Search results for "models"

Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: III. DNA separations by capillary electrophoresis in poly(N-a…

1996

Separation of DNA fragments in a novel polymer network, consisting of N-acryloylaminopropanol (AAP) is reported. The performance of this novel monomer, as a sieving liquid polymer in capillary zone electrophoresis, was evaluated. In 50 microns ID capillaries, an 8% solution of poly (AAP) can afford apex-resolution of the 123/124 bp adjacent pair of DNA fragments in marker V, typically unresolved in any poly (acrylamide) formulation. It is proposed that the distal-OH group in the AAP molecule can form transient H-bonds with the DNA double helix. Molecular modeling shows a meandering structure for poly (AAP), lacing the walls of half a cylinder, with kinks protruding at regular intervals, pot…

Heterocyclic rearrangements in constrained media. A zeolite-directed photorearrangement of 1,2,4-oxadiazoles

2005

[reaction: see text] The first intrazeolite-photoinduced rearrangement of a five-membered heterocycle is reported. A completely different behavior compared to solution irradiations has been observed. The zeolite's role in directing the photoreaction of 3-phenyl-1,2,4-oxadiazoles toward the formation of the corresponding 1,3,4-oxadiazoles in a ring contraction-ringexpansion route is discussed.

Copper-O2 reactivity of tyrosinase models towards external monophenolic substrates: molecular mechanism and comparison with the enzyme.

2011

The critical review describes the known dicopper systems mediating the aromatic hydroxylation of monophenolic substrates. Such systems are of interest as structural and functional models of the type 3 copper enzyme tyrosinase, which catalyzes the ortho-hydroxylation of tyrosine to DOPA and the subsequent two-electron oxidation to dopaquinone. Small-molecule systems involving μ-η²:η² peroxo, bis-μ-oxo and trans-μ-1,2 peroxo dicopper cores are considered separately. These tyrosinase models are contrasted to copper–dioxygen systems inducing radical reactions, and the different mechanistic pathways are discussed. In addition to considering the stoichiometric conversion of phenolic substrates, t…

tRNA stabilization by modified nucleotides.

2010

Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation …

High speed X-ray analysis of plant enzymes at room temperature.

2013

X-ray measurements at room temperature (295 K) deliver high quality data sets with unprecedented speed (2 min), as shown for crystallized raucaffricine-O-β-D-glucosidase (RG), its mutant RG-Glu186Gln and several ligand complexes of the enzyme which participates in alkaloid biosynthesis in the plant Rauvolfia. The data obtained are compared with data sets measured under typical cryo conditions (100K). Under both conditions, density maps are highly comparable and favor the described protocol for room temperature measurements, potentially paving the way for future crystallographic studies capturing biosynthetic pathway intermediates.

A quantum mechanics/molecular mechanics study of the protein-ligand interaction for inhibitors of HIV-1 integrase.

2007

Human immunodeficiency virus type-1 integrase (HIV-1 IN) is an essential enzyme for effective viral replication. Diketo acids such as L-731,988 and S-1360 are potent and selective inhibitors of HIV-1 IN. In this study, we used molecular dynamics simulations, within the hybrid quantum mechanics/molecular mechanics (QM/MM) approach, to determine the protein-ligand interaction energy between HIV-1 IN and L-731,988 and 10 of its derivatives and analogues. This hybrid methodology has the advantage that it includes quantum effects such as ligand polarisation upon binding, which can be very important when highly polarisable groups are embedded in anisotropic environments, as for example in metal-c…

Amino acid sequence and homology modeling of obtustatin, a novel non-RGD-containing short disintegrin isolated from the venom of Vipera lebetina obtu…

2003

Disintegrins represent a group of cysteine-rich peptides occurring in Crotalidae and Viperidae snake venoms, and are potent antagonists of several integrin receptors. A novel disintegrin, obtustatin, was isolated from the venom of the Vipera lebetina obtusa viper, and represents the first potent and selective inhibitor of the binding of integrin alpha(1)beta(1) to collagen IV. The primary structure of obtustatin contains 41 amino acids and is the shortest disintegrin described to date. Obtustatin shares the pattern of cysteines of other short disintegrins. However, in contrast to known short disintegrins, the integrin-binding loop of obtustatin is two residues shorter and does not express t…

Building molecular models using screw-on bottle caps

2013

Chemical models can be built using screw-on bottle caps. Two identical caps can be joined together by thermal welding to form atoms, and the resulting atoms can be joined together by welding or by hot polymer glue to form molecules. The method is easy, can be applied at every level of chemical education, and gives access to an unlimited number of models at almost no cost. It inspires hands-on activity of pupils and can be used to show the dependence between the three-dimensional structure of molecules and their chemical, physical, and biological features.

Numerical–Analytical Model for Nanotube‐Reinforced Nanocomposites

2013

Polyunsaturated fatty acids in the modulation of T-cell signalling

2009

n-3 polyunsaturated fatty acids (PUFA) have been shown to modulate immune responses. These agents, being considered as adjuvant immunosuppressants, have been used in the treatment of various inflammatory and autoimmune diseases. However, the molecular mechanisms of action of n-3 PUFA-induced immunosuppressive effects are not well-understood. Since exogenous n-3 PUFA, under in vitro and in vivo conditions, are efficiently incorporated into T-cell plasma membranes, a number of recent studies have demonstrated that these agents may modulate T-cell signalling. In this review, the interactions of n-3 PUFA with the second messenger cascade initiated during early and late events of T-cell activati…