Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukary- otic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is du…
Computational and experimental studies of size and shape related physical properties of hydroxyapatite nanoparticles
2011
In this work, the properties of hydroxyapatite (HAP) nanoparticles (NPs) have been studied both theoretically and experimentally focusing on computational analysis. HAP is widely used to fabricate implants, for drug delivery, etc. The physical properties of the nanosized HAP particles play an important role in the interaction with cells in the human body and are of great interest. Computer simulation was employed to understand the properties of HAP clusters (Ca(5)(PO(4))(3)OH) including formation energies, dipole moments and polarization (surface charges) by molecular mechanics (MM + , OPLS) and mostly by quantum semi-empirical Hartree-Fock (PM3) methods. The size of the simulated cluster i…
On the Catalytic Effect of Water in the Intramolecular Diels–Alder Reaction of Quinone Systems: A Theoretical Study
2012
The mechanism of the intramolecular Diels#8211;Alder (IMDA) reaction of benzoquinone 1, in the absence and in the presence of three water molecules, 1w, has been studied by means of density functional theory (DFT) methods, using the M05-2X and B3LYP functionals for exploration of the potential energy surface (PES). The energy and geometrical results obtained are complemented with a population analysis using the NBO method, and an analysis based on the global, local and group electrophilicity and nucleophilicity indices. Both implicit and explicit solvation emphasize the increase of the polarity of the reaction and the reduction of activation free energies associated with the transition stat…
Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin
2005
We performed a room temperature molecular dynamics (MD) simulation on a system containing 1 carboxy-myoglobin (MbCO) molecule in a sucrose–water matrix of identical composition (89% [sucrose/(sucrose + water)] w/w) as for a previous trehalose–water–MbCO simulation (Cottone et al., Biophys J 2001;80:931–938). Results show that, as for trehalose, the amplitude of protein atomic mean-square fluctuations, on the nanosecond timescale, is reduced with respect to aqueous solutions also in sucrose. A detailed comparison as a function of residue number evidences mobility differences along the protein backbone, which can be related to a different efficacy in bioprotection. Different heme pocket struc…
Aminobisphenolate supported tungsten disulphido and dithiolene complexes
2015
Dioxotungsten(vi) complexes with tetradentate amino bisphenolates were converted into the corresponding Cs-symmetric amino bisphenolate disulphido complexes by a reaction with either Lawesson's reagent or P2S5. Further reaction with diethyl acetylenedicarboxylate leads to the formation of diamagnetic tungsten(iv) dithiolene compounds. The syntheses, crystal structures, spectroscopic and electrochemical characterization of such disulphido and dithiolene complexes are presented.
Structural basis of the migfilin-filamin interaction and competition with integrin beta tails.
2008
A link between sites of cell adhesion and the cytoskeleton is essential for regulation of cell shape, motility, and signaling. Migfilin is a recently identified adaptor protein that localizes at cell-cell and cell-extracellular matrix adhesion sites, where it is thought to provide a link to the cytoskeleton by interacting with the actin cross-linking protein filamin. Here we have used x-ray crystallography, NMR spectroscopy, and protein-protein interaction studies to investigate the molecular basis of migfilin binding to filamin. We report that the N-terminal portion of migfilin can bind all three human filamins (FLNa, -b, or -c) and that there are multiple migfilin-binding sites in FLNa. H…
Nuclear magnetic resonance spectroscopic study of beta-lactoglobulin interactions with two flavor compounds, gamma-decalactone and beta-ionone.
2002
Interactions between a well-characterized protein, beta-lactoglobulin, and two flavor compounds, beta-ionone and gamma-decalactone, were studied by 2D NMR spectroscopy. NMR spectra were recorded in aqueous solution (pH 2.0, 12 mM NaCl, 10% D(2)O) under conditions such that beta-lactoglobulin is present in a monomeric state. TOCSY and NOESY spectra were recorded on the protein and the complexes between protein and ligands. The spectra of the NH-CH(alpha) region showed the cross-signals due to the coupling between N- and C-bonded protons in the polypeptide backbone. The observed chemical shift variations in the presence of ligands can be assigned to changes in the protein conformation. It app…
Crystal structure of lactitol (4-O-beta-D-galactopyranosyl-D-glucitol).
1992
Abstract Lacitol, C 12 H 24 O 11 , is monoclinic, space group P 2 1 with cell dimensions a = 7.614(1), b = 10.757(1), c = 9.370(1) A, β = 108.19(1)°, and V = 729.0(1) A 3 ; Z = 2, D x = 1.57 Mg.m −3 , λ(Cu- K α ) = 1.5406 A, μ = 1.166 mm −1 , F (000) = 368, and T = 23°. The structure was solved by direct methods and refined by least-squares calculations to R = 0.048 for 1510 unique observed reflections. There are one intra- and eight inter-molecular hydrogen bonds in the structure. Bond lengths and angles accord well with the mean values of related structures. The galactopyranosyl ring has a chair conformation.
Structure and Dynamics of RNA Guanine Quadruplexes in SARS-CoV-2 Genome. Original Strategies against Emerging Viruses
2021
Guanine quadruplex (G4) structures in the viral genome have a key role in modulating viruses' biological activity. While several DNA G4 structures have been experimentally resolved, RNA G4s are definitely less explored. We report the first calculated G4 structure of the RG-1 RNA sequence of SARS-CoV-2 genome, obtained by using a multiscale approach combining quantum and classical molecular modeling and corroborated by the excellent agreement between the corresponding calculated and experimental circular dichroism spectra. We prove the stability of the RG-1 G4 arrangement as well as its interaction with G4 ligands potentially inhibiting viral protein translation.
Three-Component Entanglements Consisting of Three Crescent-Shaped Bidentate Ligands Coordinated to an Octahedral Metal Centre
2007
3,3'-biisoquinoline ligands (biiq) L, bearing aromatic substituents on their 8 and 8' positions, have been used to generate interwoven systems consisting of three crescent-shaped ligands disposed around an octahedral metal centre. Mono-ligand complexes of the type [ReL(CO)3py]+ (py: pyridine) have also been prepared, leading to sterically non-hindering complexes in spite of the endotopic nature of the chelate used. The three-component entanglements have been prepared by using either FeII or RuII as gathering metal centre. The synthetic procedure is simple and efficient, affording fully characterised complexes as their PF6 or SbCl6 salts. X-ray crystallography clearly shows that the crescent…