Articles in 2013

A mRNA-interactome capture approach in embryonic stem cells (ESCs) has led to the identification of 283 novel RNA-binding protein (RBP) candidates, of which 68 are preferentially expressed in ESCs. Validation of two known E3 ubiquitin ligases as RBPs reveals an intriguing potential link between RNA biology and protein-modification pathways.

The activity of PLK1, a key mitotic regulator, is tightly regulated during the cell cycle through both phosphorylation and protein-protein interactions. The crystal structure of PLK1's kinase domain bound to the polo-box domain now provides a structural framework for the regulation of PLK1 through autoinhibition.

Calmodulin (CaM) regulates a variety of membrane channels in response to Ca2+, but the precise mechanisms are still unclear. Now a combination of single-particle EM, molecular dynamics simulations and functional assays is used to elucidate the structure of Ca2+–CaM bound to the full-length aquaporin AQP0, revealing a cytoplasmic gate that is closed upon CaM binding to control channel permeability in an allosteric manner.

The Arp2/3 complex regulates the actin cytoskeleton by nucleating branched actin filaments in response to cellular signals and is in turn controlled by regulators including GMF. The crystal structure of GMF bound to Arp2/3 provides insight into how GMF inhibits actin nucleation and dissembles branches.

HP1 proteins bind methylated histone H3 Lys9, a hallmark of heterochromatin, and mediate heterochromatin spreading by recruiting histone methyltransferase activities. New studies have now identified a long noncoding RNA called BORDERLINE that prevents spreading of the HP1 protein Swi6 and histone H3 Lys9 methylation beyond the pericentromeric repeat region of fission yeast chromosome 1.

Combined with kinetic analyses, the high resolution structure of kinesin-1 bound to a tubulin dimer offers a much-anticipated view of the motor-microtubule interface that illuminates the key step of neck-linker docking and of the structural basis for microtubule-accelerated ATP hydrolysis and motility.

Initiation factors eIF1 and eIF1A are key determinants of ribosomal scanning and initiation-codon selection during translation initiation. The structure of Tetrahymena thermophila 40S ribosome in complex with eIF1 and eIF1A reveals the conformational changes that accompany initiation-factor binding and provides new insights into the mechanism of start-codon recognition.

In dimeric RING E3 ligases, the tail domain of the second subunit primes the transfer reaction. The crystal structure of human Tyr363-phosphorylated CBL-B in complex with ubiquitin-linked E2 UbcH5Band a peptide substrate now shows that a phosphorylated residue can act as the priming element in monomeric RING E3s.

In immune cells, CRAC channels in the plasma membrane regulate store-operated Ca²⁺ entry in response to STIM1, a sensor protein located in the endoplasmic reticulum (ER) membrane. New biophysical assays show how dimerization of STIM1's ER-luminal domains causes extension of its cytoplasmic domains toward the plasma membrane to contact the ORAI pore and activate the channel, revealing the structural dynamics of this Ca²⁺-signaling mechanism.

Eukaryotic DNA replication begins with recruitment of the ring helicase MCM2-7 by the origin recognition complex (ORC) in a reaction facilitated by initiation factors Cdc6 and Cdt1. A new cryo-EM structure of a helicase loading intermediate, the ORC–Cdc6–Cdt1–MCM2-7 complex, unexpectedly reveals both MCM2-7 and ORC hexamers encircling the DNA, and shows the arrangement of all 14 subunits within the helicase-loader complex.

Most mammalian promoters are inherently bidirectional, but transcription only elongates productively in one direction. Data presented in this paper demonstrate that at least part of the answer lies in the asymmetric distribution of polyadenylation-site sequences around human gene promoters causing termination of upstream antisense transcription.

The general transcription factor TFIID comprises TATA-binding protein (TBP) and TBP-associated factors (TAFs). The high-resolution structure of yeast TBP in complex with yeast TAF1 containing both transcriptionally activating and repressing regions reveals detailed and specific molecular patterns of interactions with TBP and their significance for transcriptional regulation.

The mitochondrial inner membrane generates a proton-motive force (PMF) that drives cellular processes. Using a high-resolution fluorescence mapping approach combined with kinetic analyses, changes in the PMF are now shown to drive marked structural changes in the Tim23 channel of the TIM23 protein-translocation complex that are important for channel gating.

The RNA helicase UPF1 has been implicated in various functions including nonsense-mediated decay (NMD). Transcriptome-wide analysis of UPF1-binding sites in translationally active versus inhibited cells provides evidence for translation-independent UPF1-RNA interactions and also suggests that UPF1 bound to coding sequence may be displaced by translating ribosomes and that NMD substrate selection may occur after UPF1-RNA interaction.

A shield of glycans coats the viral-envelope proteins of HIV. Recent work shows how broadly neutralizing antibodies can recognize this shield despite structural variation in these 'self' carbohydrate structures.

Multiple Argonaute proteins are implicated in gene silencing by RNA interference (RNAi), but only one is known to be an endonuclease that can cleave target mRNAs. Chimeric Argonaute proteins now reveal an unexpected mechanism by which mutations distal to the catalytic center can unmask intrinsic catalytic activity, results hinting at structurally mediated regulation.

The anaphase-promoting complex/cyclosome (APC/C) is restricted by metazoan protein early mitotic inhibitor 1 (EMI1), a natural, potent inhibitor. New findings suggest that the multimodal inhibitory mechanisms of EMI1 control APC/C-dependent ubiquitylation.