Volume 10 Issue 1, January 2014

Advances in genome sequencing and structural biology mean that we are now buried under an avalanche of predicted domains and structures of proteins with unknown functions. Two groups have used different methods to unearth the functions of previously cryptic bacterial enzymes, illuminating new reactions and metabolic pathways.

A highly original and sensitive method using clickable bioorthogonal fatty acids and in situ proximity ligation enables the visualization of the palmitoylation of not only Wnt but also its fatty acyltransferase Porcupine in cells.

Altered glycosylation of cancer cells confers phenotypic changes that promote spread and evasion of immune responses. A new method for engineering cell surface glycans is providing insights into these mechanisms.

Iron is essential for biological systems but can also damage or kill cells, leading to a variety of disease states. A review of mechanisms leading to Fe- and ROS-dependent cell death highlights the vast array of open questions in this complex field.

Partial agonists are generally thought to promote GPCR conformations that signal suboptimally. Analysis of bifunctional muscarinic M₂ receptor ligands now shows that partial agonism can also be predictably defined by a single ligand binding two receptor populations in different orientations.

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.

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⁺.

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.

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.

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.

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.

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.

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.