Search results for "Dimer"
showing 10 items of 558 documents
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…
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.
Hydrogen-bond-mediated self-assembly of 26-membered diaza tetraester crowns of 3,5-disubstituted 1 h -pyrazole. Dimerization study in the solid state…
2011
By using an improved synthetic method reported earlier, the cyclic stannoxanes obtained from RN-diethanolamine (R = Me, Bu) and dibutyltin oxide have been reacted with 1H-pyrazole-3,5-dicarbonyl dichloride to afford 26-membered diaza tetraester crowns (1, R = Me; 3, R = Bu) and 39-membered triaza hexaester crowns (2, R = Me; 4, R = Bu). The new structures were identified from their analytical and spectroscopic (1H and 13C NMR, FAB-MS, and/or ESI-MS) data. Both diaza tetraester crowns (1 and 3), containing two 1H-pyrazole units, self-assemble into dimeric species through the formation of four hydrogen bonds involving the two NH pyrazole groups and the two tertiary amine groups of both crowns…
Determining the Geometry of Hydrogen Bonds in Solids with Picometer Accuracy by Quantum-Chemical Calculations and NMR Spectroscopy
2005
The structure of multiply hydrogen-bonded systems is determined with picometer accuracy by a combined solid-state NMR and quantum-chemical approach. On the experimental side, advanced 1H-15N dipolar recoupling NMR techniques are capable of providing proton-nitrogen distances of up to about 250 pm with an accuracy level of +/-1 pm for short distances (i.e., around 100 pm) and +/-5 pm for longer ones (i.e., 180 to 250 pm). The experiments were performed under fast magic-angle spinning, which ensures sufficient dipolar decoupling and spectral resolution of the 1H resonance lines. On the quantum-chemical side, the structures of the hydrogen-bonded systems were computationally optimised, yieldin…
Conformational and structural analysis of the equilibrium between single- and double-strand ?-helix of aD,L-alternating oligonorleucine
2004
Alternating sequences of D and L residues in peptides are directly related to the formation of several kinds of regular helical conformations usually called beta-helices. The major feature of these structures is that they can be associated with the transmembrane ion-conducting channel activity in some natural antibacterial peptides. The study of alternating D,L synthetic peptides is critical to understand how factors such as surrounding media, main chain length, type of side chain and terminal groups, among others, can determine the adoption of a specific kind of beta-helix. Early studies pointed out that the peptides Boc-(D-NLeu-L-NLeu)(6)-D-MeNLe-L-Nl-D-Nl-L-Nl-OMe (Boc: tert-butyloxycarb…
Experimental and Theoretical Study on the Cycloreversion of a Nucleobase-Derived Azetidine by Photoinduced Electron Transfer.
2018
[EN] Azetidines are interesting compounds in medicine and chemistry as bioactive scaffolds and synthetic intermediates. However, photochemical processes involved in the generation and fate of azetidine-derived radical ions have scarcely been reported. In this context, the photoreduction of this four-membered heterocycle might be relevant in connection with the DNA (6-4) photoproduct obtained from photolyase. Herein, a stable azabipyrimidinic azetidine (AZT(m)), obtained from cycloaddition between thymine and 6-azauracil units, is considered to be an interesting model of the proposed azetidine-like intermediate. Hence, its photoreduction and photo-oxidation are thoroughly investigated throug…
The Role of Adenine Excimers in the Photophysics of Oligonucleotides
2009
Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intra…
A Ser residue influences the structure and stability of a Pro-kinked transmembrane helix dimer
2012
AbstractWhen localized adjacent to a Pro-kink, Thr and Ser residues can form hydrogen bonds between their polar hydroxyl group and a backbone carbonyl oxygen and thereby modulate the actual bending angle of a distorted transmembrane α-helix. We have used the homo-dimeric transmembrane cytochrome b559′ to analyze the potential role of a highly conserved Ser residue for assembly and stabilization of transmembrane proteins. Mutation of the conserved Ser residue to Ala resulted in altered heme binding properties and in increased stability of the holo-protein, most likely by tolerating subtle structural rearrangements upon heme binding. The results suggest a crucial impact of an intrahelical Ser…
Structural basis for the sheddase function of human meprin β metalloproteinase at the plasma membrane.
2012
Ectodomain shedding at the cell surface is a major mechanism to regulate the extracellular and circulatory concentration or the activities of signaling proteins at the plasma membrane. Human meprin β is a 145-kDa disulfide-linked homodimeric multidomain type-I membrane metallopeptidase that sheds membrane-bound cytokines and growth factors, thereby contributing to inflammatory diseases, angiogenesis, and tumor progression. In addition, it cleaves amyloid precursor protein (APP) at the β-secretase site, giving rise to amyloidogenic peptides. We have solved the X-ray crystal structure of a major fragment of the meprin β ectoprotein, the first of a multidomain oligomeric transmembrane sheddase…