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Dodecins, a group of flavin-binding proteins with a dodecameric quaternary structure, are able to incorporate two flavins within each of their six identical binding pockets building an aromatic tetrade with two tryptophan residues. Dodecin from the archaeal Halobacterium salinarum is a riboflavin storage device. We demonstrate that unwanted side reactions induced by reactive riboflavin species and degradation of riboflavin are avoided by ultrafast depopulation of the reactive excited state of riboflavin. Intriguingly, in this process, the staggered riboflavin dimers do not interact in ground and photoexcited states. Rather, within the tetrade assembly, each riboflavin is kept under the control of the respective adjacent tryptophan, which suggests that the stacked arrangement is a matter of optimizing the flavin load. We further identify an electron transfer in combination with a proton transfer as a central element of the effective excited state depopulation mechanism. Structural and functional comparisons of the archaeal dodecin with bacterial homologs reveal diverging evolution. Bacterial dodecins bind the flavin FMN instead of riboflavin and exhibit a clearly different binding pocket design with inverse incorporations of flavin dimers. The different adoption of flavin changes photochemical properties, making bacterial dodecin a comparably less efficient quencher of flavins. This supports a functional role different for bacterial and archaeal dodecins.
Ubiquitin ligases and beyond
(2012)
First paragraph (this article has no abstract): In a review published in 2004 [1] and that still repays reading today, Cecile Pickart traced the evolution of research on ubiquitination from its origins in the proteasomal degradation of proteins through the revelation that it has a central role in cell cycle regulation and the recognition of regulatory roles for ubiquitin in intracellular membrane transport, cell signalling, transcription, translation, and DNA repair.
The title complex, [PdCl2(C18H15P)2]·0.5C6H6, has the PdII ion in a square-planar coordination mode (r.m.s. deviation for Pd, P and Cl atoms = 0.024 Å) with the PPh3 and Cl ligands mutually trans. The benzene solvent molecule is located about a crystallographic inversion centre. The title complex is isostructural with trans-dichloridobis(triphenylphosphane)palladium(II) 1,4-dichlorobenzene sesquisolvate [Kitano et al. (1983 [triangle]). Acta Cryst. C39, 1015–1017].
A metal–organic framework (MOF) material, [Zn2(adc)2(dabco)] (adc = anthracene-9,10-dicarboxylate, dabco = 1,4-diazabicyclo[2.2.2]octane), the fluorescence of which depends on the loading of its nanopores, was synthesized in two forms: as free-flowing nanocrystals with different shapes and as surface-attached MOFs (SURMOFs). For the latter, we used self-assembled monolayers (SAMs) bearing functional groups, such as carboxylate and pyridyl groups, capable of coordinating to the constituents of the MOF. It could be demonstrated that this directed coordination also orients the nanocrystals deposited at the surface. Using two different patterning methods, i.e., microcontact printing and electron-beam lithography, the lateral distribution of the functional groups could be determined in such a way that the highly localized deposition of the SURMOF films became possible.
Infrared spectroscopy in combination with a specially developed attenuated total reflection (ATR) flow cell and multivariate analysis was used for the quantitative analysis of beer and other beverages. IR spectra of samples were obtained in the range from below 1000 cm-1 to 4000 cm-1 and subjected to a multivariate analysis based on calibration sets with laboratory reference standards. In the case of beer, this calibration set included 240 beer samples spanning the entire range of ethanol content, extract and CO2. Based on this calibration, an infrared and UV/Vis spectroscopy-based sensor for the quick and quantitative quality control of beer was developed and subjected to extensive tests in breweries. This sensor meets and exceeds all requirements from brewers for the routine control in the production and bottling. Its use for other beverages, for example wine, juices or apple wine, requires only another set of calibration data for the specific beverage.
Protein-tyrosine phosphatases (PTPs) and protein-tyrosine kinases co-regulate cellular processes. In pathogenic bacteria, they are frequently exploited to act as key virulence factors for human diseases. Mycobacterium tuberculosis, the causative organism of tuberculosis, secretes a low molecular weight PTP (LMW-PTP), MptpA, which is required for its survival upon infection of host macrophages. Although there is otherwise no sequence similarity of LMW-PTPs to other classes of PTPs, the phosphate binding loop (P-loop) CX5R and the loop containing a critical aspartic acid residue (D-loop), required for the catalytic activity, are well conserved. In most high molecular weight PTPs, ligand binding to the P-loop triggers a large conformational reorientation of the D-loop, in which it moves ∼10 Å, from an “open” to a “closed” conformation. Until now, there have been no ligand-free structures of LMW-PTPs described, and hence the dynamics of the D-loop have remained largely unknown for these PTPs. Here, we present a high resolution solution NMR structure of the free form of the MptpA LMW-PTP. In the absence of ligand and phosphate ions, the D-loop adopts an open conformation. Furthermore, we characterized the binding site of phosphate, a competitive inhibitor of LMW-PTPs, on MptpA and elucidated the involvement of both the P- and D-loop in phosphate binding. Notably, in LMW-PTPs, the phosphorylation status of two well conserved tyrosine residues, typically located in the D-loop, regulates the enzyme activity. PtkA, the kinase complementary to MptpA, phosphorylates these two tyrosine residues in MptpA. We characterized the MptpA-PtkA interaction by NMR spectroscopy to show that both the P- and D-loop form part of the binding interface.
Perchlorinated polysilanes were synthesized by polymerization of tetrachlorosilane under cold plasma conditions with hydrogen as a reducing agent. Subsequent selective cleavage of the resulting polymer yielded oligochlorosilanes SinCl2n+2 (n = 2, 3) from which the octachlorotrisilane (n = 3, Cl8Si3, OCTS) was used as a novel precursor for the synthesis of single-crystalline Si nanowires (NW) by the well-established vapor–liquid–solid (VLS) mechanism. By adding doping agents, specifically BBr3 and PCl3, we achieved highly p- and n-type doped Si-NWs by means of atmospheric-pressure chemical vapor deposition (APCVD). These as grown NWs were investigated by means of scanning electron microscopy (SEM) and transmission electron microscopy (TEM), as well as electrical measurements of the NWs integrated in four-terminal and back-gated MOSFET modules. The intrinsic NWs appeared to be highly crystalline, with a preferred growth direction of [111] and a specific resistivity of ρ = 6 kΩ·cm. The doped NWs appeared to be [112] oriented with a specific resistivity of ρ = 198 mΩ·cm for p-type Si-NWs and ρ = 2.7 mΩ·cm for n-doped Si-NWs, revealing excellent dopant activation.
Folding of RNA molecules into their functional three-dimensional structures is often supported by RNA chaperones, some of which can catalyse the two elementary reactions helix disruption and helix formation. Hfq is one such RNA chaperone, but its strand displacement activity is controversial. Whereas some groups found Hfq to destabilize secondary structures, others did not observe such an activity with their RNA substrates. We studied Hfq’s activities using a set of short RNAs of different thermodynamic stabilities (GC-contents from 4.8% to 61.9%), but constant length. We show that Hfq’s strand displacement as well as its annealing activity are strongly dependent on the substrate’s GC-content. However, this is due to Hfq’s preferred binding of AU-rich sequences and not to the substrate’s thermodynamic stability. Importantly, Hfq catalyses both annealing and strand displacement with comparable rates for different substrates, hinting at RNA strand diffusion and annealing nucleation being rate-limiting for both reactions. Hfq’s strand displacement activity is a result of the thermodynamic destabilization of the RNA through preferred single-strand binding whereas annealing acceleration is independent from Hfq’s thermodynamic influence. Therefore, the two apparently disparate activities annealing acceleration and duplex destabilization are not in energetic conflict with each other.
Optogenetic approaches using light-activated proteins like Channelrhodopsin-2 (ChR2) enable investigating the function of populations of neurons in live Caenorhabditis elegans (and other) animals, as ChR2 expression can be targeted to these cells using specific promoters. Sub-populations of these neurons, or even single cells, can be further addressed by restricting the illumination to the cell of interest. However, this is technically demanding, particularly in free moving animals. Thus, it would be helpful if expression of ChR2 could be restricted to single neurons or neuron pairs, as even wide-field illumination would photostimulate only this particular cell. To this end we adopted the use of Cre or FLP recombinases and conditional ChR2 expression at the intersection of two promoter expression domains, i.e. in the cell of interest only. Success of this method depends on precise knowledge of the individual promoters' expression patterns and on relative expression levels of recombinase and ChR2. A bicistronic expression cassette with GFP helps to identify the correct expression pattern. Here we show specific expression in the AVA reverse command neurons and the aversive polymodal sensory ASH neurons. This approach shall enable to generate strains for optogenetic manipulation of each of the 302 C. elegans neurons. This may eventually allow to model the C. elegans nervous system in its entirety, based on functional data for each neuron.
The structure of the title compound, C14H12N2O2 {systematic name: 2,2′-[hydrazinediylidenebis(methanylylidene)]diphenol}, has already been determined in the triclinic space group P An external file that holds a picture, illustration, etc. Object name is e-68-0o255-efi1.jpg with Z = 4 [El-Medani, Aboaly, Abdalla & Ramadan (2004 [triangle]). Spectrosc. Lett. 37, 619–632]. However, the correct space group should be P21/c with Z = 4. This structure is a new polymorph of the already known monoclinic polymorph of salicyladehyde azine, which crystallizes in space group P21/n with Z = 2. The benzene rings form a dihedral angle of 46.12 (9)°. Two intramolucular O—H[cdots, three dots, centered]N hydrogen bonds occur.