Volume 17 Issue 1, January 2010

An X-ray crystal structure of an organic anion transporter identifies it as an ion channel instead. Its similarity to an unrelated family of water channels raises evolutionary questions that have been recently bubbling up around membrane proteins.

Small RNAs function within the context of RNA-induced silencing complexes (RISCs) containing Argonaute (AGO) subfamily proteins. Experiments now show that human RISC assembly is uncoupled from dicing and is facilitated by ATP to load the small RNA duplexes but is not necessary to unwind them. The four human AGO proteins show no obvious structural preferences for small RNA duplexes in contrast to the situation in flies and worms where small RNAs are actively sorted into distinct AGO proteins according to their structural features.

The Drosophila small RNA interference pathways can be triggered by dsRNA from various sources, both exogenous and endogenous. Examination of mutations in flies now shows that two RNA-binding proteins, R2D2 and Loquacious, in fact act together in a common pathway used by dsRNAs from different sources.

The structure of the formate channel FocA from Vibrio cholerae reveals a pentamer, with each monomer possessing its own substrate translocation pore. The selectivity filter consists of a central constriction ring and a cytoplasmic slit, which binds two formate ions. Surprisingly, FocA shares many similarities with aquaporin and glycerol channels.

The jumonji domain demethylases catalyze demethylation of histones, thus affecting modifications that are associated with transcription status. Structural and functional analyses of two PHF8 jumonji orthologs now indicates that the PHD domain, conserved in this family, binds H3K4me3, a modification associated with transcriptional activation, thus directing and augmenting the target of jumonji-mediated demethylation.

The voltage-gated proton channel Hv1 forms a dimer, but each monomer contains a voltage sensor domain that forms a pore for proton conduction. Now functional work using voltage clamp fluorometry, current recording and modeling reveals that the 2 pores are gated in a cooperative manner.

The voltage-gated proton channel Hv1 forms a dimer, but each monomer contains a voltage sensor domain that forms a pore for proton conduction. Now functional work with Ciona intestinalis Hv protein reveals that the two pores in the dimer are gated in a cooperative manner, and that the S4 helices from each subunit need to move in order to open the channels.

tRNA synthetases (RSs) have been implicated in functions beyond tRNA synthesis, and human TrpRS has been implicated in inhibiting angiogenesis. Tryptophan residues implicated in homotypic interactions on VE-cadherin are now shown to bind the active site of a naturally truncated TrpRS, indicating how this enzyme has been repurposed.

MLL fusions are linked to leukemias and retain the CXXC domain, which binds unmethylated DNA. The NMR structure of CXXC–DNA now indicates the interactions underlying binding. Mutation of a key residue to a nonbinding form decreases proliferation caused by an MLL-AF9 fusion and leukemias induced by MLL-AF9 expression in mice.

Dpp, a member of the TGF-β signaling family, is a key regulator during Drosophila development. An activation element upstream of the dad gene is now shown to operate by integrating repressive and activating inputs and allows the identification of other Dpp target genes.

MCAK is a mitotic kinesin that binds to and slides along microtubules (MT) to reach their ends, where MCAK disassembles MTs into tubulin dimers. Now the kinetics of MCAK-MT interaction are directly observed in a single-molecule setup, dissecting the contributions of different MCAK regions to on-rates and tubulin disassembly activity.

During the HIV-1 life cycle, the tRNA₃^Lys from the host cell serves as a primer for reverse transcription and to facilitate strand transfer to the 3′ region of the viral RNA. Now a long insertion with similarity to the tRNA₃^Lys gene is identified in the 3′ region of HIV-1, HIV-2 and SIV, but not the more distant FIV, and shown to play a role in strand transfer in vitro.

The Cys-loop receptors are pentameric ligand-gated ion channels important in fast synaptic transmission. By examining the pentamerization properties of membrane domain point mutants and split GlyR and 5HT3A subunits, the precise geometry of transmembrane helix packing is seen to crucially define the closed pentameric stoichiometry.

The polymorphous trigger loop is a key component of RNA polymerase (RNAP) that promotes polymerization when folded into a “trigger helices” (TH) conformation. The role of the TH in pausing and nucleotide addition for the bacterial RNAP is now teased apart using mutagenesis and biochemical analyses.

Some pathogenic viruses target the CUL4-DDB1 ubiquitin ligase machinery and subvert it. Multiple structures of viral protein fragments in complex with DDB1 reveal that they bind DDB1 through an α-helical motif similar to that used for DDB1 interaction by the cellular factor DCAF9.

Store-operated calcium entry involves two proteins: Stim1 and Orai1, but are they sufficient for gating CRAC channels or are other factors required? Mammal systems have failed to provide a conclusive answer but yeast-based assay does: Stim1 and Orai1 are the only essential components of CRAC channel activity.

THAP family proteins bind DNA and are involved in diverse DNA processes. The structure of the DNA-bound Drosophila P element transposase THAP domain now shows that the conserved β-sheet docks into the major groove, while a C-terminal basic loop binds the minor groove, a mode that is likely conserved and indicates the basis of bipartite sequence recognition.

Cellular infection with measles virus starts with the binding of the viral hemagglutinin (MV-H) to host cell receptors (CD46 or SLAM, depending on the measles strain). The crystal structure of MV-H bound to the membrane distal extracellular domains of CD46 (SCR1 and SCR2) is now described, shedding light on this important interaction.

Helicobacter pylori is a strong risk factor for stomach cancer. The CagA effector protein is translocated into host cells by a type IV secretion system and is a key virulence factor. Its effects are mediated in part through the host polarity kinase PAR1b/MARK2, which CagA binds and inhibits. The crystal structure of a complex between CagA peptide and MARK2 reveals that the CagA peptide mimics targets of this kinase family.

GFP fluorescence can be modulated in mammalian cells by binding to single-chain antibodies (nanobodies), selected to make GFP brighter or dimmer; these changes are explained by the crystal structures of the GFP-nanobody complexes. The applications of such nanobodies to monitor protein expression and subcellular localization in real time are explored.