Articles in 2011

One of the most versatile regulators of actin assembly, the WASP homology 2 (WH2) domain, reveals previously unknown facets by combining with a newly discovered actin-nucleating dimeric structure in the effector protein VopL from Vibrio parahaemolyticus.

Inositol 1,4,5-triphosphate (InsP₃) receptors are ligand-activated calcium channels in the endoplasmic reticulum membrane, and they are responsible for the cytoplasmic Ca²⁺ efflux that triggers many cellular processes. The crystal structures of the ligand-binding domain of rat type I InsP3R in its apo and ligand-bound form reveal the conformational changes that ultimately control channel gating.

Hsp90 is a molecular chaperone with a wide array of client proteins, including the tumor suppressor p53. Now the structure and interaction of p53 DNA-binding domain with full-length Hsp90 or Hsp90 fragments have been studied by NMR and other biophysical methods. The results indicate that p53 interacts with multiple domains of Hsp90 and adopts a native-like state.

Rad50 is part of the Mre11 complex, which plays a central role in DNA damage response and repair. Rad50 has a long coiled-coil region that links its globular DNA-binding domain and hook. Now the role of this region is tested by a series of truncations and functional analyses, which reveal that the HR and NHEJ functions of the Mre11 can be separated.

Previous analyses have indicated that heterochromatin assembly in Schizosaccharomyces pombe involves an RNAi-mediated mechanism. Analyses aimed at elucidating the targeting of heterochromatin at centromeres now show that RNAi-independent mechanisms exist that also exploit transcription and non-coding RNAs to promote heterochromatin formation.

Post-transcriptional maturation of pre-mRNAs involves a number of processes that are now known to interact with transcription itself. Mutations affecting early spliceosome assembly, but not a drug targeting a catalytic step of splicing, are now shown to lead to nascent transcript retention and pausing of RNA polymerase II predominantly at the 3′ end of the gene, suggesting cross-talk between splicing and transcriptional termination.

Pathogen proteins targeting the actin cytoskeleton often serve as model systems to understand their eukaryotic analogs. Structure-function studies of the bacterial actin nucleator VopL suggest that dimerization and pointed-end binding play crucial roles in VopL-mediated nucleation, by enabling the formation of a hexameric pointed end actin nucleus, and that eukaryotic actin nucleators may also function as dimers or higher oligomers.

VopL is a bacterial actin nucleation factor that induces actin stress fibers when injected by bacteria into eukaryotic host cells. Biochemical and structural analyses of VopL-mediated actin nucleation suggest a model in which contacts between the Wiskott-Aldrich homology 2 motifs and the C-terminal domain of VopL stabilize interstrand contacts between the initial actin monomers to create a filament nucleus.

The contributions that tRNA-ribosome interactions make to the dynamics of translocation are now assessed using single-molecule FRET analysis. The analysis indicates that the flexibility of tRNA plays a key role in tuning the dynamics of pre-translocation complex during translocation.

In the RNA world, there would have been ribozymes able to catalyze RNA replication. An artificial ribozyme able to catalyze RNA-templated RNA polymerization has been developed. Now biochemical work and crystal structures of this ribozyme's catalytic core trapped in a state prior to catalysis reveal the complex catalytic strategies it employs.

Toll-like receptors (TLRs) recognize pathogens and initiate innate immune responses. TLR4 associates with adaptor molecule MD-2 to recognize LPS, and this complex is regulated by a homologous complex, RP105–MD-1. The crystal structure of RP105–MD-1 reveals a unique organization, suggesting a mechanism for regulation of TLR4 response to LPS.

RNF4 is an E3 ligase involved in ubiquitinating poly-SUMOylated proteins. The structure of the RNF4 dimer, along with modeling and functional analyses, now indicate that the dimer itself, rather than acting as a scaffold, plays a specific role in recognition by binding the E2~ubiquitin thioester and activating it for catalysis.

Resection of DNA 5′ ends is the initial step for repair of double-strand breaks via homologous recombination. DNA resection is controlled in a cell-cycle dependent manner, with yeast Cdk1 known to control Sae2, a nuclease that initiates resection. Now recruitment to DNA damage sites of Dna2, a nuclease responsible for extensive resection, is also shown to be controlled by Cdk1.

The pseudokinase JH2 domain of JAK2 is a negative regulator of JAK2 activity, but the mechanism for this is unclear. Now it is shown that JH2 is actually an active kinase that phosphorylates negative regulatory sites on JAK2, thus inhibiting JAK2 signaling.