Articles in 2014

Spinach is an RNA aptamer analog of GFP that is widely used for fluorescent labeling of cellular RNAs. Crystal structures of Spinach–fluorophore complexes uncover an unusual G-quadruplex RNA fold that is involved in ligand recognition and tuning of Spinach fluorescence properties.

The combination of synthetic ligands, luminescent proteins and binding proteins converts a well-established ligand-sensing system into a tunable and quantitative reporter for drug concentrations in blood, as demonstrated with six different drugs and using a simple digital camera.

PIP₂ binds via electrostatic interactions to the N terminus of the dopamine transporter (DAT) to modulate its function in dopamine efflux. This regulation is necessary for Drosophila locomotor activity induced by the DAT substrate amphetamine.

The serotonin receptor 5-HT₆ interacts with a network of proteins that includes Cdk5. Functionally, Cdk5 phosphorylates the receptor at S350 and modulates its activity in inducing neuronal differentiation in a model neuroblastoma cell line and neurite growth in primary neurons.

Structure-guided peptide phage display combined with activity-based sorting results in the identification of zymogen activator peptides (ZAPtides) that selectively bind and activate the serine protease–like pro-HGF zymogen to promote Met signaling.

The allosteric binding of MSI-1436 to the intrinsically disordered C-terminal region of PTP1B promotes a conformational change to generate a compact inactive structure, validating the use of MSI-1436 to inhibit HER2-mediated tumorigenesis.

5-hydroxymethyluracil (hmU) is an oxidative DNA lesion and a potential intermediate in DNA repair–coupled DNA demethylation pathways. Isotopic labeling and MS reveal that hmU is produced directly by Tet-mediated oxidation of thymine in mouse embryonic stem cells, suggesting a functional role for hmU in stem cells.

An array of approximately 300 different carbohydrate structures from select gut bacteria was generated and probed with mouse and rabbit IgG samples. The binding results indicate that galectins 3, 4 and 8 of the innate immune system can recognize certain microbes only if they express self-like antigens.

Abscisic acid (ABA), a small-molecule hormone that regulates stress responses in plants, initiates signaling by nucleating ABA receptor–PP2C interactions. A structure-guided approach has produced a class of 3′-S-alkylated ABA derivatives that prevent PP2C binding to ABA receptors by blocking a solvent-exposed channel.

A cyclic dinucleotide binds to a ‘C-linker pocket’ of the HCN4 ion channel, a site that is distinct from the cyclic nucleotide binding site used for channel regulation. A small molecule found to interact with the C-linker pocket can antagonize cAMP regulation of the channel.

β-Aminobutyric acid (BABA) is a small-molecule activator of plant disease resistance. Binding of (R)-BABA to IBI1—an aspartyl-tRNA synthetase (AspRS)—primes noncanonical defense pathways, resulting in broad-spectrum disease resistance. Ligand binding also blocks AspRS activity, leading to accumulation of aspartic acid and uncharged tRNA, which activate a second plant stress response.

Endosomes and lysosomes are electrically excitable, and this is conferred by a new family of atypical voltage-gated sodium channels, lysoNa_Vs, formed by TPC1, which has similar mechanisms for gating as canonical voltage-gated channels and is sensitive to pH, appropriate for its localization in acidic compartments.

In silico screening identifies a small molecule that stabilizes the interaction between retromer components Vps35 and Vps29. The compound increases traffic of APP away from the endosomal compartment to limit generation of the Aβ peptides involved in Alzheimer's disease pathology.

Functional assessments and applications of polysaccharides are hampered by broad product distributions. Neutral drift libraries now identify specific amino acids and binding sites that determine product outcome in a polysialyltransferase, allowing the preparation of glycan chains with defined lengths.

Directed evolution of the final enzyme in the lovastatin biosynthetic pathway yields a variant with 29 mutations that does not require a carrier protein and displays altered dynamics of the catalytic residues, spending more time in the catalytically active conformation.

De novo enzyme designs have generally tried to optimize multiple aspects of enzyme function simultaneously. Focusing only on positioning of active site residues to generate a nucleophilic serine as assessed by activity-based protein profiling now leads to a successful intermediate design.

Certain oxygen-tolerant hydrogenases contain a unique [4Fe-3S] cluster near the catalytic site, but the role of this cofactor is not fully understood. Crystallographic, spectroscopic and computational data now provide evidence for redox-dependent transformations of this cluster, potentially explaining how specialized hydrogenases can safely reduce inhibitory O₂.

NMR structural data and biophysical and biological experiments show that the antifungal compound amphotericin is toxic because it acts as a sterol sponge by interacting with ergosterol on the fungal membrane and extracting it from within the membrane to the surface of the membrane.

High-resolution microscopy and biochemistry show that homoclusters of GPI-anchored proteins (GPI-APs) in the Golgi arrive at the apical membrane of polarized cells and then coalesce into larger heteroclusters. Therefore, sorting at the Golgi determines organization of GPI-APs at the plasma membrane.

Histone post-translational modifications are important regulators of chromatin structure and gene expression. Lysine 2-hydroxisobutyrylation sites, discovered by MS and validated by chemical synthesis, are found in active chromatin and associated with male germ cell differentiation.