Research articles

Thioredoxins (Trxs) reduce disulfide bonds via a Michaelis-Menten mechanism. Upon substrate stretching at high forces, an S_N2 reaction can be used by bacterial Trxs. A third mechanism, single-electron transfer, is now revealed in Trxs of either bacterial or eukaryotic origin, and is correlated with the depth of the Trx substrate-binding groove.

Covalent histone modifications have been linked to many DNA processes. The repertoire of modifications is still growing, and histone H3K64 trimethylation is now shown to be localized to pericentric chromatin and its levels dynamically altered during developmental reprogramming in both embryos and primordial germ cells.

Transient receptor potential channels are involved in sensory perception, and TRPV1 is a sensor of burning pain signals and can be modulated by acidic pH, capsaicin and heat. Substituted cysteine accessibility is used to probe state-dependent structural arrangements of the presumed pore-lining S6 helix, revealing two constrictions that participate in gating activity of the channel pore.

Hedgehog (Hh) proteins are involved in multiple developmental processes. Hedgehog-interacting proteins (Hhips) bind and inhibit vertebrate Hh proteins. A structure of HHIP in complex with human SHH now shows a distinct binding site from previous ligand structures, with the pseudocatalytic site having a key role in binding.

Hedgehog (Hh) signaling molecules are involved in multiple developmental processes. Hedgehog-interacting protein (Hhip) binds and inhibits vertebrate Hh proteins. Structures of HHIP in complex with SHH and DHH now show a distinct binding site from previous ligand structures, with metal-binding sites having a role in interaction.

Exogenously applied small RNAs have previously been shown to inhibit transcriptional levels when targeted to promoters. They are now shown to alter the ratio of alternative splice forms. The features of splice form alteration are reminiscent of transcriptional gene silencing by siRNAs.

Clostridium botulinum neurotoxins (BoNTs) cleave proteins involved in neurotransmitter release, with different serotypes showing distinct cleavage specificity. The structure of BoNT F with peptide inhibitors based on the VAMP substrate give insight into residues crucial for substrate binding and catalysis.

The lamprey adaptive immune system is evolutionarily distinct from ours and based on recognition by leucine-rich repeat proteins rather than antibodies. The crystal structure of a lamprey variable lymphocyte receptor in complex with a protein antigen now gives insight into how a distinct adaptive immune molecule recognizes a protein antigen.

AID is a DNA cytidine deaminase that participates in the generation of antibody diversity. AID's mutagenic activity is carefully controlled by transcriptional and post-translational mechanisms. Now the enzyme's intrinsic catalytic activity is found to have been kept low during evolution, and in vitro–selected AID upmutants can cause genetic instability.

The contribution of hydrogen bonding to the thermodynamics of protein folding is not well understood. The strength of hydrogen bonds is now found to depend on the polarity of their microenvironment, being stronger in non-polar surroundings. Thus, the burial or solvent exposure of a few hydrogen bonds near the surface of a protein can significantly stabilize or destabilize its native state.

Telomeres alternate between telomerase-extendable and telomerase-unextendable states. Now this switch is reconstituted in vitro, using DNA templates and purified telomeric proteins from yeast. The molecular chaperone Hsp82 is shown to have a role in this switch by modulating the DNA binding activity of Cdc13.

ESCRT-III proteins play important roles in multivesicular body (MVB) formation, cytokinesis, and enveloped virus budding. The structure of Ist1, which also functions in cytokinesis and MVB sorting, reveals that it, too, is an ESCRT-III family member and suggests that this protein family uses a common mode of autoinhibition.

The Brr2 ATPase is a large DExD/H-box helicase required for key snRNA-remodeling steps during the splicing reaction. The structure of part of Brr2, in conjunction with modeling and functional analysis, indicates that it probably resembles the Hel308 DNA helicase and may share a similar helicase mechanism.

Nonsense-mediated decay is a surveillance pathway that removes transcripts containing a premature stop codon. UPF3 is unusual among the trans-acting factors in the pathway because there are two distinct homologs, UPF3A and UPF3B. Given that patients with reduced UPF3B contain upregulated levels of UPF3A, a regulatory interplay between the two factors is uncovered, where competition for UPF2 binding destabilizes the unbound factor.

The nuclear pore complex mediates nucleocytoplasmic transport and consists of an assembly of multiple copies of ∼30 different proteins called nucleoporins. Kampmann and Blobel describe the structure and flexibility of the heptameric Nup84 complex by single-particle, negative-stain EM. They find that the arrangement of β-propeller and α-solenoid folds within the heptamer resembles that of the clathrin triskelion, which has been proposed to share a common evolutionary origin with the heptameric complex.

Covalent histone modifications can affect the structure of chromatin. Expression of underlying monomethylated histone H3K27 is associated with chromocenters in Arabidopsis, but its presence is unaffected by mutations in the expected methyltransferases. Data now indicate that this modification is catalyzed by Arabidopsis ATRX5 and ATXR6 and is required for silencing, but in a pathway independent of that involving DNA methyltransferases.

The box H/ACA pseudouridine synthase complex guides modification of small nucleolar and Cajal body ribonucleoproteins (sno/scaRNAs), which are essential for maturation of the ribosome and spliceosome. The structure of a functional H/ACA complex containing L7Ae, Nop1 and Cbf5 proteins bound to the substrate and guide RNAs and with a catalytically rearranged substrate in the active site is now presented.

Protein kinase C epsilon (PKCε) priming involves phosphorylation of the kinase domain at 3 different sites. Whether these phosphorylation events were autocatalytic was unclear. Now Parker and colleagues use different PKCε mutants and inhibitors to demonstrate that the occupancy of the nucleotide binding pocket, and not catalytic activity, promote priming of PKCε.

The signaling adaptor TRAF6 is a ubiquitin E3 ligase whose activity can lead to activation of NF-κB and MAPK pathways. New data based on the structure of TRAF6 in complex with the ubiquitin E2 Ubc13 suggest that other TRAFs do not interact with Ubc13 and that oligomerization of TRAF6 is needed for downstream signal transduction.

The amino-terminal domain (ATD) of ionotropic glutamate receptors (iGluRs) mediates their assembly into AMPA-, kainate- and NMDA-sensitive subtypes. The crystal structure of the ATD from the kainate receptor GluR6 reveals a dimeric organization and likely determinants for subtype-selective assembly.