Search results for " LAB"
showing 10 items of 2393 documents
Mitochondrial DNA haplotype frequencies in natural and experimental populations of Drosophila subobscura.
1998
Abstract The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (>96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima's neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic back…
MODELLING THE DISPERSION PROPERTIES OF MASS LINEAR CHAINS: EXPERIMENTS AND SIMULATIONS
2009
We analyze and discuss the results of an experiment with the goal of revealing the phonon-like acoustic dispersion curve. The experimental apparatus consists of a sonometer and an electromagnetic driver connected to a signal generator in order to establish standing waves along a stretched metal string (a guitar string) upon which a set of beads (used normally for fishing) has been fixed. The oscillation amplitude is measured by means of a detector connected to an MBL interface. We detect the resonance frequencies as function of the wave-number and obtain the corresponding dispersion curve. The results show that deviations from linearity occur when the wavelength is comparable with the dista…
Determination of enrichment factors for modified RNA in MeRIP experiments
2019
In the growing field of RNA modification, precipitation techniques using antibodies play an important role. However, little is known about their specificities and protocols are missing to assess their effectiveness. Here we present a method to assess enrichment factors after MeRIP-type pulldown experiments, here exemplified with a commercial antibody against N6-methyladenosine (m6A). Testing different pulldown and elution conditions, we measure enrichment factors of 4-5 using m6A-containing mRNAs against an unmodified control of identical sequence. Both types of mRNA carry 32P labels at different nucleotides, allowing their relative quantification in a mixture after digestion to nucleotides…
2,8-Diazido-ATP — a short-length bifunctional photoaffinity label for photoaffinity cross-linking of a stable F1 in ATP synthase (from thermophilic b…
1995
Abstract To demonstrate the direct interfacial position of nucleotide binding sites between subunits of proteins we have synthesized the bifunctional photoaffinity label 2,8-diazidoadenosine 5′-triphosphate (2,8-DiN3ATP). UV irradiation of the F1-ATPase (TF1) from the thermophilic bacterium PS3 in the presence of 2,8-DiN3ATP results in a nucleotide-dependent inactivation of the enzyme and in a nucleotide-dependent formation of α-β crosslinks. The results confirm an interfacial localization of all the nucleotide binding sites on TF1.
Site-by-site tracking of signal transduction in an azidophenylalanine-labeled bacteriophytochrome with step-scan FTIR spectroscopy
2021
Signal propagation in photosensory proteins is a complex and multidimensional event. Unraveling such mechanisms site-specifically in real time is an eligible but a challenging goal. Here, we elucidate the site-specific events in a red-light sensing phytochrome using the unnatural amino acid azidophenylalanine, vibrationally distinguishable from all other protein signals. In canonical phytochromes, signal transduction starts with isomerization of an excited bilin chromophore, initiating a multitude of processes in the photosensory unit of the protein, which eventually control the biochemical activity of the output domain, nanometers away from the chromophore. By implementing the label in pri…
Heme Binding Constricts the Conformational Dynamics of the Cytochrome b559′ Heme Binding Cavity
2012
Cytochrome b(559)' is a transmembrane protein formed by homodimerization of the 44-residue PsbF polypeptide and noncovalent binding of a heme cofactor. The PsbF polypeptide can dimerize in the absence and presence of heme. To monitor structural alterations associated with binding of heme to the apo-cytochrome, we analyzed the apo- and holo-cytochrome structure by electron paramagnetic resonance spectroscopy. Spin labeling of amino acids located close to the heme binding domain of the cytochrome revealed that the structure of the heme binding domain is unconstrained in the absence of heme. Heme binding restricts the conformational dynamics of the heme binding domain, resulting in the structu…
Solid state NMR analysis of peptides in membranes: Influence of dynamics and labeling scheme.
2010
The functional state of a membrane-active peptide is often defined by its conformation, molecular orientation, and its oligomeric state in the lipid bilayer. These "static" structural properties can be routinely studied by solid state NMR using isotope-labeled peptides. In the highly dynamic environment of a liquid crystalline biomembrane, however, the whole-body fluctuations of a peptide are also of paramount importance, although difficult to address and most often ignored. Yet it turns out that disregarding such motional averaging in calculating the molecular alignment from orientational NMR-constraints may give a misleading, if not false picture of the system. Here, we demonstrate that t…
Fluidity of liposome membranes doped with metalloporphyrins: An ESR study
2008
Changes in membrane fluidity of porphyrin-doped liposomes have been investigated to assess the kinetics of the fluidization process. Metal complexes of tert-butylphenyl mesosubstituted porphyrin, containing ions of Mg, Mn, Fe, Co, Ni and Cu, were used as dopants. Liposomes were obtained by sonication of hen egg yolk lecithin (EYL). Electron paramagnetic resonance (ESR) was applied using two spin probes, TEMPO (2,2,6,6-tetramethylpiperidine- 1-oxyl) and 16-DOXYL-stearic acid [2-ethyl-2-(15-methoxy-15-oxopentadecyl)-4,4- dimethyl-3-oxazolidinyloxyl], localized at different sites within the membrane to determine the spectroscopic parameters: partition (F) and rotation correlation time (τ), rel…
Vibrational spectrum of the spin crossover complex [Fe(phen)(2)(NCS)(2)] studied by IR and Raman spectroscopy, nuclear inelastic scattering and DFT c…
2006
The vibrational modes of the low-spin and high-spin isomers of the spin crossover complex [Fe(phen)(2)(NCS)(2)] (phen = 1,10-phenanthroline) have been measured by IR and Raman spectroscopy and by nuclear inelastic scattering. The vibrational frequencies and normal modes and the IR and Raman intensities have been calculated by density functional methods. The vibrational entropy difference between the two isomers, DeltaS(vib), which is--together with the electronic entropy difference DeltaS(el)--the driving force for the spin-transition, has been determined from the measured and from the calculated frequencies. The calculated difference (DeltaS(vib) = 57-70 J mol(-1) K(-1), depending on the m…
Synthesis of a potent photoreactive acidic γ-secretase modulator for target identification in cells.
2012
Supramolecular self-assembly of amyloidogenic peptides is closely associated with numerous pathological conditions. For instance, Alzheimer´s disease (AD) is characterized by abundant amyloid plaques originating from the proteolytic cleavage of the amyloid precursor protein (APP) by β- and γ-secretases. Compounds named γ-secretase modulators (GSMs) can shift the substrate cleavage specificity of γ-secretase toward the production of non-amyloidogenic, shorter Aβ fragments. Herein, we describe the synthesis of highly potent acidic GSMs, equipped with a photoreactive diazirine moiety for photoaffinity labeling. The probes labeled the N-terminal fragment of presenilin (the catalytic subunit of …