Articles in 2011

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.

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.

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.