Articles in 2011

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.

The lack of sequence-specificity of DNA replication origins in most eukaryotes poses a challenge for its identification. Through BrdU labeling followed by high-throughput sequencing, supported by ChIP-chip to locate ORC1 and CDC6, the origins of replication in Arabidopsis thaliana are now mapped and their contexts analyzed.

CP29 is one of the minor light-harvesting complexes from plant photosystem II; it absorbs and transfers solar energy for photosynthesis. Now the crystal structure of spinach CP29 is solved, revealing a network of pigments and offering insights into energy transfer pathways.

Xrn1 is a 5′-3′ exoribonuclease that is implicated in a range of regulated mRNA decay processes in eukaryotes. The structure of Xrn1 is now presented, indicating that it unexpectedly carries repeated structural domains with similarities to the Tudor, Chromo and other domains. These may stabilize the active site and form a platform for protein recruitment.

The C. elegans microRNA let-7 regulates developmental progression, and human let-7 has been implicated in disease. Examination of endogenous let-7 expression in C. elegans now reveals a complex regulation process whereby pri-let-7 is regulated transcriptionally with oscillations during each larval stage, and co-transcriptionally by LIN-28 which prevents mature microRNA accumulation during early larval stages.

In this issue, two papers present contrasting models for the machinations of the measles virus attachment protein. Here we discuss how these reports illuminate possible intersubunit motions made by the protein as it drives the fusion of viral and cellular membranes during infection and further our understanding of this global scourge.

The interaction of autotaxin with its substrates leads to the production of lysophosphatidic acids (LPA), bioactive lipids with an emerging prominent role in inflammation and cancer. Two papers in this issue tell the previously unknown story of autotaxin, from substrate discrimination to highly efficient local delivery of LPA to target receptors.

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.

Hsp70 chaperones interact with many proteins through a substrate-trapping mechanism that requires ATP. Hsp70s have a lid over the substrate-binding cleft, whose function is controversial. Using cysteine cross-linking and EPR in the Escherichia coli Hsp70 DnaK, it is now shown that helix B of the lid subdomain can adopt three major conformational states and that it does not necessarily close over bound substrates, allowing binding of natively folded states.

FliJ interacts with many flagellar proteins involved in protein export, but its function was unclear. Now the crystal structure of FliJ shows it is a homolog of the F1-ATPase γ-subunit. Binding of FliI to FliJ promotes FliI hexameric ring formation, suggesting that flagellar type III protein export systems and F1-ATP synthase use a similar mechanism.

Hsc70 disassembles the coats of clathrin-coated vesicles, remodels a number of other protein complexes, and facilitates protein folding. The dynamics of clathrin uncoating promoted by Hsc70 have now been monitored with single-particle fluorescence imaging. The results suggest that disassembly is driven by trapping of small conformational fluctuations.

MutS scans DNA for mismatches; once a lesion is recognized, MutS initiates a cascade of events that ultimately results in mismatch excision and repair. Now the behavior of MutS on DNA is studied using smFRET, revealing that mismatch recognition triggers ATP binding that switches MutS from a transient scanning clamp to a very stable sliding clamp.

The structural and thermodynamic changes caused by substrate binding were followed using a combination of techniques. The approach reveals that allosteric communication between the two active sites of a homodimeric enzyme occurs through two opposing mechanisms. One follows a classical paradigm and the other involves a recently-proposed interplay of folding and binding.

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.

Serpins disable their target proteases by formation of an inhibitory complex in which the serpin experiences major structural reordering. How local unfolding allows the serpin to remodel its structure is now mapped by chemical probing. The evolution of functionally important conformationally labile regions has exposed serpins to a risk of aggregation, and indeed many serpinopathy-linked mutations map to the identified labile region.

APOBEC1 is involved in conversion of a specific C to U in apolipoprotein B mRNA, a classic example of RNA editing. With a comparative RNA-Seq screen, numerous additional targets of APOBEC1 editing are found. Editing sites tend to be located in AU-rich regions of 3′ UTRs, and analysis identifies common features that prove predictive of additional targets.

microRNAs bind Argonaute proteins, guiding silencing of target mRNAs. CLIP-seq has now been used to map microRNA targets bound by Ago2 in a Dicer-dependent fashion in mouse ES cells. The study reveals that certain sets of transcripts, such as TGF-β signaling pathway components, tend to be targeted, and also identifies a G-rich motif in targets that may modulate regulation.

:Autotaxin (ATX) is a secreted enzyme that produces lysophosphatidic acid (LPA), which in turn activates GPCRs to elicit cellular responses. The crystal structures of mouse ATX in its apo state and bound to different LPAs and functional work reveal a hydrophobic tunnel that could participate in direct delivery of the product to its cognate GPCRs.

Nucleotide excision repair is one of the main pathways for removal of damaged DNA. UvrA, which finds the damaged DNA, has broad specificity. The first crystal structure of UvrA in complex with DNA shows that the UvrA dimer does not contact the lesion directly but instead probes the conformation of the DNA around the modified residue.