Research articles

TRF2 is a member of the telosome/shelterin complex, which helps maintain telomere integrity. Using an oriented peptide library based on a previously identified TRF2-interaction region to define a consensus sequence for binding, new proteins have been identified as TRF2 interactors and implicated in telomeric functions. This suggests that TRF2 acts as a hub for recruiting different proteins to the telomere via a distinct linear sequence.

Methylation at particular residues on histone tails has been associated with various functions and, in the case of dimethylated histone H3 arginine 2 (H3R2), cross-talk with methylation of a nearby lysine has been shown to be linked to transcriptional repression. Budding yeast monomethylated H3R2 is now shown to be associated with active loci and involved in activation of meiotic genes upon induction of sporulation.

The huntingtin protein (HTT) contains a polyQ tract preceded by an N-terminal flanking sequence (HTT^NT) that contributes to HTT aggregation. Now the role of HTT^NT in aggregation is explored in vitro, revealing a complex, multistep pathway initiated when polyQ disrupts HTT^NT structure, enhancing the latter's assembly into prefibrillar aggregates. Within these intermediates, subsequent interactions of the polyQ moieties drive further assembly into compact amyloid aggregates.

NAD⁺ is an essential cofactor in energy metabolism and redox reactions and is a regulator of different cellular processes. Kinetic and structural studies of the M. tuberculosis glutamine-dependent NAD⁺ synthetase suggests a tight coupling of the catalytic sites that catalyzes the ATP-dependent formation of NAD⁺ at the synthetase domain using the ammonia derived from the L-glutamine and glutaminase domain.

Although the dimensions of the ribosomal exit tunnel are cramped, it is known that some structural elements can begin folding there. The tertiary folding of an α-helical hairpin and a β-hairpin are now probed within the ribosomal exit tunnel, indicating that minimal tertiary interactions can be explored close to the exit of the tunnel.

Im7 is a small Escherichia coli colicin binding protein that uses a remarkably complex folding pathway. Analysis of the Im7 folding landscape reveals details of the earliest transition state in its folding pathway and indicates that the formation of non-native contacts that result in intermediate folding states is necessary to maintain elements essential to the protein's function.

Riboswitches are RNA domains that alter gene expression in response to ligand binding. The structure of the Bacillus subtilis preQ1 ribsoswitch, which recognizes the conserved modified nucleobase preQ1, in complex with its ligand indicates how an RNA of only 34 nucleotides recognizes its ligand.

The Hsp90 chaperone is responsible for the stabilization of a large variety of regulatory proteins. Single-molecule FRET was used to examine the conformational dynamics of Hsp90 in its different nucleotide-bound states. The findings suggest that, in the absence of substrate and cochaperone proteins, Hsp90's conformational changes are not strongly coupled to ATP hydrolysis.

A group of neutralizing monoclonal antibodies (mAbs) targeting the influenza A hemagglutinin has been selected and characterized. Remarkably, these mAbs were able to neutralize a broad array of group 1 strains and could protect mice from infection when given prophylactically or therapeutically. The crystal structure of one such mAb in complex with hemagglutinin provides insight into its mechanism of neutralization and broad specificity.

Mammalian gene silencing is associated with both histone and DNA methylation. The PRMT5 arginine histone methyltransferase is now found to affect DNA methylation at the γ-globin locus in mice. This is mediated by an effect on recruitment of the DNA methyltransferase DNMT3A, but through interaction with the product of PRMT5 activity. This suggests that DNMT3A reads the histone methylation, coupling it to nearby DNA methylation.

The Hsp90 chaperone is responsible for the stabilization of a large variety of regulatory proteins. By labeling the subunits in the Hsp90 homodimer with different dyes and in different positions, the kinetics of Hsp90 conformational changes along the ATPase cycle was characterized, revealing different intermediate states and the different roles of cochaperones.

The G9a-like lysine methyltransferases can be inhibited by the small molecule BIX-01294, recently identified through a chemical screen and shown to be capable of replacing Oct3/4. The structure of GLP in complex with BIX-01294 indicates an overlap with the known position of histone peptide binding, and further work indicates that the drug inhibits methylation of DNMT1, indicating that it is enzyme specific but non specific with regard to substrate.

Mek1 and Mek2 are kinases that phosphorylate Erk, participating in the signal transduction pathway controlling cellular growth and adhesion. Though closely related, there are clear functional differences, with Mek1 being subject to negative-feedback regulation via phosphorylation by Erk. Now Mek1 and Mek2 are shown to form a heterodimer in vivo, in which Mek2 activity is also controlled by Erk phosphorylation of Mek1.

The DEAD-box protein DBP5 is involved in yeast mRNA export, though the mechanism by which it helps to remodel and release transcripts on the cytoplasmic face of the nuclear pore complex has been unclear. The structures of DBP5 in complex with the mRNA and AMPPNP, as well as with the nucleoporin NUP214, indicate that the transcript and nucleoporin compete for the same binding site, suggesting a model for the sequence of events occurring at the last step of export.

Photosystem II (PSII) catalyzes the first light-dependent step in photosynthesis. An improved structural model of a cyanobacterial PSII provides complete assignment of all subunits in the complex and reveals possible channels used for the transport of protons, oxygen and water to the thylakoid lumen.

KSRP is involved in mRNA instability, a role that is repressed upon AKT kinase–mediated phosphorylation, which promotes 14-3-3 interaction. This modification site is now shown to be exposed upon AKT phosphorylation through unfolding of the KH1 domain of KSRP, an event that allows 14-3-3 interaction, which in turn affects nuclear cytoplasmic partitioning.

The ATPase and the microtubule binding domains of dynein are separated by a long stalk coiled coil, which has to communicate and coordinate the activities of these domains along the mechanochemical cycle. Now this communication is shown to occur via sliding of the α-helices of the coiled coil.

Rare codons along transcripts have been proposed to influence the local rate of translation and the folding of nascent polypeptide chains. Now this idea is demonstrated for a bacterial protein: rare-codon clusters are shown to affect translation rates, and this was important for efficient protein folding in vitro and in vivo.

Meiosis is a highly conserved and tightly regulated process in which one round of DNA synthesis is followed by two rounds of division. By studying the expression of crs1 pre-mRNA, a meiotic cyclin in fission yeast, Wise and co-workers found that increased RNA accumulation during meiosis is not due to an increase in transcription but rather is a result of RNA processing and turnover. Moreover, they found that polyadenylation of crs1 is linked to splicing, a coupling previously thought to occur only in mammals. They suggest that this highly integrated crs1 regulatory system may allow a rapid response to adverse conditions.

Nucleosomes can be closely spaced in vivo, suggesting that they may on occasion approach one another or even meet. Using in vitro dinucleosomal model systems, positioned nucleosomes, as well as nucleosomes in the process of being repositioned, are now shown to overlap, forming single, compact particles, with one histone dimer ejected in the process. The potential relevance to remodeling processes is discussed.