Research articles

A magnetic tweezer system that arrests the rotary ATP synthase F1 at the ATP-hydrolysis step provides an order of events to the chemomechanical cycle involving ADP release before phosphate release upon F1 rotation in ATP-hydrolysis mode.

The identification or development of enzymes with new functions remains a significant challenge. A new strategy uses rationally selected sequences anticipated to serve as functional motifs to search the wealth of available genomic data, successfully yielding 17 (R)-selective amine transaminases.

Some cyclodipeptides are unusual in that their cyclic scaffold is created from activated, amino-acid–loaded tRNA substrates. Structural and biochemical evidence now demonstrates that the enzymes that perform this reaction are homologous to tRNA synthetases and use a covalently bound intermediate.

Purine catabolism is typically thought to yield metabolic waste material. However, bioinformatics analysis, coupled with structural and biochemical investigations, now demonstrates that the central carbons of the purine ring can be recycled into glycine in B. subtilis and other bacteria.

Enzymatic conversion of adenosine to inosine is an RNA editing mechanism for post-transcriptional diversification of mRNA. A new chemical tagging–reverse transcription method leads to the identification of new A-to-I RNA editing sites in the human genome.

Secretion of strigolactone from plant roots mediates mutualistic fungal interactions but also facilitates parasitic plant invasion. A screen in Arabidopsis thaliana has identified compounds that perturb strigolactone levels and link this hormone to light signaling pathways in host plants.

The multiple lysines that can link ubiquitin chains have created challenges in studying these important biopolymers. The ribosomal incorporation of a protected lysine analog now allows the specific construction of native K6- and K29-linked diubiquitin chains, enabling structural analysis and deubiquitinase profiling.

Iron-sulfur clusters are essential components of many proteins and are assembled in a hierarchical pathway. Tah18 is a diflavin reductase that transfers electrons to the [2Fe-2S] cluster of Dre2 in an early step of iron-sulfur cluster biogenesis in the cytoplasm of eukaryotes.

Structure-specific flap endonuclease 1 (FEN1) is known to interact with multiple nuclear proteins involved in DNA metabolism. Arginine methylation in FEN1 blocks phosphorylation of a nearby serine and enhances FEN1 binding to PCNA, which serves to channel FEN1 toward DNA replication and repair pathways.

Polymerase exclusion of ribonucleotides during DNA replication is imperfect. New data indicate that DNA polymerase ϵ incorporates into DNA ribonucleotides that are repaired by an RNase H2–dependent process and that defective repair results in replicative stress and genome instability.

Although FPPS is a potential anti-cancer target, the high bone affinity of nitrogen-containing bisphosphonates, FPPS inhibitors used clinically to treat bone disease, has prevented their development as cancer therapeutics. Using fragment-based drug discovery, non-bisphosphonate inhibitors were discovered that bind in a previously undescribed allosteric pocket.

A chemical array screen identifies a small-molecule inhibitor of pirin that inhibits its interaction with the oncoprotein Bcl3 and decreases the expression of the tumor mobility protein SNAI2. As a result, the compound perturbs the migration of melanoma cells that have high pirin expression levels.

Biotin synthesis is known to include a pimelate intermediate, the construction of which is controversial. Genetic manipulations and chemical feeding now demonstrate that the two mystery enzymes in the process create and cleave a methyl ester that sends a biotin precursor into the fatty acid synthesis machinery.

Probing the biological location and function of transition metals has proven difficult. X-ray fluorescence microscopy in combination with an array of metal chelators now provides a way to interrogate zinc in maturing mouse oocytes, demonstrating a role for this metal in cell division.

A variety of natural C-nitroso compounds are known, but the path to these important functional groups has been a mystery. Elucidation of the biosynthetic route to an iron chelator now reveals a tyrosinase-like copper-containing monooxygenase as responsible for the transformation.

Instability of (CTG)•(CAG) repeats in microsatellite DNA has been linked to numerous neurological diseases. Probing trinucleotide repeat structures using engineered zinc-finger nucleases provides evidence that DNA hairpins form in vivo and are linked to replication-dependent genomic instability.

Current methods to investigate glycosylation allow the identification of modification sites but provide limited additional information. A new strategy using polymers to label specific sugars now shows a huge variety in the occupancy of known glycosylation sites as well as unexpected interplay between post-translational modifications.

Proteins rely on a combination of intramolecular forces to form and stabilize their structures. A careful comparison of computational analysis and high-resolution crystal structures now indicates that the n→π* interaction merits inclusion in this group.

Evidence for the existence and importance of GPCR dimers and oligomers is mounting, but direct detection of these species has been challenging. The development of improved fluorescent ligands for time-resolved spectroscopy confirms their presence across GPCR families and in native tissue.

Proteomic analysis in dendritic cells identifies three palmitoylation sites within IFITM3, an innate immunity protein involved in inhibition of early replication of several viruses. Palmitoylation of IFITM3 regulates its clustering in membranes and is crucial for inhibition of influenza virus infection.