Research articles

The nuclear pore complex (NPC) is key to nucleocytoplasmic transport and is based on a stable scaffold involving multiple heptameric Y complexes. The structure of the Nup84–Nup145C–Sec13 component of the Y complex now indicates that the Nup84–Nup145C and Sec31 homotypic interface in the COPII lattice are analogous, suggesting a lattice NPC model.

The poxvirus 2L protein binds tumor necrosis factor-α (TNFα). Structural data now indicate that 2L interacts with TNFα at a site overlapping with that for its receptor, arguing for the basis of inhibition of receptor interaction and TNFα-induced immune responses.

The SARS coronavirus protein nsp1 can suppress host gene expression at a post-transcriptional level, with previous work showing a reduction in mRNA abundance. Now a direct effect on protein synthesis is revealed, as nsp1 modifies transcripts and also inactivates the 40S ribosomal subunit.

Hsp90 is a molecular chaperone essential for the maintenance of cellular homeostasis. Now multiple approaches are used to study the deleterious effects of mutations in β-strand 8 of the N domain of Hsp90 and the role of the charged linker between N and M domains in mediating such effects.

miRNAs can repress transcripts through decay. Mammalian miRNA-mediated deadenylation is now shown to involve both the Pan2–Pan3 and the Ccr4–Caf1 deadenylases. Such deadenylation can be triggered by tethered Ago or TNRC6 and is followed by decapping of the reporter.

Screening a library of artificial zinc fingers for transcriptional activators in mammalian cells can be laborious. Now a strategy is described that couples the screening to production of retroviral particles that will carry the positive clones, allowing iterative rounds of selection.

Sialic acid is the most abundant terminal monosaccharide on mammalian cell surface glycoconjugates. The crystal structures of a mammalian sialyltransferase, that of porcine ST3Gal-I, in the apo form and bound to analogues of the donor and acceptor substrate are now described, providing insights into the catalytic mechanism and for inhibitor design.

Rates of in vivo transcription have proven hard to pin down, especially across long mammalian genes that can contain lengthy introns. Using DRB inhibition followed by release, the rates of transcription of multiple human genes are now measured and splicing rates of both U2- and U12-dependent introns are assessed.

Studying protein interactions at membranes is a technical challenge. A quantitative approach to measuring the interaction between the apoptotic proteins tBid and Bcl using fluorescence correlation spectroscopy reveals that membranes have an active role in modulating BCL2 protein interactions.

Despite the importance of small RNA–mediated silencing, no structural information exists for complexes of known function. Using single-particle EM, the structure of the minimal functional unit for RNAi in humans (AGO2, Dicer and TRBP) is now presented.

Increasing evidence indicates that membrane protein function can be affected by the surrounding membrane bilayer. A new study on voltage-gated potassium channels using tarantula toxins suggests that lipid interaction with the voltage sensor can influence channel function.

F₁F_o ATP synthases produce ATP using proton- or sodium-motive force to drive ions through the membrane-embedded F_o complex, causing rotation of its c-ring rotor leading to ATP synthesis. The first high-resolution crystal structure of the c-ring from a proton-translocating F₁F_o-ATP synthase reveals the architecture of the proton-binding site and provides insight into the mechanism of proton transport.

Some p53 mutations result in gain-of-function variants that can contribute to tumorigenesis. Three such mutants, R175H, R273H and R280K p53, are now shown to cooperate with transcription factor E2F1 to upregulate the expression of ID4, which in turn stabilizes the transcripts from pro-angiogenic factors IL-8 and GRO-α.

Identifying physiological substrates of proteases still poses a challenge. An unbiased approach using the heterologous Escherichia coli proteome now identifies the structural and sequence determinants for caspase-3 substrates, revealing a kinetic threshold that can distinguish relevant substrates.

Transcription initiation involves recruitment of key factors to promoters. Yeast TATA-binding protein (TBP) turnover is now examined genome-wide and genes transcribed by the three RNA polymerases found to have distinct signatures. Further analyses suggest that TBP dynamics, rather than DNA sequence affinity per se, is key to gene expression.

Rhesus macaque monkeys can inhibit retroviral replication via TRIMCyp, a variant of TRIM5a with an insertion of the cyclophilin A cDNA. Cyclophilin A binds to HIV-1 capsid, whereas TRIMCyp restricts HIV-2. How the change in specificity of this domain occurred is now revealed through biophysical and structural studies.

An improved method for detecting proteins phosphorylated by the ERK kinase reveals multiple new in vitro ERK substrates, including three nucleoporin proteins. Nup50 is phosphorylated in FG repeats by ERK2 in vivo and in vitro, suggesting a new mechanism by which MAP kinase signaling controls nuclear translocation of proteins.

Colicins are secreted bacterial toxins. To avoid killing the producer organism, each colicin is coexpressed with a high-affinity inhibitor, or immunity protein (Im). The evolution of Im-Colicin interfaces and the evolvability traits of protein-protein interactions are now examined using in vitro evolution and structural analyses.

The maturation of tRNAs involves folding into their L shape and nucleotide modifications at several positions. Some modifying enzymes require an L-shaped substrate, and the crystal structure of methylase Trm5 in complex with AdoMet and tRNA now reveals how the substrate tertiary structure is sensed.

Alternative splicing increases genome coding potential and is affected by factors including the hnRNPs. The effect of altering splice site strength on splicing activity is now found to be antagonized by nearby hnRNP H binding sites. Other splicing factor sites may have similar effects and may thus have influenced splice form evolution.