Volume 18 Issue 10, October 2011

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.

ADARs deaminate adenosines to inosines in double-stranded RNA (dsRNA). Interestingly, effects seen when ADARs are knocked out can be suppressed by additional knockout of RNAi machinery, suggesting competition between the two pathways. Genome-wide identification of ADAR targets shows that ADAR edits heavily in regions that generate siRNAs when ADAR is absent, indicating a role for ADAR in regulating dsRNA accumulation and thus siRNA production.

Solvent dynamics are an often overlooked component in enzymatic activity. Terahertz spectroscopy, X-ray absorption analysis and molecular dynamics simulations show that solvent movement is tightly correlated with formation of a productive enzyme–substrate complex, but not an enzyme–inhibitor complex, in a metalloprotease, indicating that solvent motions may assist catalysis.

Collagen is highly abundant in the biosphere but is not easily degraded by proteases. The crystal structure of Clostridium histolyticum collagenase G reveals a pathway of recognition, unraveling and degradation for collagen breakdown.

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.

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.

A single miRNA can target hundreds of distinct transcripts, but some miRNAs such as C. elegans lsy-6 have very low target proficiency. The reasons behind this are now identified as weak seed-pairing stability and high target-site abundance. These findings have implications for understanding off-target effects of siRNAs and improving miRNA target predictions.

Endoplasmic reticulum-associated degradation (ERAD) substrates must be dislocated across the ER membrane through a process driven by the ATPase p97/VCP, and Derlins are thought to be part of the dislocation machinery. New data identify Derlin-1 as an inactive member of the rhomboid family that facilitates the release of ERAD substrates from the ER, following their transfer across the membrane.

It has been unclear how fly Dicer-1 exclusively recognizes pre-miRNAs. New analyses show that fly Dicer-1 recognizes the single-stranded terminal loop structure of pre-miRNAs through its N-terminal helicase domain, checks the loop size and measures the distance between the 3′ overhang and the terminal loop. This unique mechanism allows fly Dicer-1 to inspect the authenticity of pre-miRNA structures.

For each ATP molecule, the Na/K pump extrudes three Na⁺ and imports two K⁺ ions by alternating between outward- and inward-facing conformations that preferentially bind K⁺ or Na⁺, respectively. Molecular dynamics simulations based on atomic models, together with electrophysiological experiments, show that protonation of several acidic residues that form the cation-binding sites is crucial to achieve K⁺ selectivity.

Yra1 is an export factor known to link 3′ end formation of mRNAs to export through interaction with Pcf11, a subunit of the cleavage-polyadenylation factor CF1A. Yra1 is now found to regulate assembly of CF1A and affect poly(A) site choice.

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.

The online game Foldit invites players to solve problems involving protein structure prediction. Now Foldit players have been recruited to work on a modeling problem and ultimately solve the crystal structure of a retroviral protease that had resisted previous determination.