ChemBioChem

The cover picture shows the enzyme–inhibitor complex of a bacterial fucosidase derived from human microbiota. Fucose is implicated in many diseases, notably cancer and human fucosidosis, consequently there is evolving interest in the inhibition and manipulation of enzymes involved in fucose processing. 3D structural analysis complemented by kinetics and isothermal titration calorimetry paint a portrait of fucosidase inhibitor binding in which pH effects within the active centre (red) modify binding properties. Manipulation of “aglycon-mimicking” chemistries and inhibitor pK_a values are likely routes to optimal fucosidase inhibition in the context of cellular and mechanistic probes and potential therapeutic agents. For more information see the communication by G. Davies et al. on p. 1971 ff. Background photo of B. thetaiotaomicron adapted from L. Gross, PLoS Biol.2007, 5, e199, as permitted under the Creative Commons Attribution License Agreement.

The inside cover picture shows the molecular structure of a DAG lactone derivative on top of the inner leaflet of a DMPC bilayer. The confocal microscopy image illustrates DAG-lactone-stimulated membrane localization of PKCδ-ECFP in living cells, while the space-filling model shows the surface of the C1B domain of PKCδ, the target of the lactone. For more information, see the paper by V. E. Marquez, S. Corbalan-Garcia, R. Jelinek et al. on p. 2003 ff.

Nature's glycosylating agents: The glycosyltransferases (GTs) are of great interest in chemistry, biology and medicine both for synthetic applications and as therapeutic targets. Herein, a brief introduction to the biology of GTs and the recent advances in the development of GT bioassays is given; this is a key prerequisite for the investigation of this exciting enzyme class.

Recent advances in our understanding of cell-migration inhibition and cytotoxicity of the glutarimide-containing polyketides are highlighted. Independent mode of action studies now make it possible to correlate specific structural features to specific intracellular binding interactions and their downstream results.

Directing the formation of macromolecular complexes offers important opportunities for understanding and engineering cellular fate and function. Small synthetic components can be used to nucleate the formation of desired cellular machines. A great deal of control over cellular processes and more could be available by applying this concept to couple orthogonal scaffolds to elicit desired outcomes.

Just do it: Directed evolution enables efficient enzymatic synthesis of catalytically active RNA as well as highly functionalized C5-modified DNA. The DNA polymerase variant that is proficient in incorporating nucleobase and sugar-modified nucleotides was identified by a chip-based protein library screening assay.

The state you're in: GABARAP, a protein relevant for autophagic processes, has been enzymatically coupled to phosphatidylethanolamine in a ubiquitin-like modification cascade. The lipidation state of GABARAP defines its subcellular localization pattern and is crucial to its functional integrity.

What contributes what? The inhibition of an α-L-fucosidase by two imino-sugar inhibitors is studied through the X-ray crystallography of enzyme–inhibitor complexes and thermodynamic dissection of binding over a range of pH values.

Promiscuous proteins: The identification and characterization of a wild-type promiscuous hydrolase that efficiently catalyzes the hydrolysis of ester bonds and haloacids in a single protein has been reported. This study has demonstrated the utility of metagenomics to access novel catalytic activities.

A two-pronged approach using fluorescence-based probes and chemically controlled dimerization was successfully implemented to study the functional effects of Shank3 PDZ domain ligand binding in vitro. Overall, Shank3 PDZ-domain dimerization induces an eight- to 30-fold enhancement of PDZ domain binding affinity for the fluorescent probe and the native nonfluorescent GKAP ligand.

Plasmid DNA molecules in polyplexes with poly(L-lysine) (PLL) and multiarm PEG-installed PLL (maPEG–PLL) adopted condensed and noncondensed states, respectively. maPEG–PLL polyplexes showed comparable cell-free gene expression with naked pDNA. The inhibition ability of DNA condensation of maPEG–PLL provided not only the recovery of cell-free gene expression but also elevated the gene expression of cultured cells.

Ferritin encapsulation inside lipid vesicles reveals the spontaneous formation of protein-rich vesicles. The solute distribution inside the vesicles follows a power law. The important conclusion for origins-of-life scenarios is that the dynamics of membrane closure allow the accumulation of solutes inside primitive cells, thus providing an explanation for the origins of early functional cells.

Switching conformations: The important role that α-synuclein plays in some neurodegenerative diseases arises from its ability to undergo conformational switching between low-detergent-concentration fibrillization and a high-concentration homogenous structure. Here we use ¹⁹F NMR spectroscopy to probe the conformational switch of α-variants containing site-specifically incorporated fluorinated amino acid analogues.

Heparin blocks membrane interactions of an amyloid peptide: Glycosaminoglycans (GAGs) induced divergent fibrillation pathways in a prion amyloidogenic fragment. The extent of fibril formation/inhibition is closely dependent upon the ratio between the GAG and the peptide, and a model is proposed to account for the aggregation phenomena.

At anchor: The biological activities of charged diacylglycerol (DAG)-lactones exhibiting different alkyl groups attached to the heterocyclic nitrogen of an α-pyridylalkylidene chain appear highly correlated to their interactions with the cell membrane (see figure). The results highlight the fundamental role of membrane anchoring in determining the biological profiles of synthetic DAG-lactone ligands.

The influence of temperature and pH on the stability and catalytic activity of dihydrofolate reductase from the cold-adapted deep-sea bacterium Moritella profunda has been studied. Our results demonstrate adaptation of Moritella profunda dihydrofolate reductase to its environment and indicate compromises between enthalpic and entropic contributions to the reaction free energy and between k_cat and K_M.

Sugar-capturing polymers: An oriented glyco-capturing macroligand was synthesized by site-specific immobilization of an O-cyanate chain-end-functionalized boronic acid containing polymer (boropolymer) onto an amine surface. Oriented and covalent immobilization of the O-cyanate chain-end-functionalized boropolymer onto amine-modified solid surfaces and its specific glyco-capturing capacity were confirmed by QCM and AFM.

Fluorous helpers: A collection of iminoalditols with unusual N substituents containing highly fluorinated structural moieties was prepared. These compounds exhibit attractive interactions with glycosidases and can serve as leads towards novel pharmacological chaperones.

Route ginger: Dehydrogingerdione analogues were produced by a recombinant E. coli strain that has an “artificial” biosynthesis pathway for dehydrogingerdione that is not based on the original biosynthesis pathway of gingerol derivatives in plants. At least theoretically, more than 100 dehydrogingerdione analogues could be produced by this system.

Pore defense: Alamethicin strongly induces a hypersensitive-like local response and systemic lesions in Arabidopsis thaliana. The amplitude of the defense response is related to the presence of the helicogenic α-aminoisobutyric acid residues (U) in the alamethicin sequence and to the ability of this peptaibol to form pores in plasma membranes.

Wiley-VCH, Weinheim 2010, XXI+335 pp., hardcover € 99.00.—ISBN 978-3-527-32541-2

Humana Press, Totowa 2010, XII+276 pp., hardcover $ 99.00.—ISBN 978-1-58829-950-5