Search results for " Simulation"
showing 10 items of 4034 documents
Surface plasmons and vibrations of self-assembled silver nanocolumns
2006
6 pags. ; 5 figs. 1 tab.
Conformational Changes in the Nucleosome Followed by the Selective Accessibility of Histone Glutamines in the Transglutaminase Reaction: Effects of …
2001
Transglutaminases, the enzymes that catalyze the acyl-transfer reaction between glutamine and primary amines, have been used to introduce probes into proteins in order to perform structural studies using physical techniques. Here we use an original approach in which the increasing accessibility of the glutamines of core histones to TGase is used to monitor the salt-induced conformational changes of the nucleosome. The rationale of this strategy is that the accessibility of a glutamine to transglutaminase depends on the blockage due to the presence of either other histones or DNA. At low ionic strength, only glutamines on the N-terminal tails of H2B and H3 are labeled with monodansylcadaveri…
Mechanically interlocked calix[4]arene dimers display reversible bond breakage under force.
2009
The physics of nanoscopic systems is strongly governed by thermal fluctuations that produce significant deviations from the behaviour of large ensembles1,2. Stretching experiments of single molecules offer a unique way to study fundamental theories of statistical mechanics, as recently shown for the unzipping of RNA hairpins3. Here, we report a molecular design based on oligo calix[4]arene catenanes—calixarene dimers held together by 16 hydrogen bridges—in which loops within the molecules limit how far the calixarene nanocapsules can be separated. This mechanically locked structure tunes the energy landscape of dimers, thus permitting the reversible rupture and rejoining of the individual n…
Influence of Whole-Body Dynamics on 15N PISEMA NMR Spectra of Membrane Proteins: A Theoretical Analysis
2009
AbstractMembrane proteins and peptides exhibit a preferred orientation in the lipid bilayer while fluctuating in an anisotropic manner. Both the orientation and the dynamics have direct functional implications, but motions are usually not accessible, and structural descriptions are generally static. Using simulated data, we analyze systematically the impact of whole-body motions on the peptide orientations calculated from two-dimensional polarization inversion spin exchange at the magic angle (PISEMA) NMR. Fluctuations are found to have a significant effect on the observed spectra. Nevertheless, wheel-like patterns are still preserved, and it is possible to determine the average peptide til…
New antitumoral acetogenin ‘Guanacone type’ derivatives: Isolation and bioactivity. Molecular dynamics simulation of diacetyl-guanacone
2007
We describe herein the isolation and semisynthesis of four acetogenin derivatives (1-4) as well as their ability to inhibit the mitochondrial respiratory chain and several tumor cell lines. In addition, four nanoseconds (ns) of MD simulation of compound 4, in a fully hydrated POPC bilayer, is reported.
Hydrogen bonding in dimers of tritolyl and tritosylurea derivatives of triphenylmethanes.
2006
The crystal structure of the homodimer formed by the tritolylurea 3a proves the existence of a belt of six bifurcated hydrogen bonds between both NH and the O=C groups of the adjacent urea residues. For the tritosylurea 3b, four additional three-center hydrogen bonds, also involving the SO2 oxygen, are found in the crystalline state. Molecular dynamics simulations in a chloroform box confirm these patterns of the hydrogen bonds and the resulting elongation of the dimer 3b. 3b in comparison to 3a x 3a. The calculated complexation energies for the three dimeric combinations are nearly identical in agreement with the simultaneous formation of heterodimer 3a x 3b in a mixture of 3a and 3b.
Effects of static and dynamic perturbations on isotropic hyperfine coupling constants in some quinone radicals.
2004
The effects of solvent dielectric response on the isotropic hyperfine coupling constants of the 1,4-benzoquinone, 1,4-naphthoquinone and 9,10-anthraquinone anions and 1,4-naphthalenediol cation radicals were studied by electron spin resonance (ESR) spectroscopy and by the theoretical density functional method within the polarizable continuum model. Experimental results demonstrate that the isotropic hyperfine coupling constants can be obtained with high accuracy and that the effects of solvent impurities can be minimized by careful sample preparation. The results obtained correlate well with theoretical predictions from density functional theory calculations. For 1,4-naphthalenediol both th…
Antimicrobial Peptides and Their Superior Fluorinated Analogues: Structure-Activity Relationships as Revealed by NMR Spectroscopy and MD Calculations
2010
9 pag., 6 fig, 3 tab.
Orientational landscapes of peptides in membranes: prediction of (2)H NMR couplings in a dynamic context.
2009
Unlike soluble proteins, membrane polypeptides face an anisotropic milieu. This imposes restraints on their orientation and provides a reference that makes structure prediction tractable by minimalistic thermodynamic models. Here we use this framework to build orientational distributions of monomeric membrane-bound peptides and to predict their expected solid-state (2)H NMR quadrupolar couplings when labeled at specific side chain positions. Using a complete rigid-body sampling of configurations relative to an implicit lipid membrane, peptide free energy landscapes are calculated. This allows us to obtain probability distributions of the peptide tilt, azimuthal rotation, and depth of membra…
NMR study of hexanucleotide d(CCGCGG)2 containing two triplet repeats of fragile X syndrome
2003
Abstract Long repeated stretches of d(CCG) and tri-nucleotide are crucial mutations that cause hereditary forms of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) di-nucleotide is one of the candidates for Z-DNA conformation. Solution NMR structure of d(CCGCGG) 2 has been solved and is discussed. The determined NMR solution structure is a distorted highly bent B-DNA conformation with increased flexibility in both terminal residues. This conformation differs significantly from the Z-DNA tetramer structure reported for the same hexamer in the crystal state at similar ionic strength by Malinina and co-workers. Crystal structure of d(CCGCGG) 2 at high salt concentration …