Polypeptides and polynucleotides are natural programmable biopolymers that can self-assemble into complex tertiary structures. We describe a system analogous to designed DNA nanostructures in which ...protein coiled-coil (CC) dimers serve as building blocks for modular de novo design of polyhedral protein cages that efficiently self-assemble in vitro and in vivo. We produced and characterized >20 single-chain protein cages in three shapes-tetrahedron, four-sided pyramid, and triangular prism-with the largest containing >700 amino-acid residues and measuring 11 nm in diameter. Their stability and folding kinetics were similar to those of natural proteins. Solution small-angle X-ray scattering (SAXS), electron microscopy (EM), and biophysical analysis confirmed agreement of the expressed structures with the designs. We also demonstrated self-assembly of a tetrahedral structure in bacteria, mammalian cells, and mice without evidence of inflammation. A semi-automated computational design platform and a toolbox of CC building modules are provided to enable the design of protein cages in any polyhedral shape.
We consider the duality between the four-dimensional S-matrix of planar maximally supersymmetric Yang-Mills theory and the expectation value of polygonal shaped Wilson loops in the same theory. We ...extend the duality to amplitudes with arbitrary helicity states by introducing a suitable supersymmetric extension of the Wilson loop. We show that this object is determined by a host of recursion relations, which are valid at tree level and at loop level for a certain “loop integrand” defined within the Lagrangian insertion procedure. These recursion relations reproduce the BCFW ones obeyed by tree-level scattering amplitudes, as well as their extension to loop integrands which appeared recently in the literature, establishing the duality to all orders in perturbation theory. Finally, we propose that a certain set of finite correlation functions can be used to compute all first derivatives of the logarithm of MHV amplitudes.
Protein export through the bacterial Sec pathway Tsirigotaki, Alexandra; De Geyter, Jozefien; Šoštaric, Nikolina ...
Nature reviews. Microbiology,
01/2017, Letnik:
15, Številka:
1
Journal Article
Recenzirano
The general secretory (Sec) pathway comprises an essential, ubiquitous and universal export machinery for most proteins that integrate into, or translocate through, the plasma membrane. Sec exportome ...polypeptides are synthesized as pre-proteins that have cleavable signal peptides fused to the exported mature domains. Recent advances have re-evaluated the interaction networks of pre-proteins with chaperones that are involved in pre-protein targeting from the ribosome to the SecYEG channel and have identified conformational signals as checkpoints for high-fidelity targeting and translocation. The recent structural and mechanistic insights into the channel and its ATPase motor SecA are important steps towards the elucidation of the allosteric crosstalk that mediates secretion. In this Review, we discuss recent biochemical, structural and mechanistic insights into the consecutive steps of the Sec pathway - sorting and targeting, translocation and release - in both co-translational and post-translational modes of export. The architecture and conformational dynamics of the SecYEG channel and its regulation by ribosomes, SecA and pre-proteins are highlighted. Moreover, we present conceptual models of the mechanisms and energetics of the Sec-pathway dependent secretion process in bacteria.
The assumption of an ecological limit to the number of species in a given region is frequently invoked in evolutionary studies, yet its empirical basis is remarkably meager. We explore this ...assumption by integrating data on geographical distributions and phylogenetic relationships of nearly six thousand terrestrial vertebrate species. In particular, we test whether sympatry with closely-related species leads to decreasing speciation rates. We introduce the concept of clade density, which is the sum of the areas of overlap between a given species and other members of its higher taxon, weighted by their phylogenetic distance. Our results showed that, regardless of the chosen taxon and uncertainty in the phylogenetic relationships between the studied species, there is no significant relationship between clade density and speciation rate. We argue that the mechanistic foundation of diversity-dependent diversification is fragile, and that a better understanding of the mechanisms driving regional species pools is sorely needed.
Direct interactions among species are only possible if there is some overlap in their geographical distributions. However, despite intense focus of macroecological research on species geographical ...ranges, relatively little theoretical and empirical work has been done on the evolution of range overlap. In this study we explore a simple model of range overlap based on a log-normal distribution of species range sizes along a one-dimensional domain, with or without absorbing boundary conditions. In particular, we focus on the mean and variance of range overlap distributions, as well as the topology of the resulting overlap networks with respect to their degree distribution, evenness, and betweenness scores. According to the model, there is an approximately linear relationship between many aspects of the distribution of range overlaps and their underlying species distributions, such as their mean and variance. However, the expected mean number of non-zero range overlaps for a given species varied from linear to convex depending on the variance of the underlying geographical range distribution. The expected topology of range overlap networks varied substantially depending on the mean and variance in the corresponding geographical distributions, particularly in the case of the degree and closeness distributions. Finally, we test the expectations of our model against five datasets of altitudinal distributions of Neotropical birds. We found strong departures from the expectations based on our model, which could potentially result from phylogenetic niche conservatism related to altitudinal gradients in environmental conditions, or from the asymmetric colonization of mountains by species from lowlands. Potential applications of range overlap networks to a variety of ecological and evolutionary phenomena are discussed.
Little is currently known about the relationship between the parental diet during pregnancy and the growth of the child from early childhood until early adulthood. This study was designed to examine ...whether the dietary patterns of the parents during a pregnancy and of the respective child at 3 years are associated with the length/height-for-age z-score of child at birth, 3 years of age and at 19 years of age.
Dietary patterns of pregnant women and their partners, and offspring at 3 years that were enroled in the 1990-1991 period in the Czech part of the European Longitudinal Study of Pregnancy and Childhood. Multivariable linear regression models were used to estimate the relationship between the dietary patterns of parents (835 child-mother-father trios) during pregnancy and the length/height-for-age z-score of their offspring at birth, 3 years and 19 years.
The maternal health-conscious food pattern was found to predict lower child height at 3 years, but not at birth nor at 19 years of age. An increase in the health-conscious pattern score of the maternal diet was associated with significantly lower height-for-age z-score at 3 years; however, the observed effect lost its significance after the adjustment for diet of the child at 3 years.
After full adjustment, the only significant predictors of the height-for-age z-score of the child at 3 years were the heights of both parents and maternal education. More research into the association of maternal diet in pregnancy and height of child is necessary.
We present a combined report on the results of three editions of the Cell Tracking Challenge, an ongoing initiative aimed at promoting the development and objective evaluation of cell segmentation ...and tracking algorithms. With 21 participating algorithms and a data repository consisting of 13 data sets from various microscopy modalities, the challenge displays today's state-of-the-art methodology in the field. We analyzed the challenge results using performance measures for segmentation and tracking that rank all participating methods. We also analyzed the performance of all of the algorithms in terms of biological measures and practical usability. Although some methods scored high in all technical aspects, none obtained fully correct solutions. We found that methods that either take prior information into account using learning strategies or analyze cells in a global spatiotemporal video context performed better than other methods under the segmentation and tracking scenarios included in the challenge.
A
bstract
Dark matter (DM) interacting with the SM fields via a
Z
′-boson (‘
Z
′-portal’) remains one of the most attractive WIMP scenarios, both from the theoretical and the phenomenological points ...of view. In order to avoid the strong constraints from direct detection and dilepton production, it is highly convenient that the
Z
′ has axial coupling to DM and leptophobic couplings to the SM particles, respectively. The latter implies that the associated U(1) coincides with baryon number in the SM sector. In this paper we completely classify the possible anomaly-free leptophobic
Z
′ with minimal dark sector, including the cases where the coupling to DM is axial. The resulting scenario is very predictive and perfectly viable from the present constraints from DM detection, EW observables and LHC data (di-lepton, di-jet and mono-jet production). We analyze all these constraints, obtaining the allowed areas in the parameter space, which generically prefer
m
Z
′
≲ 500 GeV, apart from resonant regions. The best chances to test these viable areas come from future LHC measurements.
Huntington's disease is a fatal neurodegenerative disorder that is caused by CAG-CAA repeat expansion, encoding polyglutamine, in the huntingtin (HTT) gene. Current age-of-clinical-onset prediction ...models for Huntington's disease are based on polyglutamine length and explain only a proportion of the variability in age of onset observed between patients. These length-based assays do not interrogate the underlying genetic variation, because known genetic variants in this region do not alter the protein coding sequence. Given that individuals with identical repeat lengths can present with Huntington's disease decades apart, the search for genetic modifiers of clinical age of onset has become an active area of research.
Results from three independent genetic studies of Huntington's disease have shown that glutamine-encoding CAA variants that interrupt DNA CAG repeat tracts, but do not alter polyglutamine length or polyglutamine homogeneity, are associated with substantial differences in age of onset of Huntington's disease in carriers. A variant that results in the loss of CAA interruption is associated with early onset and is particularly relevant to individuals that carry alleles in the reduced penetrance range (ie, CAG 36–39). Approximately a third of clinically manifesting carriers of reduced penetrance alleles, defined by current diagnostics, carry this variant. Somatic repeat instability, modified by interrupted CAG tracts, is the most probable cause mediating this effect. This relationship is supported by genome-wide screens for disease modifiers, which have revealed the importance of DNA-repair genes in Huntington's disease (ie, FAN1, LIG1, MLH1, MSH3, PMS1, and PMS2).
Focus needs to be placed on refining our understanding of the effect of the loss-of-interruption and duplication-of-interruption variants and other interrupting sequence variants on age of onset, and assessing their effect in disease-relevant brain tissues, as well as in diverse population groups, such as individuals from Africa and Asia. Diagnostic tests should be augmented or updated, since current tests do not assess the underlying DNA sequence variation, especially when assessing individuals that carry alleles in the reduced penetrance range. Future studies should explore somatic repeat instability and DNA repair as new therapeutic targets to modify age of onset in Huntington's disease and in other repeat-mediated disorders. Disease-modifying therapies could potentially be developed by therapeutically targeting these processes. Promising approaches include therapeutically targeting the expanded repeat or directly perturbing key DNA-repair genes (eg, with antisense oligonucleotides or small molecules). Targeting the CAG repeat directly with naphthyridine-azaquinolone, a compound that induces contractions, and altering the expression of MSH3, represent two viable therapeutic strategies. However, as a first step, the capability of such novel therapeutic approaches to delay clinical onset in animal models should be assessed.
Transglutaminase type 2 (TG2) is a ubiquitously expressed member of the transglutaminase family, capable of mediating a transamidation reaction between a variety of protein substrates. TG2 also has a ...unique role as a G-protein with GTPase activity. In response to GDP/GTP binding and increases in intracellular calcium levels, TG2 can undergo a large conformational change that reciprocally modulates the enzymatic activities of TG2. We have generated a TG2 biosensor that allows for quantitative assessment of TG2 conformational changes in live cells using Förster resonance energy transfer (FRET), as measured by fluorescence lifetime imaging microscopy (FLIM). Quantifying FRET efficiency with this biosensor provides a robust assay to quickly measure the effects of cell stress, changes in calcium levels, point mutations and chemical inhibitors on the conformation and localization of TG2 in living cells. The TG2 FRET biosensor was validated using established TG2 conformational point mutants, as well as cell stress events known to elevate intracellular calcium levels. We demonstrate in live cells that inhibitors of TG2 transamidation activity can differentially influence the conformation of the enzyme. The irreversible inhibitor of TG2, NC9, forces the enzyme into an open conformation, whereas the reversible inhibitor CP4d traps TG2 in the closed conformation. Thus, this biosensor provides new mechanistic insights into the action of two TG2 inhibitors and defines two new classes based on ability to alter TG2 conformation in addition to inhibiting transamidation activity. Future applications of this biosensor could be to discover small molecules that specifically alter TG2 conformation to affect GDP/GTP or calcium binding.
PDF
