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40 results for “substrate specificity”
Supplementary data for "Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily"
<p>Supplementary data for "Machine learning-based prediction of activity and substrate specificity for OleA enzymes in the thiolase superfamily"</p>
Computational Studies of Substrate Transport and Specificity in a Phospholipid Flippase
<p>MD trajectories of all-atom and CG simulations of PI4P activated E2P state of the Drs2p-Cdc50p complex.</p>
Data from: Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in the Drosophila mushroom body contributing to olfactory learning
<p><em>O-</em>GlcNAcylation is a dynamic post-translational modification that diversifies the proteome. Its dysregulation is associated with neurological disorders that impair cognitive function, and yet identification of phenotype-relevant candidate substrates in a brain-region-specific manner remains unfeasible. By combining an <em>O-</em>GlcNAc binding activity derived from<em> Clostridium perfringens</em> OGA (<em>Cp</em>OGA) with TurboID proximity labeling in <em>Drosophila</em>, we developed an <em>O-</em>GlcNAcylation profiling tool that translates <em>O-</em>GlcNAc modification into biotin conjugation for tissue-specific candidate substrates enrichment. We mapped the <em>O-</em>GlcNAc interactome in major brain regions of <em>Drosophila</em> and found that components of the translational machinery, particularly ribosomal subunits, were abundantly <em>O-</em>GlcNAcylated in the mushroom body of <em>Drosophila</em> brain. Hypo-<em>O-</em>GlcNAcylation induced by ectopic expression of active <em>Cp</em>OGA in the mushroom body decreased local translational activity, leading to olfactory learning deficits that could be rescued by dMyc overexpression-induced increase of protein synthesis. Our study provides a useful tool for future dissection of tissue-specific functions of <em>O-</em>GlcNAcylation in <em>Drosophila</em> and suggests a possibility that <em>O-</em>GlcNAcylation impacts cognitive function via regulating regional translational activity in the brain.</p>
Data from: Evidence for morph-specific substrate choice in a green-brown polymorphic grasshopper
<p>Orthopteran insects are characterized by high variability in body coloration, in particular featuring a widespread green-brown color polymorphism. The mechanisms that contribute to the maintenance of this apparently balanced polymorphism are not yet understood. To investigate whether morph-dependent microhabitat choice might contribute to the continued coexistence of multiple morphs, we studied substrate choice in the meadow grasshopper <i>Pseudochorthippus parallelus.</i> The meadow grasshopper occurs in multiple discrete, genetically determined color morphs that range from uniform brown to uniform green. We tested whether three common morphs preferentially choose differently colored backgrounds in an experimental arena. We found that a preference for green backgrounds was most pronounced in uniform green morphs. If differential choices improve morph-specific performance in natural habitats via crypsis and/or thermoregulatory benefits, they could help to equalize fitness differences among color morphs and potentially produce frequency-dependent microhabitat competition, though difference appear too small to serve as the only explanation. We also measured the reflectance of the grasshoppers and backgrounds and used visual modelling to quantify the detectability of the different morphs to a range of potential predators. Multiple potential predators, including birds and spiders, are predicted to distinguish between morphs chromatically, while other species, possibly including grasshoppers themselves, will perceive only differences in brightness. Our study provides the first evidence that morph-specific microhabitat choice might be relevant to the maintenance of the green-brown polymorphisms in grasshoppers and shows that visual distinctness of color morphs varies between perceivers.</p>
Data from: Evidence for morph-specific substrate choice in a green-brown polymorphic grasshopper
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Data from: Tissue-specific O-GlcNAcylation profiling identifies substrates in translational machinery in the Drosophila mushroom body contributing to olfactory learning
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The heavy chain 4F2hc modulates the substrate affinity and specificity of the light chains LAT1 and LAT2
<p>Data to Kantipudi S., Jeckelmann J.-M., Ucurum Z., Bosshart P.D. and Fotiadis D. <em>Int. J. Mol. Sci. </em>(2020) <strong>21</strong>, 7573.</p>
datasets for A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range
<p>datasets for A systematic approach to study protein-substrate specificity enables the identification of Ssh1 substrate range</p>
Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C
<p>Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.</p>
Data from: Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. X. Age-specific dynamics of adult epicuticular hyrdocarbon expression in response to different host plants
Analysis of sexual selection and sexual isolation in Drosophila mojavensis and its relatives has revealed a pervasive role of rearing substrates on adult courtship behavior when flies were reared on fermenting cactus in preadult stages. Here, we assessed expression of contact pheromones comprised of epicuticular hydrocarbons (CHCs) from eclosion to 28 days of age in adults from two populations reared on fermenting tissues of two host cacti over the entire life cycle. Flies were never exposed to laboratory food and showed significant reductions in average CHC amounts consistent with CHCs of wild-caught flies. Overall, total hydrocarbon amounts increased from eclosion to 14–18 days, well past age at sexual maturity, and then declined in older flies. Most flies did not survive past 4 weeks. Baja California and mainland populations showed significantly different age-specific CHC profiles where Baja adults showed far less age-specific changes in CHC expression. Adults from populations reared on the host cactus typically used in nature expressed more CHCs than on the alternate host. MANCOVA with age as the covariate for the first six CHC principal components showed extensive differences in CHC composition due to age, population, cactus, sex, and age × population, age × sex, and age × cactus interactions. Thus, understanding variation in CHC composition as adult D. mojavensis age requires information about population and host plant differences, with potential influences on patterns of mate choice, sexual selection, and sexual isolation, and ultimately how these pheromones are expressed in natural populations. Studies of drosophilid aging in the wild are badly needed.
Species of Acantholichen occurring only in the Neotropics show a high degree of endemism (Dal Forno et al. 2016). Of the seven species now recognized in this genus (Table 2), 71.4% (5) are known only from South America. As with Dictyonema, Acantholichen seem to be specific to substrate type and appears in the Andean small forest occurring on mosses in tree bark inhabiting mostly exposed habitats. Cyphellostereum is also represented by a high number of species restricted to the Neotropics [6 (66.6%)], while one is known only from North America, one from Southeastern United States and Puerto Rico, and another species is known only from Borneo and Fiji (Table 2). It is probably due to their unusual appearance that these lichens are getting confused with free-living cyanobacteria colonies, and that there are still undescribed species in the Neotropics. in Eight new species of lichenized Basidiomycota in the genera Acantholichen, Cyphellostereum and Dictyonema s.str. (Agaricales, Hygrophoraceae) from northern South America
Species of Acantholichen occurring only in the Neotropics show a high degree of endemism (Dal Forno et al. 2016). Of the seven species now recognized in this genus (Table 2), 71.4% (5) are known only from South America. As with Dictyonema, Acantholichen seem to be specific to substrate type and appears in the Andean small forest occurring on mosses in tree bark inhabiting mostly exposed habitats. Cyphellostereum is also represented by a high number of species restricted to the Neotropics [6 (66.6%)], while one is known only from North America, one from Southeastern United States and Puerto Rico, and another species is known only from Borneo and Fiji (Table 2). It is probably due to their unusual appearance that these lichens are getting confused with free-living cyanobacteria colonies, and that there are still undescribed species in the Neotropics.
Input data for "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses"
<p>Topologies, coordinates, input and analysis scripts for Amber20 simulations performed in "Characterisation of the mechanism of Bile Salt Hydrolase substrate specificity by experimental and computational analyses", Structure, 2023</p>
Data from: Premating isolation is determined by larval rearing substrates in cactophilic Drosophila mojavensis. X. Age-specific dynamics of adult epicuticular hyrdocarbon expression in response to different host plants
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Partitioning of Catechol Derivatives in Lipid Membranes: Implications for Substrate Specificity to Catechol-O-methyltransferase
<p>The data used for publication "Partitioning of Catechol Derivatives in Lipid Membranes: Implications for Substrate Specificity to Catechol-<em>O</em>-methyltransferase" in ACS Chemical Neuroscience (2020), 11(6), 969-978.</p>
Data from: The evolution of fungal substrate specificity in a widespread group of crustose lichens
Lichens exhibit varying degrees of specialization with regard to the surfaces they colonize, ranging from substrate generalists to strict substrate specialists. Though long recognized, the causes and consequences of substrate specialization are poorly known. Using a phylogeny of a 150-200 MYA clade of lichen fungi, we asked whether substrate niche is phylogenetically conserved, which substrates are ancestral, whether specialists arise from generalists or vice versa, and how specialization affects speciation/extinction processes. We found strong phylogenetic signal for niche conservatism. Specialists evolved into generalists and back again, but transitions from generalism to specialism were more common than the reverse. Our models suggest that for this group of fungi, "escape" from specialization for soil, rock and bark occurred, but specialization for wood foreclosed evolution away from that substrate type. In parallel, speciation models showed positive diversification rates for soil and rock dwellers but not other specialists. Patterns in the studied group suggest that fungal substrate specificity is a key determinant of evolutionary trajectory for the entire lichen symbiosis.
Data from: Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli
Evolutionary adaptation to a constant environment is often accompanied by specialization and a reduction of fitness in other environments. We assayed the ability of the Lenski Escherichia coli populations to grow on a range of carbon sources after 50,000 generations of adaptation on glucose. Using direct measurements of growth rates, we demonstrated that declines in performance were much less widespread than suggested by previous results from Biolog assays of cellular respiration. Surprisingly, there were many performance increases on a variety of substrates. In addition to the now famous example of citrate, we observed several other novel gains of function for organic acids that the ancestral strain only marginally utilized. Quantitative growth data also showed that strains with higher mutation rate exhibited significantly more declines, suggesting that most metabolic erosion was driven by mutation accumulation and not by physiological tradeoffs. These reductions in growth by mutator strains were ameliorated by growth at lower temperature, consistent with the hypothesis that this metabolic erosion is largely caused by destabilizing mutations to the associated enzymes. We further hypothesized that reductions in growth rate would be greatest for substrates used most differently from glucose, and we used flux balance analysis to formulate this question quantitatively. To our surprise, we found no significant relationship between decreases in growth and dissimilarity to glucose metabolism. Taken as a whole, these data suggest that in a single resource environment, specialization does not mainly result as an inevitable consequence of adaptive tradeoffs, but rather due to the gradual accumulation of disabling mutations in unused portions of the genome.
Data from: The evolution of fungal substrate specificity in a widespread group of crustose lichens
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Data from: Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli
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Novel Non-catalytic Substrate-selective p38α-specific MAPK Inhibitors with Endothelial-Stabilizing and Anti-inflammatory Activity
GEO Series GSE93330. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
RNA-seq reveals that Air1 and Air2 control TRAMP substrate specificity for nuclear RNA surveillance
GEO Series GSE42231. Saccharomyces cerevisiae. 8 samples. Type: Expression profiling by high throughput sequencing.
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