Articles in 2010

A high-resolution structure of an off-pathway misfolded intermediate state of a PDZ domain is now obtained, through a combination of phi-value analysis and computational modeling. The structure reveals that a misfolded intermediate can look quite similar to the native state.

Mutations in BRCA2 are associated with higher susceptibility to some forms of cancer. BRCA2 is known to play a central role in the repair of DNA breaks via homologous recombination. Now a role for BRCA2 in telomere integrity is revealed, indicating that BRCA2 can contribute to genome stability in multiple ways.

tRNA and mRNA translocation on the ribosome is catalyzed by the GTPase EF-G. Using single-molecule FRET analysis, this process is examined, indicating that GTP hydrolysis does not affect translation through promoting a ribosomal unlocked state, but that constraining the conformation of EF-G to a high-affinity interaction with the ribosome is key to translocation rate.

In yeast cells, short telomeres are preferentially elongated by the telomerase complex in a process that requires Tel1. Now low levels of telomerase inhibitory protein Rif2 and the absence of Mec1 are shown to mark short telomeres for Tel1 binding and elongation rather than double-strand break repair.

The anthrax lethal toxin protein transporter consists of protective antigen (PA) and lethal factor (LF), with LF unfolding for translocation into the host cell. Structural and functional analyses now indicate how each of four LFs unfolds and binds into amphipathic clefts on the surface of the PA octomer.

Open channel blockers are very different in their chemistry and structure. Now GLIC, a bacterial model for pentameric ligand-gated channels, is used to investigate the structural basis of open channel block. The work identifies two extended interaction sites, with large blockers binding to the center of the membrane and small blockers binding to the narrow intracellular region.

A genome-wide analysis of replication profiles in different budding yeast mutants reveals that the alternative clamp loader component Ctf18 has a key role in the DNA replication checkpoint, acting together with Mrc1 to promote Rad53 phosphorylation.

Notch signaling regulates key developmental events, and aberrant Notch signaling has been linked to disease. The structure of a dimeric Notch transcription complex with DNA is presented, revealing how dimer-binding sites with different spacers may be recognized. Cryptic dimer-binding sites are also uncovered, which might account for differential sensitivity of promoters to cooperative assembly of complexes.

Vesicle tethering is the least well understood step of vesicular transport. The core conserved oligomeric Golgi (COG) vesicle tethering complex from yeast, consisting of the four essential subunits Cog1–4, is now reconstituted and characterized by negative stain EM and single particle analysis. The COG complex forms a y-shaped structure, whose central region and the distal regions of at least two legs all participate in interactions with other components of the intracellular trafficking machinery.

How a variety of nuclear export signals (NESs) are recognized by their receptor CRM1 is now examined by crystallography, NMR spectroscopy, biochemistry and cellular approaches. The work reveals that the different NES peptides adopt different conformations to fit into five rigid hydrophobic binding pockets on CRM1, and redefines an NES consensus.

Alternative splicing can be affected by transcription elongation rate and genotoxic stress. Camptothecin is now shown to induce MDM2 exon skipping in a p53-independent and reversible manner. This process involves disrupting EWS and YB-1 interaction, which are Pol II and spliceosome-associated factors, respectively.

Yeast possesses eight multisubunit vesicle tethering complexes, including TRAPPI and TRAPPII. The TRAPPII complex functions in the late Golgi and consists of all TRAPPI and three specific subunits. Purified native yeast TRAPPII is now characterized by single-particle electron microscopy, providing insights into the molecular basis for human pathologies resulting from defective TRAPP complex function.

The prokaryotic ubiquitin-like protein Pup is involved in the Mycobacterium tuberculosis proteasome pathway but is an intrinsically disordered protein, unlike eukaryotic Ub. Structural data now indicate that the Mycobacterium proteasomal ATPase (Mpa) binds Pup in an α-helical form, indicative of binding-induced folding of Pup upon reaching the proteasome in this system.

Understanding the genesis of histone may give functional insight and elucidate maintenance of post-translational histone modifications. Using biochemical purification and characterization from human cell fractions, the authors examine pre-deposition histone complexes, giving insight into processes from assembly through to nuclear import.

Nuclear HIV-1 mRNA export is mediated by cooperative Rev protein binding to the Rev response element (RRE) RNA, forming a complex recognized by the Crm1 host export factor. A structure of a Rev dimer now shows that the organization of Rev monomers within a dimer defines the RRE recognition interface, with the other side likely binding Crm1.

The crystal structure of the complex formed by the death domains from Fas and FADD at physiological pH is now solved, revealing a 5:5 complex that is supported by electron microscopy data. Along with mutagenesis and mass spectrometry analyses, the work provide insight into Fas mutations that cause autoimmune lymphoproliferative syndrome.

Electron cryo-microscopy images of actin filaments (F-actin) allow the visualization of different conformational states, which can be classified into different groups. Further analyses reveal the plasticity of the subdomain 2 region and suggest that missense mutations related to disease affect F-actin structural dynamics.

A complex substrate containing mobile double Holliday junctions is now used to show that yeast proteins Sgs1 (DNA helicase) and Top3 (topoisomerase) act together to dissolve the junctions and avoid crossing over; the protein Rmi1 stimulates this process.

Rad51 plays a central role in homologous recombination pathways. Now work with Xenopus laevis egg extracts shows that Rad51 prevents formation of DNA gaps at or behind replication forks, which are dependent on Mre11 nuclease activity.

The NoGo decay pathway involves the Dom34–Hbs1 complex and targets mRNAs that are stalled during translational elongation for cleavage. The structure of the Dom34–Hbs1 complex now reveals its structural similarity to release and elongation factor complexes. Upon binding Hbs1, Doom34 adopts a tRNA-like conformational change that suggests it would act to terminate translation.