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Protein synthesis by the ribosome involves large-scale rearrangements of the “small” subunit (SSU; ∼1 MDa), which include inter- and intra-subunit rotational motions. With more than 1000 structures of ribosomes and ribosomal subunits now publicly available, it is becoming increasingly difficult to design precise experiments that are based on a comprehensive analysis of all known rotation states. To overcome this limitation, we present the Ribosome Angle Decomposition (RAD) method, where the orientation of each small subunit head and body is described in terms of three angular coordinates (rotation, tilt and tilt direction) and a single translation. To demonstrate the utility of the accompanying software (RADtool) we applied it to all published ribosome and mitoribosome structures. This identified and analyzed 1077 fully-assembled ribosome complexes, as well as 280 isolated small subunits from 48 organisms. The RAD approach quantitatively distinguishes between previously described qualitative rotational features, determines when rotation-only descriptions are insufficient, and shows that tilt-like rearrangements of the SSU head and body are pervasive in both prokaryotic and eukaryotic ribosomes. Together, the presented database and technique provide a robust platform for systematically analyzing, visualizing, and comparing subunit orientations of ribosomes from all kingdoms of life. Accordingly, the RAD resource establishes a common foundation with which structural, simulation, single-molecule and biochemical efforts can precisely interrogate the dynamics of this prototypical molecular machine.

Novel hydroxy, methyl and methoxy ring-trisubstituted 2-methoxyethyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH2OCH3 (where R is 2,3-dimethyl-4-methoxy, 2,5-dimethyl-4-methoxy, 2,4-dimethoxy-6-methyl, 3,5-dimethoxy-4-hydroxy, 4-hydoxy-3,5-dimethyl, 2,3,4-trimethoxy, 2,4,5-trimethoxy, 2,4,6-trimethoxy, 3,4,5-trimethoxy) were prepared and copolymerized with styrene. The acrylates were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-trisubstituted benzaldehydes and 2-methoxyethyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the acrylates were copolymerized with styrene in solution with radical initiation (ABCN) at 70C. The compositions of the copolymers were calculated from nitrogen analysis.

A critical step in data analysis for many different types of experiments is the identification of features with theoretically defined shapes in N-dimensional datasets; examples of this process include finding peaks in multi-dimensional molecular spectra or emitters in fluorescence microscopy images. Identifying such features involves determining if the overall shape of the data is consistent with an expected shape; however, it is generally unclear how to quantitatively make this determination. In practice, many analysis methods employ subjective, heuristic approaches, which complicates the validation of any ensuing results—especially as the amount and dimensionality of the data increase. Here, we present a probabilistic solution to this problem by using Bayes’ rule to calculate the probability that the data have any one of several potential shapes. This probabilistic approach may be used to objectively compare how well different theories describe a dataset, identify changes between datasets and detect features within data using a corollary method called Bayesian Inference-based Template Search; several proof-of-principle examples are provided. Altogether, this mathematical framework serves as an automated ‘engine’ capable of computationally executing analysis decisions currently made by visual inspection across the sciences.

Obstructive sleep apnea (OSA) remains a prominent disease state characterized by the recurrent collapse of the upper airway while sleeping. To date, current treatment may include continuous positive airway pressure (CPAP), lifestyle changes, behavioral modification, mandibular advancement devices, and surgical treatment. However, due to the desire for a more convenient mode of management, pharmacological treatment has been thoroughly investigated as a means for a potential alternative in OSA treatment. OSA can be distinguished into various endotypic or phenotypic classes, allowing pharmacological treatment to better target the root cause or symptoms of OSA. Some medications available for use include antidepressants, CNS stimulants, nasal decongestants, carbonic anhydrase inhibitors, and potassium channel blockers. This review will cover the findings of currently available and future study medications that could potentially play a role in OSA therapy.

Novel trisubstituted ethylenes, methyl and methoxy ring-trisubstituted 2-methoxyethyl phenylcyanoacrylates, RPhCH=C(CN)CO2CH2CH2OCH3 (where R is 2,3-dimethyl-4-methoxy, 2,5-dimethyl-4-methoxy, 2,4-dimethoxy-6-methyl, 3,5-dimethoxy-4-hydroxy, 4-hydoxy-3,5-dimethyl, 2,3,4-trimethoxy, 2,4,5-trimethoxy, 2,4,6-trimethoxy, 3,4,5-trimethoxy) were prepared and copolymerized with styrene. The ethylenes were synthesized by the piperidine catalyzed Knoevenagel condensation of ring-substituted benzaldehydes and 2-methoxyethyl cyanoacetate, and characterized by CHN analysis, IR, 1H and 13C NMR. All the ethylenes were copolymerized with styrene in solution with radical initiation (ABCN) at 70°C. The compositions of the copolymers were calculated from nitrogen analysis.

Stunning advances in the structural biology of multicomponent biomolecular complexes (MBCs) have ushered in an era of intense, structure-guided mechanistic and functional studies of these complexes. Nonetheless, existing methods to site-specifically conjugate MBCs with biochemical and biophysical labels are notoriously impracticable and/or significantly perturb MBC assembly and function. To overcome these limitations, we have developed a general, multiplexed method in which we genomically encode non-canonical amino acids (ncAAs) into multiple, structure-informed, individual sites within a target MBC; select for ncAA-containing MBC variants that assemble and function like the wildtype MBC; and site-specifically conjugate biochemical or biophysical labels to these ncAAs. As a proof-of-principle, we have used this method to generate unique single-molecule fluorescence resonance energy transfer (smFRET) signals reporting on ribosome structural dynamics that have thus far remained inaccessible to smFRET studies of translation.

During unfavorable cellular conditions (e.g., tumor hypoxia, viral infection, nutrient deprivation, etc.), the canonical, cap-dependent translation initiation pathway in human cells is suppressed by sequestration of the cap-binding protein, eukaryotic initiation factor (eIF) 4E, by 4E-binding proteins. Additionally, the expression levels of eIF4G and its cellular homolog, death associated protein 5 (DAP5), are elevated. Under these conditions, a subset of cellular mRNAs, including many encoding proteins with important roles in human health and disease, (e.g. HIF-1α, FGF-9, and p53) is translated in a cap-independent manner. Despite their physiological importance, however, the molecular mechanisms underlying cap-independent initiation of this subset of cellular mRNAs remain unknown. Here, we have used fluorescence anisotropy-based equilibrium binding assays developed in our laboratories to demonstrate that an N-terminal truncated form of human eIF4G1 that cannot interact with eIF4E (ΔN-4G1) or DAP5 directly bind to the 5’ untranslated regions (UTRs) of these mRNAs. Specifically, we have measured the differential affinities with which ΔN-4G1 and DAP5 interact with the 5’ UTRs of four distinct members of this subset of cellular mRNAs. Using a luciferase-based gene expression reporter assay, we further demonstrate that these same 5’ UTRs can promote cap-independent initiation in an ΔN-4G1 or DAP5-dependent manner in a rabbit reticulocyte lysate-based in vitro translation system. Integrating the results of our quantitative binding- and in vitro translation studies, we propose a model specifying how a subset of cellular mRNAs switch from cap-dependent to cap-independent modes of translation initiation Significance Under cellular stress conditions (e.g., tumor hypoxia, viral infection, etc.), the canonical, cap-dependent initiation of eukaryotic protein synthesis, or translation, of a subset of cellular mRNAs switches to a cap-independent mechanism. Despite the important role they play in human health and disease, the mechanisms regulating this switch remain unknown. We have found that a variant of eukaryotic initiation factor (eIF) 4G1 and its homolog, DAP5, factors that are upregulated under stress conditions, bind with high affinity and specificity to the 5’ untranslated regions of these mRNAs and upregulate their translation. These results suggest that binding of eIF4G1 or DAP5 to these mRNAs plays an important role in regulating the switch between the cap-dependent and cap-independent initiation of these mRNAs.

A complete understanding of the determinants that restrict D-amino acid incorporation by the ribosome, which is of interest to both basic biologists as well as the protein engineering community, remains elusive. Previously, we demonstrated that D-amino acids are successfully incorporated into the C-terminus of the nascent polypeptide chain. Ribosomes carrying the resulting peptidyl-D-aminoacyl-tRNA (peptidyl-D-aa-tRNA) donor substrate, however, partition into subpopulations that either undergo translation arrest through inactivation of the ribosomal peptidyl-transferase center (PTC) or remain translationally competent. The proportion of each subpopulation is determined by the identity of the D-amino acid sidechain. Here, we demonstrate that the identity of the aminoacyl-tRNA (aa-tRNA) acceptor substrate that is delivered to ribosomes carrying a peptidyl-D-aa-tRNA donor further modulates this partitioning. Our discovery demonstrates that it is the pairing of the peptidyl-D-aa-tRNA donor and the aa-tRNA acceptor that determines the activity of the PTC. Moreover, we provide evidence that both the amino acid and tRNA components of the aa-tRNA donor contribute synergistically to the extent of arrest. The results of this work deepen our understanding of the mechanism of D-amino acid-mediated translation arrest and how cells avoid this precarious obstacle, reveal similarities to other translation arrest mechanisms involving the PTC, and provide a new route for improving the yields of engineered proteins containing D-amino acids.

Correction to: Nature Communications https://doi.org/10.1038/s41467-017-02380-9 , published online 22 January 2018 In the originally published version of this Article, the af fi liation details for Santi González, Jian ’ an Luan and Claudia Langenberg were inadvertently omitted. Santi González should have been af fi liated with 'Barcelona Supercomputing Center (BSC), Joint BSC-CRG-IRB Research Program in Computational Biology, 08034 Barcelona, Spain ’ , and Jian ’ an Luan and Claudia Langenberg should have been af fi liated with ‘ MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK ’ . Furthermore, the abstract contained an error in the SNP ID for the rare variant in chromosome Xq23, which was incorrectly given as rs146662057 and should have been rs146662075. These errors have now been corrected in both the PDF and HTML versions of the Article.