Research articles

Tubulin undergoes cycles of removal or addition of a C-terminal tyrosine residue to the C-terminus of α-tubulin within the α-β heterodimer. Crystal structures of tubulin tyrosine ligase (TTL), along with SAXS and functional analyses, reveal that TTL interacts with the C-terminal tail of α-tubulin and also with its longitudinal face, preventing incorporation of the α–β tubulin dimer into the microtubule lattice.

Dimerization, ligand-binding and co-confinement are all expected to contribute to erbB1 signaling, but the level of their contribution has not yet been fully appreciated. Two-color quantum-dot tracking in live cells now shows that ligand-binding (two ligands with two receptors) stabilizes erbB1 dimers, whereas actin networks influence dimer mobility and promote repeated encounters between erbB1 monomers.

TiaS catalyzes the transfer of agmatine onto the first position cytidine of the tRNAIle2 anticodon in archaea, ensuring proper translation of the matching codon. Now the crystal structures of the TiaS–tRNAIle2 complex with ATP, or with AMPCPP and agmatine, reveal a novel kinase domain and show how TiaS selects the correct tRNA while segregating the target cytidine until agmatine is bound.

Monoclonal antibody 2F5 recognizes the membrane proximal external region (MPER) in GP41 and has broad neutralization activity against HIV-1 strains. NMR, EPR and HDX/MS analyses now show that 2F5 extracts MPER from the membrane using a scoop-like movement.

Archaea use a tRNA^Ile with agmatine conjugated at the C34 position to decode the AUA codon. The enzyme that catalyzes this reaction, TiaS, has been previously identified, and it is now shown that it uses a novel kinase domain to hydrolyze ATP into AMP and pyrophosphate before phosphorylating itself and the tRNA on its way to conjugating the agmatine.

Eukaryotic initiation factor eIF2 binds initiator Met-tRNA_i^Met to the P site of the 40S ribosomal subunit. Hydroxyl radical probing analyses allowed mapping of the binding of eIF2 on the ribosome and on Met-tRNA_i^Met. Interestingly, despite having structural similarities to elongation factor EF-Tu, which delivers aminoacyl-tRNAs to the A site of 70S elongating ribosomes, eIF2 binds tRNA in a substantially different manner.

Organism-wide RNA interference (RNAi) is due to the movement of mobile RNA species throughout the organism. New genetic evidence shows that double-stranded RNA (dsRNA), which triggers RNAi, and at least one dsRNA intermediate produced during RNAi can act as or generate mobile silencing RNAs in Caenorhabditis elegans. Interestingly, single-stranded primary and amplified secondary siRNAs do not generate mobile silencing RNAs.

Aprataxin is a DNA deadenylase that processes DNA molecules with 5'-AMP termini that result from abortive ligation reactions. The crystal structures of the Schizosaccharomyces pombe ortholog Hnt3 in its apo state, bound to DNA or DNA and AMP, provide insight into how this enzyme recognizes and processes its substrate.

NuA4 is an essential and conserved histone acetyltransferase (HAT) complex. Using electron microscopy supported by biochemical analyses, insights are now gained into its interaction with the nucleosome core particle (NCP). These data indicate that the Epl1 subunit is essential for NCP interaction, whereas the Yng2 subunit positions the acetyltransferase complex relative to specific histone tails.

Deficiencies in aprataxin, which reverses 5′-adenylate DNA adducts, can lead to the neurodegenerative disorder AOA1. Mutagenesis analyses and the crystal structure of the aprataxin ortholog from Schizosaccharomyces pombe in complex with DNA, AMP and Zn²⁺ reveal the mechanisms by which this enzyme processes DNA lesions and maintains genome integrity.

LRP5/6 is a Wnt co-receptor essential for Wnt/β-catenin signaling. X-ray crystallography and electron microscopy analyses now reveal that the LRP6 extracellular ligand-binding domain is composed of two pairs of rigid blocks connected by a short hinge. The structure of the LRP6–DKK1c complex also shows how DKK1 may potently inhibit Wnt/β-catenin signaling through its binding to these structural blocks.

The GW182 protein, which binds poly(A)-binding protein (PABP) and is part of the miRNA-induced silencing complex, effects translational repression and deadenylation of target mRNAs. New data indicate that GW182 independently interacts with the PAN2–PAN3 and CCR4–NOT deadenylase complexes and that interaction of GW182 with CCR4–NOT is PABP-independent and occurs through discrete binding sites with distinct roles in miRNA-mediated deadenylation.

The function of GW182 proteins in miRNA-mediated gene silencing has been unclear. Studies in human and fly cells now identify tryptophan-containing motifs as important repressive elements. These motifs, which are dispersed throughout GW182 proteins, function additively by recruiting deadenylase complexes to repress both poly(A)⁺ and poly(A)⁻ mRNAs, suggesting that recruitment, in addition to catalyzing deadenylation, also mediates translational repression.

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.

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.

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.

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.

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.

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.

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.