ChemBioChem

The cover picture shows the binding of the bacterial messenger cyclic di-GMP (c-di-GMP) to a protein-based fluorescent biosensor. C-di-GMP plays important roles in many pathogenic bacteria by mediating biofilm formation and virulence (a biofilm formed by P. aeruginosa is shown in the background), and bacterial cells usually contain multiple diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) to regulate the cellular concentration of c-di-GMP. Certain proteins are now being considered as novel targets for the development of antibacterial agents. The development of facile methods of assaying enzymatic activity and screening inhibitors will facilitate the lead discovery processes. On p. 2753 ff, Z.-X. Liang et al. describe the design of a fluorescent biosensor that responds to c-di-GMP with sub-micromolar sensitivity in a real-time fashion. The biosensor can be used in enzyme assays for DGCs and c-di-GMP PDEs as well as the high-throughput screening of inhibitors.

The inside cover picture shows the first molecular identification of autoproteolytic fragments of the Parkinson's disease protein α-synuclein, in particular, the highly aggregation-prone fragment (72–140). On p. 2740 ff, M. Przybylski et al. explain how the gas-phase separation capability of ion-mobility mass spectrometry allowed these fragments to be identified.

LynF prenylates, but the prenyl migrates: Schmidt and co-workers have demonstrated that LynF from Lyngbya aestuarii is a reverse O-prenyl transferase. However, a forward C-prenylated product is obtained through a non-enzymatic Claisen rearrangement. The elucidation of this unprecedented two-step process is a significant contribution to our understanding of the biosynthesis of complex macrocyclic peptides.

No-bias binding: The abiotic template-directed synthesis of RNA could have been a key process in the origins of life on Earth. Recreating this process in the laboratory has been challenging, yet a combination of strategies has given rise to a synthesis that is both efficient and unbiased against any of the four nucleotides.

Do not disturb! As an environment-sensitive fluorescent amino acid, L-(7-hydroxycoumarin-4-yl) ethylglycine (7HC) is genetically encodable in E. coli containing a suppressor tRNA and a cognate 7HC-specific tRNA synthetase. Its incorporation into a full-length protein allows the detection of a nearby phosphorylation event with minimum influence on protein structures and functions, thereby serving as the smallest phosphorylation sensor.

Control yourself! A two-color molecular beacon with non-nucleosidic chromophores in a triplex stem is presented. Pyrene and PDI fluorophores act as mutual quenchers by formation of a donor–acceptor complex in the closed form. Hybridization with the target results in two independent fluorescence signals. The two-color read-out provides a “self-control” feature, which helps to eliminate false positive signals in imaging and screening applications.

Open and closed: The characterization of protein mobility is crucial for the understanding of biological functions. We have applied NMR spectroscopy to study the conformational dynamics of the 80 kDa enzyme prolyl oligopeptidase (POP). Our results revealed that POP is highly dynamic and that inhibition of catalytic activity shifts this conformational equilibrium towards a less dynamic state.

Gas-phase protein separation by ion mobility: With its ability to separate the Parkinson's disease protein α-synuclein and its autoproteolytic products—despite the small concentrations of the latter—ion-mobility MS has enabled the characterization of intermediate fragments in in vitro oligomerization-aggregation. In particular, a possible key fragment, the highly aggregating C-terminal fragment, αSyn(72–140), has been revealed.

We report the sensitive detection of telomerase activity by using exonuclease III-aided target recycling to amplify the signal produced by a chimeric LNA–DNA molecular beacon. We demonstrate the specific detection of as few as 30 telomerase-positive breast cancer cells in a single-measurement fluorescence assay that avoids the problematic PCR and gel analysis of the current “gold-standard” assay.

Seeing below the surface: A small-molecule droplet array platform on an NADH-immobilized solid surface and a biotinylated acetophenone derivative were developed to identify the substrate candidates for soluble P450 enzymes of interest. This methodology is thought to be easily applicable to other class I P450 systems, including those that use NADPH as cofactor.

Messenger bagged: The design of a fluorophore-labeled protein biosensor for the bacterial messenger cyclic di-GMP is described. The biosensor responds to c-di-GMP with sub-micromolar sensitivity in a real-time fashion. The biosensor can be used for enzyme assays for diguanylate cyclases and c-di-GMP phosphodiesterases as well as the high-throughput screening of inhibitors.

Don't stick around: A screen of eukaryotic kinase inhibitors for molecules that modulate bacterial biofilm development revealed that the protein kinase C inhibitor, palmitoyl-dl-carnitine, blocks biofilm formation by the opportunistic pathogen, Pseudomonas aeruginosa (see figure). The molecule stimulates motility, blocks quorum sensing and overrides at least two biofilm-stimulatory cues.

Additional epoxidation: A two-component flavin-dependent monooxygenase, the ActVA-ORF5/ActVB system, functioning as a quinone-forming C-6 oxygenase for actinorhodin biosynthesis in Streptomyces coelicolor, was revealed to have an additional epoxidation activity in vitro. This additional function is possibly a result of the adaptable structural features of the two-component system.

Conformational preferences for potential transport of nucleosides across biological membranes is reported. Human concentrative nucleoside transporters (hCNTs) showed preference for nucleosides in the Northern conformation in both inhibition and transport assays and human equilibrative nucleoside transporters (hENTs) showed preference for nucleosides in the Southern conformation in inhibition assays.

Suppression of the photoinduced electron transfer (PET) in a new fluorescent probe (HP Green) for hydrogen peroxide uses a naphthalimide fluorophore coupled to p-anisidine (as a redoxactive group). It has been shown to enable rapid and highly sensitive enzymatic assays for L-lactate (limit of detection, LOD, 162 nM) and D-glucose (LOD 0.64 μM).

Balance of powers: Mutation studies of the Drosophila HP1α chromodomain were used to determine the relative contributions of electrostatic and hydrogen-bonding interactions to the recognition of di- and trimethyllysine. The findings provide insight into how nature achieves selectivity for these two closely related post-translational modifications, and has relevance to inhibitor design as well.

Simple and efficient: Conjugation of carbohydrates synthesized by automation or in solution is achieved during the DNA synthetic cycle to produce DNA–carbohydrate conjugates. B-form duplexes constructed from modified single strands present carbohydrates through the major groove for lectin-binding studies.

Switching bioactivity: Changes in the configurations at the two chiral centers of sparsomycin, especially at the chiral carbon, can affect its capability to promote ribosomal translocation. Incorporation of the pseudo-uracil moiety of sparsomycin into linezolid confers the ability to promote ribosomal translocation onto linezolid derivatives, thereby confirming the importance of this moiety in promoting translocation.

A neat click: We have synthesized a mono-ubiquitinated proliferating cell nuclear antigen analogue (PCNA–Ub, see figure) using click chemistry. The artificial amino acid azidohomoalanine, which has an azide, was incorporated into ubiquitin, and the pyrrolysine analogue, Plk, which has an alkyne, was incorporated into PCNA. These were linked by the Cu^I-catalyzed Huisgen cycloaddition to yield site-selectively mono-ubiquitinated PCNA.

Taking the Rab: Expressed protein ligation allows site-specific incorporation of unnatural functionalities, such as fluorophores, into proteins. This requires synthesis of peptides with such functionalities and their subsequent ligation onto proteins. To construct a library of fluorescent RabGTPase sensors we developed an alternative approach in which proteins are labeled on a free cysteine and then ligated to an unlabeled peptide.

Artificial genetic switches: Our novel synthetic pyrrole (P)–imidazole (I) polyamides conjugated with SAHA, a histone deacetylase (HDAC) inhibitor, triggered transcriptionally permissive chromatin modifications and differential activation of pluripotentcy gene expression. These programmable DNA-binding small molecules could potentially be developed as genetic “ON” switches to modulate specific gene(s) of interest.

Display article: A structural vaccinology approach could lead to a new generation of vaccine candidates, based upon conformationally constrained epitope mimetics. Here a β-hairpin mimetic of the HIV-1V3 loop is rendered immunogenic by multivalent display on the surface of synthetic virus-like particles (SVLPs).

Targeting Zn fingers? Zn-finger proteins are involved in various cellular processes and thus, in principle, are a large class of targets for a variety of diseases. We address whether it is possible to identify small molecules that are selective against these targets using NMR-based approaches.

Where and why: Hemin binding to polymer-bound short peptide sequences was evaluated by a combinatorial approach in conjunction with UV/Vis spectroscopy and electrophysiological measurements (see graph). Selected peptides efficiently competed with the ion channel hSlo1 for hemin binding. The method revealed features of potential heme-interacting proteins in vivo.

Polarity exploration: A method to create giant protein vesicles (GPVs) is described. Fluorescence microscopy is used to characterize GPV morphology and protein–lipid hydrophobic interactions. Specifically, we employed generalized polarization imaging to monitor the polarity around the protein transmembrane region of aquaporins labeled with the polarity-sensitive probe Badan.

A double sensing strategy for detecting mismatching in polypurine oligonucleotides has been developed. Double sensing by the oligonucleotide sequence allows single mutations of target oligonucleotides to be detected by monitoring changes in pyrene fluorescence. The high specificities of the probes are maintained over a wide temperature range without sacrificing hybridization kinetics.

A binary photocontrolled nucleic acid probe that contained a nucleotide modified with one photolabile unit and two hybridization-sensitive fluorescent dyes has been designed for area-specific fluorescence imaging of RNA in a cell. Only probes in the defined irradiation area were activated by uncaging irradiation; subnuclear mRNA diffusion in a living cell was monitored.