ChemBioChem

The cover picture highlights structure–activity relationship studies of dMMO2–d5SICS, one of the most promising unnatural base pairs. Because the ortho substituents of the constituent nucleobase analogues are required for continued primer extension after synthesis of the unnatural base pair, these studies, described on p. 2394 ff. by F. E. Romesberg and Y. J. Seo, focused on meta and/or para substituents of the dMMO2 scaffold. These derivatives are expected to be positioned in the developing major groove, and the results suggest that they have both steric and electrostatic effects on replication. The results also reveal several approaches by which the unnatural base pair might be used to site-specifically label DNA with a functionality of interest. Similar modifications of the d5SICS nucleobase analogue should allow for the site-specific labeling of DNA with two different functionalities, and the previously demonstrated efficient transcription of the unnatural base pair suggests that derivatives might similarly enable site-specific labeling of RNA.

The inside cover picture shows a few examples of small molecules investigated for biofilm control that either inhibit biofilm formation or disperse existing bacterial biofilms. The confocal images show P. aeruginosa:gfp bacteria that have formed a biofilm (upper left) in comparison to a biofilm population dispersed by a 2-aminoimidazole derivative (lower right). For more details, see the Minireview by C. Melander and J. J. Richards on p. 2287 ff.

Films you don't want to see: The medical community faces a tremendous challenge in overcoming diseases stemming from the formation and persistence of bacterial biofilms. A concise review of current approaches employed to control bacterial biofilms is discussed.

Five easy steps: Phenazines are redox-active bacterial secondary metabolites that possess broad-specificity antibiotic activity and can also play an important role as virulence factors in infectious disease. Their biosynthesis from two molecules of chorismic acid is catalyzed by enzymes encoded in the conserved phz operon.

Lethal weapon: The X-ray crystal structure of a cytotoxic pore-forming complex revealed brilliant new insights into the mechanism and structure of an all-α-helical toxin.

Grab the remote: New generation biomaterials are capable of recruiting, programming, and dispersing host cells in situ to target locations for tissue maintenance, regeneration, or destructive purposes.

Recognize this? Based on predictions from mRNA expression of lipoproteins from Staphylococcus aureus, lipopeptide fragments were chemically synthesized, and their TLR2-stimulatory activities and cytokine-induction capabilities were analyzed. All the lipopeptides activated TLR2, but the activities varied depending on their peptide sequences.

Selective double click labeling: The determination of nanomolar concentrations of matrix metalloproteinase II is made possible through the use of a nanoprobe that consists of fluorescently doped silica nanoparticles to which a FRET-based enzyme substrate has been conjugated through sequential click reactions.

Searching for polyphenolic keys: Immobilization of the polyphenolic molecule (−)-vescalin onto a carboxylated dextran-coated gold surface enabled the determination by surface plasmon resonance (SPR) of its strong (subnanomolar) affinity to the human DNA topoisomerase IIα protein target without perturbations from nonspecific complexation phenomena.

Fungal decoration: The gene fgaAT, which was identified in the biosynthetic gene cluster of fumigaclavine C in Aspergillus fumigatus, was cloned and over-expressed in E. coli. Structure elucidation of the enzymatic product showed that FgaAT catalyses the acetylation of fumigaclavine B in the presence of acetyl coenzyme A.

Live electrochemistry: Shewanella is an electrogenic microbe that has a significant content of c-type cytochromes in its outer-cell membrane. By using the specific binding affinity of nitric monoxide, we demonstrate the first electrochemical identification and electron-transfer kinetics of cytochromes under living conditions. The results revealed an unusually efficient respiratory electron-transfer chain at the cell/electrode interfaces.

Mechanism makeover: We remodeled sucrose phosphorylase to mimic the active-site characteristics of a retaining glycosyltransferase. Thus, an enzymatic reaction coordinate for α-retaining glucosyl transfer through a covalent β-glucosyl enzyme intermediate was changed into one in which configurational retention appeared to be achieved through a direct front-side nucleophilic displacement reaction.

How deep does it go? The characterization of interactions between antimicrobial peptides and membranes is important for the understanding of their biological activities and functions. This study describes an NMR method for determining insertion depths and orientations of peptides embedded in micelles. We have translated paramagnetic relaxation enhancements (PREs) of peptide atoms inside micelles into distance restraints for structure calculations.

Life under pressure: We compare the X-ray crystal structures and pressure dependence of the catalytic parameters of dihydrofolate reductase (DHFR) from E. coli and M. profunda and find no obvious evidence for pressure adaptation in the piezophilic MpDHFR.

Glu stick: A conserved Glu residue in the cyclotide family of plant defence peptides is crucial for biological activity. NMR studies show that this residue forms a network of hydrogen bonds that stabilise a protruding loop. Methylation of the Glu carboxyl in the cyclotide cycloviolacin O2 significantly disrupts the structure of this loop. The increased flexibility likely prevents selfaggregation in membranes, and this explains the lack of activity of the analogue.

On top of the POP: Dipeptidyl phosphonate activity-based probes were designed and synthesized. One probe, which is shown in the figure, allowed selective detection of the endogenous activity of prolyl oligopeptidase (POP) both by using in-gel analysis and mass spectrometry.

Stable SMase inhibitors: The first structure–activity-relationship studies for the inhibition of acid sphingomyelinase by phosphatidylinositol-3,5-bisphosphate did not show any variable parts in the inositol moiety. The phosphatidic acid part, however, was substituted by a monoalkyl sulfone; this led to potent phospholipase-stable inhibitors with improved biophysical properties.

Turn it OFF: A combination of mechanism-guided library design and dual genetic selection provided OFF riboswitches that repress gene expression in response to thiamine pyrophosphate (TPP) in E. coli. Two classes of riboswitches that function by controlling the accessibility of the Shine-Dalgarno sequence by the ribosome were selected and characterized.

Radical departure: Isomerisation of littorine (1) to hyoscyamine involves an oxidation/rearrangement catalysed by CYP80F1. We have probed this mechanism with deutero and arylfluoro analogues of littorine. The data suggest that hydroxylation takes place via a benzylic carbocation intermediate, whereas the product profile arising from rearrangement is more consistent with a benzylic radical intermediate.

It's unnatural: To optimize the d5SICS: dMMO2 unnatural base pair, five dMMO2 derivatives with different substituents at the position meta to the glycosidic linkage have been synthesized and analyzed. During replication, only triphosphate insertion is sensitive to derivatization; this reflects changes in sterics, dipole moment, and polarizability. These results should help optimize the unnatural base pair and identify strategies to site-specifically label DNA and RNA.