Articles in 2011

A quantitative covalent labeling strategy reveals that multiple ligand-specific conformational states are present in the G protein–coupled β₂-adrenergic receptor. Their existence may underlie 'biased agonism', which describes the differential abilities of agonists to activate distinct signaling mechanisms downstream of GPCRs.

A systematic analysis of possible substrates for reverse glycosyltransferase reactions reveals thermodynamically favored pathways to the traditional 'activated' sugar donors, enabling high-yielding enzymatically coupled sugar transfers and a general colorimetric assay for sugar nucleotide formation and utilization.

The first high-resolution structures of transaldolase with bound intermediates both define active site residues that necessitate a revision of the current reaction pathway and point to a high-energy intermediate structure and protein conformational changes as mechanisms to promote product formation.

Purine base binding specificity in adenine and guanine riboswitches is governed primarily by specific base pairing interactions in the ligand-binding site. A series of 2′-deoxyguanosine riboswitch structures reveals remodeling of the ligand-binding site and remote regions of the structure to accommodate the sugar moiety of the nucleoside substrate.

The combination of several biochemical analyses, including determination of kinetic isotope effects and linear free energy relationships, offer the first detailed insights into a natural S_Ni-like reaction mechanism and provide compelling evidence for a frontal nucleophilic substitution in a retaining glycosyltransferase.

The identification of cellular targets for natural products that potently inhibit the growth of cancer cell lines implicates oxysterol-binding proteins in the growth of cancer cells. These natural products, termed ORPphilins, also affect sphingomyelin biosynthesis.

FlAsH fluorescence and thioflavin-to-FlAsH FRET are used to distinguish amyloid-β oligomer formation from fibril formation, supporting rapid oligomer formation prior to fibril formation—consistent with a nucleated conformational conversion mechanism—that can be modulated by certain Alzheimer's disease–linked mutations or lipids.

Salt bridges between positively charged residues within the S4 transmembrane segment of the voltage-sensing potassium channel, Shaker, and acidic residues in S2 and S3 segments are not necessary during channel gating; rather, two of the acidic residues may occupy a hydrophilic water-filled vestibule that creates an energetically favorable environment for S4 movement during channel gating.

Based on a BRET readout, dopamine D2 receptor agonist NPA is more potent at activating Gα_i when the D2 receptor forms a heteromer with the related D1 receptor than if it forms D2 receptor homomers, suggesting that GPCR heteromerization can result in functional selectivity.

Polo-like kinase 1 (Plk1) regulates multiple processes that are important for cell proliferation, and it is a promising anticancer drug target. Efforts to inhibit Plk1 function by disrupting interactions that are essential for its proper localization identify a high-affinity alkylated phosphopeptide ligand specific for Plk1.

Overabundance of the eIF2–GTP–Met-tRNAi translational initiation complex has been linked to malignant transformation. N,N'-diarylurea chemical probes that block ternary complex assembly through heme-regulated inhibitor kinase activation validate translational initiation pathways as a potential anti-cancer targets.

Protein lysine methyltransferases modulate the activities of chromatin and non-chromatin proteins by specific methylation of lysine side chains. A large-scale structure-based design approach has yielded a new chemical probe that potently and selectively inhibits G9a and GLP methyltransferases in cells.

The synthetic compound Shield-1 can already be used to protect designed fusion proteins from degradation. The development of a new protein domain that is degraded upon addition of Shield-1 expands the compound's utility in controlling protein function and allows the simultaneous degradation and stabilization of different constructs.

A search through hydrophobic chemical space identifies an adamantane tag that targets dehalogenase fusion proteins for degradation, as demonstrated for both cytosolic and transmembrane proteins; and in zebrafish and mice. This molecule provides a new tool to study protein function with precise control.

Plutonium (Pu), a radiotoxic element, enters cells via an unknown mechanism. Solution structures and X-ray imaging studies reveal that Pu binds transferrin, and the complex can be taken up by cells via receptor-mediated endocytosis only if iron is contained in transferrin's N-lobe.

Protein-focused lead-identification strategies may be limited in their ability to identify small molecules that bind to cellular RNAs. Docking small molecules against the structural ensemble substantially improves the docking accuracy of TAR and has led to the identification of six new TAR binders, one of which inhibits HIV-1 replication.

Compounds identified from a high-content screen implicate RTK activation as well as GSK-3 inhibition in regulating SMN levels and point to a therapeutic strategy for treating spinal muscular atrophy.

A quantitative sensor of spatial and temporal dynamics of activity of the protein tyrosine kinase Src shows that its activity peaks 1–2 μm from the leading edge of cells undergoing lamellipodial membrane extension, and the activation is correlated with protrusion velocity.

Investigations of reveromycin biosynthesis, including metabolite analysis, feeding experiments and in vitro tests of enzyme function, point to a two-step mechanism for formation of the central spiroacetal, in which RevG oxidizes a stable acyclic precursor and RevJ catalyzes the stereocontrolled cyclization.

Phosphorylation of the Huntington's disease protein Htt by CK2 leads to Htt nuclear translocation in response to stress. Inhibition of other kinase pathways can restore phosphorylation to hypophosphorylated Htt in Huntington's disease and may lead to a therapeutic strategy.