Brief Communications

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.

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.

RING E3 ligases mediate transfer of ubiquitin-like proteins from an E2 ligase to a substrate, but how this occurs is a long-standing mystery. Docking E2-RING structures onto a new crystal structure of the C-terminal domain of the E3-RING CUL1 in complex with the RBX1 RING protein now shows how a conformational change in RBX1 allows for the transfer by closing a gap between CUL1 and the E2.

Eisosomes are essential for plasma membrane organization in yeast. Structural, biochemical and cell biological studies now reveal that the main eisosome components are part of the conserved BAR-domain family of proteins, which bind and shape membranes.

Ash2L is part of a complex involved in histone H3 lysine 4 trimethylation, linked to active transcription. Ash2L is now found to contain a helix-wing-helix DNA binding domain that is needed for targeting and H3K4 trimethylation at the β-globin locus control region in vivo.

Cooperativity is a universal property of biological macromolecules that is widely exploited in their regulation and function. Simulations and single-molecule FRET studies demonstrate that molecular heterogeneity lowers the cooperativity of ligand binding, suggesting that it is crucial to determine the cooperativity of individual molecules and the extent of heterogeneity in order to derive accurate molecular models.

Deg1 is an HtrA protease that participates in the turnover of the photosynthetic proteins in chloroplasts. Now the crystal structure of Deg1, along with functional work, reveals that Deg1 oligomerization and activation occur in response to acidic pH, which should be encountered in the thylakoid lumen when exposed to light.

An intein controlled by redox in bacteria is created by engineering a disulfide bond between the catalytic cysteine residue and the flanking polypeptide. A natural analog of this arrangement from Pyrococcus abyssi is found to respond to redox conditions in Escherichia coli, suggesting that inteins may function as biological sensors.

Hydrogen-deuterium exchange/mass spec analysis of PrP^Sc derived from mouse brains reveals that the infectious form of the prion adopts conformations that differ substantially from those previously postulated by various structural models.

A GFP-based reporter system has been developed to measure repair of DNA interstrand cross-links (ICLs) via homologous recombination. Cells defective in the Fanconi anemia pathway showed a marked defect in repair only when the reporter contained a replication origin, revealing an important role in ICL-induced homologous recombination coupled to replication.

Prior to induction, promoters tend to be depleted for nucleosomes, but the mechanism and function of this depletion has been obscure. It is now shown that in yeast, where a barrier can lead to phasing of nucleosomes, the degree of occupancy of these phased sites is predictably determined by the underlying DNA sequences; in addition, as occupancy is increased, nucleosomal removal upon induction is decreased, as is mRNA production.

The signal sequence on nascent peptides is recognized by the signal recognition particle (SRP), with subsequent targeting of the SRP-ribosomal nascent complex to the membrane. The structure of a signal sequence bound to the core SRP is presented, revealing structural changes in the SRP upon signal sequence binding.

Crystal structures of the protease domain of human HtrA1, with or without its PDZ domain, reveal that this enzyme's activity is controlled by substrate binding to its active site, via an induced-fit mechanism.

Rhodopsin is a G protein–coupled receptor (GPCR) involved in biological signaling. How the structure of the ligand is connected with larger-scale functional protein dynamics has remained elusive. Solid-state NMR relaxation shows that localized motions of the ligand retinal lead to collective fluctuations of transmembrane helices in the activation mechanism of the photoreceptor.

XMRV is a retrovirus that has been linked to prostate cancer and chronic fatigue syndrome. The crystal structure of the XMRV protease differs from the structures of other retropepsins and instead resembles those of pepsin-like enzymes, suggesting that this protease may represent a distinct evolutionary branch of the aspartic proteases.

Myotonic dystrophy type 1 (DM1), a multisystem disorder affecting skeletal and smooth muscle and other essential systems, belongs to a group of RNA gain-of-function disorders caused by the expansion of a CUG trinucleotide repeat (CUG^exp) in the 3' untranslated region of the DM protein kinase (DMPK) gene. Furling and coworkers have developed an optimized human U7-snRNA containing a poly-CAG antisense sequence to target the CUG^exp RNAs. These constructs cause specific degradation of pathogenic but not wild-type DMPK RNA products. By abolishing the RNA gain-of-function toxicity responsible for pathogenesis, these hU7-snRNAs could affect gene silencing in other RNA-dominant disorders expressing expanded repeats.

Nascent peptides with signal sequences must be recognized in order to be correctly targeted within the cell. The cryo-EM structure of the E. coli signal recognition particle in complex with its receptor and the translating ribosome is now presented, indicating conformational changes that lead to receptor recruitment.

Despite recognizing an epitope on HIV-1 gp41 that partially overlaps with those from broadly neutralizing antibodies, mAb 13H11 is non-neutralizing. Now the crystal structure and binding studies of 13H11 Fab with a gp41 peptide reveal why: the antigen assumes a helical structure consistent with the post-fusion conformation of gp41.

The 2009 pandemic flu influenza A H1N1 strain has caused great public health concern. Now the structure of H1N1 neuraminidase (NA) reveals that it lacks the characteristic additional cavity at its active site, known as the 150-cavity, found in all other known group 1 NAs.

The exon junction complex (EJC) is found on spliced mRNAs and influences post-transcriptional regulation. It is now shown that in Drosophila melanogaster, the EJC is bound to some but not all spliced junctions, suggesting that its assembly by the splicing machinery is a regulated process.