ChemBioChem

The cover picture shows the mechanism of catalysis by the tomato allene oxide synthase (syn. hydroperoxide dehydratase, EC 4.2.1.92.) LeAOS3, CYP74C3. Enzymes of this CYP74 family control the main routes of the plant lipoxygenase cascade, the source of oxylipins, which play important roles in plant signalling and defence. The primary products of allene oxide synthases are the short-lived allene oxides. For instance, the 9-hydroperoxide of linoleic acid is converted by LeAOS3 into allene oxide (12Z)-9,10-epoxy-10,12-octadecadienoic acid. Trapping experiments demonstrated that in contrast to the ordinary allene oxide synthases (CYP74A subfamily), LeAOS3 (CYP74C subfamily) is a multifunctional enzyme that catalyses not only the synthesis, but also the hydrolysis and cyclisation of allene oxide. Further details can be found in the article by A. N. Grechkin, L. S. Mukhtarova, et al. on p. 2498 ff.

Pumping iron and sulfur: Several iron–sulfur cluster ([FeS]) biogenesis systems exist. In bacteria the ISC (iron–sulfur cluster) and SUF (mobilisation of sulfur) pathways are coordinated through the transcription factor IscR. The apo form of IscR (without [FeS]) activates the expression of the suf operon, and its holo form (with [FeS]) depresses the isc operon. Iron starvation and oxidative stress affect both systems through IscR or other factors, such as Fur, OxyR and IHF.

Worth its weight: Gold nanoparticle (AuNP)-based colorimetric biosensing assays are designed for the detection of biological processes (or analytes) that can induce either AuNP aggregation (•) or redispersion (•) of AuNP aggregates. Balancing interparticle attractive and repulsive forces, which determine AuNP dispersion and aggregation stages, is key in designing such assays.

Fingers in lots of pies: For the first time a member of the CYP74 enzyme subfamily (9-AOS) from tomato has been shown by chemical and analytical approaches to catalyze multiple reactions. These multifunctional properties of 9-AOS from the oxylipin-forming lipoxygenase (LOX) pathway raise several new questions on lipid-derived signaling.

Phototcleavage of phosphorylated proteins. Phosphorylation of proteins is one of the most important mechanisms in cellular signaling and is involved in cellular processes such as metabolism, apoptosis, and differentiation. Uranyl photocleavage at high specificity as well as efficiency of proteins with phosphorylated residues was systematically analyzed. The results open the way for the detection of phosphorylation sites in proteins by uranyl photocleavage.

Precious GEM: In this communication, we demonstrate that a photosensitive gemini surfactant (AzoGEM) can be used to control the conformation of individual genomic DNA molecules at a surfactant-to-DNA charge ratio near to unity, which is 1000 times smaller than that for the systems reported to date (AzoTAB). We analyze the AzoGEM–DNA and AzoTAB–DNA interactions in terms of binding affinity and reversibility.

Prebiotic nucleotide synthesis: two for the price of one! Photoanomerization of α-D-cytidine is extremely low yielding, but irradiation of the 2′-phosphate results in efficient anomerization and nucleobase hydrolysis such that both pyrimidine nucleotides needed for prebiotic RNA synthesis are produced in a single reaction.

Watson–Crick recognition of double-helical B-form DNA by Chiral γ-PNAs: C→G-clamp (X) nucleobase substitution provides the necessary binding free energy for chiral γ-PNAs to invade mixed-sequence B-DNA.

Labeling lysine: A cascade-type labeling chemistry was developed by making use of rapid 6π-azaelectrocyclization. The whole process achieves site-selective and the nondestructive labeling of target proteins under neutral/physiological conditions, without the need for special cleavage operations directed against the affinity ligands.

Taking a turn. Short tripeptides that form stable β turns in water are remarkably stable against chemical and thermal degradation. Terminal cation–π interactions lead to stabilization of these turns that are formed independently of sequence.

In-liposome self-encoding system: A simplified system in which genetic information is replicated by a self-encoded replicase was assembled in liposomes only with defined components. This system consists of just 144 gene products, which is comparable to the hypothetical minimal requirements, and has the potential to evolve by being compartmentalized in liposomes.

Hidden peel: The interaction of α-synuclein (αS) with membranes is implicated in Parkinson's disease. Through EPR, the mobility of spin labels attached to αS was determined as a function of membrane composition. It revealed that αS peels off gradually from the membrane, an indication that the membrane interaction could be initiated at the N terminus of αS.

Electrostatic stabilization: When a native protein structure is exposed to vacuum as in native electrospray ionization (ESI), what are the very early structural changes caused by desolvation? Molecular dynamics (MD) calculations show that before global structural changes occur, the native fold can be transiently stabilized by the formation of salt bridges and ionic hydrogen bonds on the protein surface (see scheme).

A conformational switch: The solution NMR structures of both the apo and holo forms of actinorhodin acyl carrier protein (ACP) from Streptomyces coelicolor reveal a previously undetected conformational switch that involves the movement of helix III towards helix II and rearrangement of the side chain of Leu43. These changes could play a role in modulating the affinity of apo- and holo-ACP for holosynthase.

Synthetic glycoconjugates: We have developed biotinylated bi- and tetra-antennary glycoconjugates to capture and detect E. coli, and compared the binding affinity of these novel molecules to commercial polyclonal antibodies. Magnetic beads coated with glycoconjugates outperformed antibody-coated magnetic beads in sensitivity and selectivity under identical experimental conditions.

A single-point mutant of C. antarctica lipase B demonstrated a direct epoxidation reaction mechanism for the epoxidation of α,β-unsaturated aldehydes by hydrogen peroxide in aqueous and organic solution. Computational calculations showed a two-step reaction mechanism with formation of an oxyanion intermediate, and the active-site residue His224 functioning as a general acid-base catalyst with support from Asp187. The oxyanion is stabilized by two hydrogen bonds from Thr40.

Luminous beads: We have developed a solid-support fluorescein-labeling reagent that enables spacer-free C-terminal labeling of peptides for use in fluorescence polarization (FP) assays. Libraries of C- and N-terminally labeled peptides were synthesized, and their binding to two different protein domains of the GYF family was investigated by FP and confirmed by NMR experiments. This technique was then implemented in the development of high-affinity ligands.

Out of the light, into the dark: The YcgF BLUF domain undergoes global structural changes between its light- and dark-adapted states, thus indicating a reorientation of its C-terminal-joining α-helix relative to the domain surface. This movement is hypothesized to trigger temperature-dependent formation of a signaling state that controls the YcgF phosphodiesterase activity.

Insight into the biological properties of cylindramide 1 was gained from comparison with cyclopentane analogues 4, which were accessible through a convergent synthetic strategy. Residual dipolar couplings (RDCs) allowed the structure of 1 to be refined by NMR spectroscopy.

The forces of stabilization: The interaction of bradykinin (BK) with the bradykinin B2 receptor (B2R) was analyzed by using molecular modeling (MM) and molecular dynamics (MD) simulations. The specific geometries and hydrogen-bonding interactions of the inactive and active (shown) states of the BK receptor were explored in detail, and comparisons to the known partially activated rhodopsin molecule, were made.

Multitasking: Trapping experiments, concentration-dependence and time-course studies of linoleic acid (9S)-hydroperoxide conversion by recombinant tomato allene oxide synthase (CYP74C3, LeAOS3) demonstrated that LeAOS3 is a multifunctional enzyme that catalyzes sequentially the synthesis of short-lived allene oxide and then either allene oxide hydrolysis into (9R)-α-ketol or allene oxide cyclization into the cyclopentenone, rac-cis-12-oxo-PEA.

Polyene sweetners: The sugars attached to polyene natural products are important for their antifungal activity and drug-like properties. Here, we show that the reversibility of the polyene glycosyltransferases AmphDI and NysDI, in conjunction with chemoenzymatic synthesis of a set of GDP–sugar nucleotide precursors, enables the exchange of polyene sugars.

The nacre-soluble matrix of the freshwater paleoheterodont bivalve Unio pictorum exhibits carbonic anhydrase activity, an important function in calcification processes. This matrix is composed of three main proteinaceous discrete fractions, the one with the highest apparent molecular weight is a 95 kDa glycoprotein specific to the nacreous layer and possesses a glycosyl component, consisting of sulfated polysaccharides, that is involved in calcium binding. The three proteins were analysed, and the results suggest that identical peptides make up the constitutive domains of the different proteins.

Getting your vitamins: The tocochromanol compound δ-tocotrienol was produced in recombinant E. coli cells cultivated on a simple medium. The cells were successfully made to express an engineered tocochromanol pathway by incorporation of genes from Pseudomonas putida (hpd), Pantoea ananatis (crtE), Synechocystis (hpt), and Arabidopsis thaliana (cyc).

The desaturase effect: Incubation of pheromone deuterium-labelled fatty acids with dissected labial glands and direct injection of labelled substrates into Bombus lucorum males revealed that esterification of pheromone products proceeds in the labial gland. The enzyme responsible for this esterification (Δ⁹ desaturase) shows a preference for C₁₂–C₁₄ fatty acid chains.