Research articles

Coiled-coil assemblies have served as a rich resource for testing fundamental principles of protein structure and function. A semi-empirical design strategy now yields the first parallel hexamer, which also displays an internal channel that can be manipulated to direct assembly.

Conformation-specific antibodies and longitudinal tracking of individual neurons in situ identifies a toxic monomer species linked to Huntington's disease.

IMPDH and GMPR have similar active sites, but their reactions cause opposite effects on the guanine nucleotide pool. Biochemical and crystallographic evidence point to cofactor conformation as distinguishing the two reaction mechanisms and demonstrate that GMPR can substitute for IMPDH, prompting further investigations of this metabolic cycle.

GPCRs are known to initiate a variety of signaling pathways, but their full reach in coordinating cellular events is unknown. Live cell imaging using label-free and fluorescence assays to monitor the effects of GPCR ligands now surprisingly connects GPCR networks to nucleotide metabolism.

An evolutionary algorithm predicts anti-inflammatory drug combinations that have synergistic effects on IL-1β expression more efficiently than would empirical approaches of testing drug combinations individually.

N6-Methyladenosine is an abundant nucleoside in cellular mRNA that undergoes demethylation under physiological conditions by fat mass and obesity-associated protein (FTO). This new pathway suggests that RNA modifications can be reversible and potentially have an impact on RNA metabolism.

Trafficking G proteins between membranes is essential for their signaling activity. Structural and biochemical studies on the farnesylated G protein Rheb and the guanine nucleotide–dissociation inhibitor (GDI)-like PDEδ suggest an allosteric mechanism for Rheb release and identify a bona fide GDI-displacement factor (GDF).

Cells must coordinate nutrient uptake for balanced growth, but the mechanism by which this occurs was unknown. Flux measurements and biochemical assays now identify α-ketoglutarate as the key signal in this process that accumulates upon nitrogen limitation and inhibits an enzyme involved in glucose transport.

Peptidic natural products are theoretically amenable to characterization by mass spectrometry, but proteomics programs are not trained to discover these compounds. A new strategy uses mass spectrometry and bioinformatics iteratively to rapidly identify both ribosomal and nonribosomal sequences, yielding multiple new compounds.

Investigations into kanamycin biosynthesis and identification of new pathway intermediates surprisingly point to the substrate specificity of two glycosyltransferases as controlling flux into parallel pathways, allowing changes to product profiles and structures by varying these gatekeeper enzymes.

Complex polysaccharides are generally thought not to have a defined carbohydrate sequence because their synthesis is not template-directed. Detailed mass spectrometry of bikunin now counters this dogma, showing that each molecular weight species consists of only a single sequence.

Histidine kinase 4 from Arabidopsis thaliana (AHK4) is a membrane-bound receptor for cytokinins, a class of plant hormones involved in growth, development and defense. Crystal structures of the AHK4 sensor domain in complex with various natural and synthetic cytokinins reveal important features of ligand recognition by this cytokinin receptor.

Rapid reversible inhibitors of the oxygenation activity of COX-2, including ibuprofen and naproxen, selectively inhibit the enzyme with endocannabinoid 2-AG substrates but not with arachidonic acid, and this substrate-selective inhibition may be important for the analgesic activity of the drugs.

A chemical-genetic study predicts mechanisms of resistance to PI3K inhibitors. Activation of NOTCH signaling, which leads to c-MYC expression, can overcome cancer cell dependency on PI3K signaling for growth. NOTCH and PI3K have not previously been linked in breast cancer.

Mono- and digalactosyldiacylglycerols (MGDGs and DGDGs) are glycolipids that are central to plant metabolism and photosynthetic membrane biogenesis. Galvestine-1, a small molecule inhibitor of MGDG synthases that was identified in a high-throughput chemical screen in Arabidopsis thaliana, reveals a new role for these galactolipids in pollen-tube development.

A single trimethylated species is obtained in an on-resin N-methylation reaction of a cyclic hexapeptide. This regioselectivity is driven by conformation and the presence of intramolecular hydrogen bonds, and is correlated with membrane permeability of the peptides.

The inhibitor PU-H71 preferentially targets tumor-enriched Hsp90 complexes. Affinity purification using PU-H71 reveals cancer-specific protein networks in chronic myeloid leukemia and that the abundance of tumor-specific Hsp90 clients in cells can predict sensitivity to Hsp90 inhibitors.

Cleavage of peptide precursors is well known for ribosomally produced sequences. Investigation of xenocoumacin biosynthesis now points to a similar function in nonribosomal peptide synthesis clusters, explaining one source of mismatches between genetic and chemical information.

An untargeted metabolomics approach identifies C14 phosphatidylcholines (PCs) as specific cellular medium-chain substrates of the lipase ABHD3, as well as C5–C8 short-chain PCs including oxidized pro-atherosclerotic and pro-apoptotic PC phospholipids.

Nonsense suppression, or reassigning stop codons to encode for other amino acids, offers a method for expanding the genetic code of proteins. Deletion of release factor 1 in an Escherichia coli strain enables the incorporation of non-natural amino acids into proteins at multiple sites.