Articles in 2013

Crystal structures of QueE, a radical SAM enzyme that converts the purine base of GTP into a deazapurine found in natural products and tRNA, explain how the enzyme functions with a trimmed-down radical SAM enzyme fold and rationalizes its unusual Mg²⁺ dependency.

Use of a domain of unknown function as the input for bioinformatic searching reveals a new Cu-dependent family of chitinases, assigned as CAZy group AA11, that diverge in sequence but share structural homology with the existing AA9 and AA10 families.

Phenotypic screening for serine hydrolase inhibitors capable of modulating lipid storage coupled with target deconvolution identifies carboxylesterase 3 as having a role in regulating adipocyte function, with enzyme inhibition causing positive outcomes in mouse models of obesity and diabetes.

A screen for compounds that promote ES cell differentiation into pancreatic β cells identified a VMAT2- and monoamine-dependent suppression mechanism of pancreatic β-cell differentiation. VMAT2 inhibitors potentiated differentiation from Pdx1-positive pancreatic progenitor cells into Ngn3-positive endocrine precursors, and then into β cells with increased insulin production.

In the ubiquitin-proteasome system, E2 enzymes such as Cdc34A mediate the transfer of ubiquitin to protein substrates, which are thus marked for proteasomal degradation or other fates. New structural data reveal that the small-molecule inhibitor CC0651 impairs Cdc34A activity by stabilizing the normally transient Cdc34A–ubiquitin complex.

In synthetic biology designs, circuit components can generally move within the cell, meaning that functional cross-talk can cause faulty wiring. Genome mining, synthetic promoter construction and cross-reactivity screening now identify 20 orthogonal TetR repressor-promoter pairs for use in complex applications.

TR3 is an orphan nuclear receptor with roles in apoptosis. A TR3-binding compound induces mitochondrial translocation of TR3 and autophagy via the Nix–Toms–ANT1/VDAC1 pathway, providing a mechanism for cell death in melanoma cells that are resistant to spontaneous and drug-induced apoptosis.

Substrate binding to the multidrug exporter LmrP from Lactococcus lactis catalyzes proton entrance by stabilizing an outward-open conformation. Transitions between conformational states are dictated by proton passage down the transmembrane helical bundle.

Crystallographic analysis and spectroscopic studies employing the nitrile moiety of bosutinib as an IR-active probe reveal that structured water molecules, organized by the gatekeeper residues of kinases, mediate the selectivity profile of kinase inhibitor binding.

Defined phospholipid-functionalized glycopolymers serve as a new tool to identify the mechanistic connection between hypersialylation and immunoprotection, where hypersialylation of tumor cells subverts the immunosurveillance mechanism of NK cells by recruiting the lectin Siglec-7 to inhibit human NK cell activation.

Clickable fatty acids coupled with in situ proximity ligation allow visualization of Wnt as it trafficks through the secretory pathway, defining roles for palmitoylation and glycosylation in controlling Wnt activity and exploring the substrate specificity and regulation of the Wnt-modifying porcupine.

Phosphatidylinositol transfer proteins (PITPs) are important mediators of phosphoinositide signaling within cells. A small-molecule inhibitor of the PITP Sec14, identified by chemical screening and structure-based design, affects transit through the trans-Golgi network and endosomal system.

To date, five classes of naturally occurring self-cleaving ribozymes have been reported. The bioinformatic discovery in bacteria and eukaryotes of twister RNAs, a new ribozyme class that contains a double pseudoknot fold, adds to the list of catalytic RNAs that have roles in cells.

NAD(P)H-dependent enzymes are generally assumed to use a one-step hydride transfer mechanism owing to a lack of evidence for alternative proposals. Spectrophotometric and NMR data now call this assumption into question, defining a covalent substrate-cofactor species that is catalytically competent in three unrelated enzymes.

Enzyme annotations often suffer from incomplete functional information for homologous sequences. Extrapolation from one characterized enzyme to multiple possible substrate-enzyme pairs, using bioinformatics and experimental approaches, leads to four distinct β-keto acid cleavage enzyme functional motifs and assignment of 14 new activities.

Beyond its canonical role in translation, lysyl-tRNA synthetase (KRS) stabilizes the prometastatic 67-kDa laminin receptor (67LR) in the plasma membrane. A small-molecule inhibitor of the KRS-67LR interaction modulates the KRS-promoted metastatic potential of 67LR without disrupting the normal function of each protein.

The PsaA binding protein delivers Mn²⁺ to the human pathogen Streptococcus pneumoniae. Structural and biochemical studies now explain its metal specificity, showing that metal binding induces a closed complex that is reversible for the desired substrate but irreversible for the inhibitor Zn²⁺.

Drugs and antibiotics induce oxidation and mobilization of membrane-bound copper(I) ions to copper(II) species within the E. coli cytosol, causing oxidation of a single cysteine residue of the multiple antibiotic-resistance regulator MarR, that leads to formation of disulfide-bonded MarR tetramers and release of dimers from sites of transcriptional activity.

High-throughput screening systems that better mimic the physiological complexity of diseased tissues may aid the discovery of more efficacious compounds. A co-culture system that mimics the microenvironment of leukemia stem cells (LSCs) in bone marrow enables the discovery of compounds, including lovastatin, that selectively kill LSCs.

Cyclic diadenosine monophosphate (c-di-AMP) is a newly identified nucleotide second messenger in bacteria. Though protein receptors for c-di-AMP are known, the ydaO riboswitch has now been validated as a physiological sensor of cellular c-di-AMP levels.