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122 results for “structural stability”
FTD-tau S320F mutation stabilizes local structure and allosterically promotes amyloid motif-dependent aggregation
<p>Amyloid deposition of the microtubule-associated protein tau is a unifying theme in a multitude of neurodegenerative diseases. Disease-associated missense mutations in tau are associated with frontotemporal dementia (FTD) and enhance tau aggregation propensity. However, the molecular mechanism of how mutations in tau promote tau assembly into amyloids remains obscure. There is a need to understand how tau folds into pathogenic conformations to cause disease. Here we describe the structural mechanism for how an FTD-tau S320F mutation drives spontaneous aggregation. We use recombinant protein and synthetic peptide systems, computational modeling, cross-linking mass spectrometry, and cell models to investigate the mechanism of spontaneous aggregation of the S320F FTD-tau mutant. We discover that the S320F mutation drives the stabilization of a local hydrophobic cluster which allosterically exposes the <sup>306</sup>VQIVYK<sup>311</sup> amyloid motif. We identify a suppressor mutation that reverses the S320F aggregation phenotype through the reduction of S320F-based hydrophobic clustering <em>in vitro</em> and in cells. Finally, we use structure-based computational design to engineer rapidly aggregating tau sequences by optimizing nonpolar clusters in proximity to the S320 site revealing a new principle governing the regulation of tau aggregation. We uncover a mechanism for regulating aggregation that balances transient nonpolar contacts within local protective structures or in longer-range interactions that sequester amyloid motifs. The introduction of a pathogenic mutation redistributes these transient interactions to drive spontaneous aggregation. We anticipate that more profound knowledge of this process will permit control of tau aggregation into discrete structural polymorphs to aid the design of reagents that can detect disease-specific tau conformations.</p>
Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes"
<p>The dataset contains: DFT and MD Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes". </p> <p> </p> <p> </p>
Data from: Linking environmental stability with genetic diversity and population structure in two Atlantic Forest palm trees
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Data from: Seasonal variations in planktonic food web structure affect stability by shifting the distribution of energy fluxes
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Structural models and Sort-seq data for: Packing of apolar amino acids is not a strong stabilizing force in transmembrane helix dimerization
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Data from: Genetics-based interactions of foundation species affect community diversity, stability, and network structure
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Stage-structured ontogeny in resource populations generates non-additive stabilizing and de-stabilizing forces in populations and communities
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Data for: Spatial structure within root systems moderates stability of Arbuscular Mycorrhizal mutualism and plant-soil feedbacks
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Data from: Climate and local environment structure asynchrony and the stability of primary production in grasslands
<p><b>Aim</b>: Climate variability threatens to destabilize production in many ecosystems. Asynchronous species dynamics may buffer against such variability when decreased performance by some species is offset by increased performance of others. However, high climatic variability can eliminate species through stochastic extinctions or cause similar stress responses among species, reducing buffering. Local conditions, such as soil nutrients, can further alter production stability directly or by influencing asynchrony. We test these hypotheses using a globally distributed sampling experiment.</p> <p><b>Location</b>: Grasslands in North America, Europe and Australia.</p> <p><b>Time period</b>: Annual surveys over five-year intervals occurring between 2007 and 2014.</p> <p><b>Major taxa studied</b>: Herbaceous plants.</p> <p><b>Methods</b>: We annually sampled per-species cover and aboveground community biomass (net primary productivity; NPP), plus soil chemical properties, in twenty-nine grasslands. We tested how soil conditions, combined with precipitation and temperature variability, affect species richness, asynchrony and temporal stability of primary productivity. We used bivariate relationships and structural equation modeling to examine proximate and ultimate relationships.</p> <p><b>Results</b>: Climate variability strongly predicted asynchrony, whereas NPP stability was more related to soil conditions. Species richness was structured by both climate variability and soils, and in turn increased asynchrony. Temperature and precipitation variability caused a unimodal asynchrony response, with asynchrony lowest at low and high climate variability. Climate impacted stability indirectly through its effect on asynchrony, with stability increasing at higher asynchrony due to lower inter-annual NPP variability. Soil conditions had no detectable effect on asynchrony but increased stability by increasing mean NPP, especially when soil organic matter was high.</p> <p><b>Main Conclusions</b>: We found globally consistent evidence that climate modulates species asynchrony, but that the direct effect on stability is low relative to local soil conditions. Nonetheless, our observed unimodal responses to temperature and precipitation variability suggest asynchrony thresholds, beyond which there are detectable destabilizing impacts of climate on primary productivity.</p>
Data from: Across-year social stability shapes network structure in wintering migrant sparrows
Migratory birds often form flocks on their wintering grounds, but important details of social structure such as the patterns of association between individuals are virtually unknown. We analysed networks of co-membership in short-term flocks for wintering golden-crowned sparrows (Zonotrichia atricapilla) across three years and discovered social complexity unsuspected for migratory songbirds. The population was consistently clustered into distinct social communities within a relatively small area (~ 7 ha). Birds returned to the same community across years, with mortality and recruitment leading to some degree of turnover in membership. These spatiotemporal patterns were explained by the combination of space use and social preference – birds that flocked together in one year flocked together again in the subsequent year more often than were expected based on degrees of home range overlap. Our results suggest that a surprising level of social fidelity across years leads to repeatable patterns of social network structure in migratory populations.
Data from: Eighty-five million years of Pacific Ocean gyre ecosystem structure: long-term stability marked by punctuated change
While the history of taxonomic diversification in open ocean lineages of ray-finned fish and elasmobranchs is increasingly known, the evolution of their roles within the open ocean ecosystem remains poorly understood. To assess the relative importance of these groups through time, we measured the accumulation rate of microfossil fish teeth and elasmobranch dermal denticles (ichthyoliths) in deep-sea sediment cores from the North and South Pacific gyres over the past 85 million years (Myr). We find three distinct and stable open ocean ecosystem structures, each defined by the relative and absolute abundance of elasmobranch and ray-finned fish remains. The Cretaceous Ocean (pre-66 Ma) was characterized by abundant elasmobranch denticles, but low abundances of fish teeth. The Palaeogene Ocean (66–20 Ma), initiated by the Cretaceous/Palaeogene mass extinction, had nearly four times the abundance of fish teeth compared with elasmobranch denticles. This Palaeogene Ocean structure remained stable during the Eocene greenhouse (50 Ma) and the Eocene–Oligocene glaciation (34 Ma), despite large changes in the overall accumulation of both groups during those intervals, suggesting that climate change is not a primary driver of ecosystem structure. Dermal denticles virtually disappeared from open ocean ichthyolith assemblages approximately 20 Ma, while fish tooth accumulation increased dramatically in variability, marking the beginning of the Modern Ocean. Together, these results suggest that open ocean fish community structure is stable on long timescales, independent of total production and climate change. The timing of the abrupt transitions between these states suggests that the transitions may be due to interactions with other, non-preserved pelagic consumer groups.
Data from: EB Ford revisited: assessing the long-term stability of wing-spot patterns and population genetic structure of the meadow brown butterfly on the Isles of Scilly
Understanding selection in the wild remains a major aim of evolutionary ecology and work by Ford and colleagues on the meadow brown butterfly Maniola jurtina did much to ignite this agenda. A great deal of their work was conducted during the 1950s on the Isles of Scilly. They documented island-specific wing-spot patterns that remained consistent over about a decade, but patterns on some islands changed after environmental perturbation. It was suggested that these wing-spot patterns reflected island-specific selection and that there was little migration between islands. However, genetic studies to test the underlying assumption of restricted migration are lacking and it is also unknown whether the originally described wing-spot patterns have persisted over time. We therefore collected female butterflies from five of Ford's original study locations, including three large islands (St Mary's, St Martin's and Tresco) and two small islands (Tean and St Helen's). Wing-spot patterns had not changed appreciably over time on three of the islands (two large and one small), but were significantly different on the other two. Furthermore, analysis of 176 amplified fragment length polymorphisms revealed significant genome-wide differentiation among the five islands. Our findings are consistent with Ford's conclusions that despite the close proximity of these islands, there is restricted gene flow among them.
Interactions of the Ionic Liquid [C2C1Im][DCA] with Au(111) Electrodes: Interplay between Ion Adsorption, Electrode Structure and Stability
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Data set of Magnetic stability of magnetite particles with single vortex structure during low temperature oxidation
<p>Data set of Magnetic stability of magnetite particles with single vortex structure during low temperature oxidation</p>
Thriving in the heat – Lysine acetylation stabilizes the quaternary structure of a Mega-Dalton hyperthermoactive PEP-synthase
<p>Over time structural adaptations enabled proteins and enzymes to have sufficient stability and flexibility to perform the basic functions of life under various environmental conditions. The catalytic cores of key metabolic enzymes of hyperthermophilic archaea work at a temperature range of 80-120 °C, similar to the conditions wher the earliest life forms may have thrived. Here we characterize a key enzyme of the central carbon metabolism of <em>Pyrococcus furious</em>, through an integrative approach combining structural mass spectrometry, cryo-electron microscopy, mass photometry and molecular modelling with molecular dynamics simulations. From our investigation, we unveil the structural organization of phosphoenolpyruvate synthase (PPSA). Its 24-meric assembly - weighing over 2 MDa - harbors flexible distal domains, whose proper functioning and coordination depends on widespread chemical acetylation of lysine residues. This non-enzymatic post-translational modification, along with other types of lysine modifications, also occurs on most other major protein complexes of <em>P. furiosus</em>. These modifications likely originated in the chemically favorable primordial conditions and gradually became highly specialized and enzyme-driven in more distantly related mesophiles and Eukaryotes.</p> <p><strong>Molecular dynamics simulations and analysis – </strong>The all-atom structures of the full c1(X4) 24-mer PPSA models, carrying highly acetylated sites at 14 positions (106, 120,185, 187, 427, 466, 492, 496, 557, 574, 641, 726, 737, 805) or unmodified lysines were coarse grained (CG), mapping their atoms to the SIRAH force field (ff), that uses a classical Hamiltonian common to most all-atom potentials to describe particle–particle interactions, and recently extended to support the PTMs most commonly found on proteins(Garay et al., 2020). Both starting structures contained a disulfide bond between Cys42-Cys189 as well as phosphorylation of Thr440. All starting structures, simulation boxes and parameters files used for the minimization, equilibration and production are provided (Supplementary Data 5). Simulation was conducted in GROMACS 2020.4(Hess et al., 2008), for which code can be found here: <a href="https://doi.org/10.5281/zenodo.5636522">https://doi.org/10.5281/zenodo.5636522</a>. The 24-aly system consisted of 94128 CG atoms for the protein representation, solvated with 179271 WT4 CG water beads (Garay et al., 2020). A neutral charge was achieved adding 6617 NaW (Na<sup>+</sup>) and 5633 ClW (Cl<sup>-</sup>), corresponding to a concentration of approximately 150 mM NaCl concentration. The 24-lys system was also prepared accordingly and consisted of 93456 CG atoms for the protein, 186690 WT4 CG water beads and neutralized with 6503 NaW (Na<sup>+</sup>) and 5855 ClW (Cl<sup>-</sup>). Solvation was done using the default radii of 0.105 nm for atoms not present in the VdW database (vdwradii.dat) and then removing the WT4 molecules within 0.3 nm from the solute. In all cases, eventual clashes were relaxed during the solute-restrained energy minimization. Due to the length of the loops connecting the 3 domains, an alternative configuration of the tetramers where the CD-NBD domains are sitting on top of the neighboring PPSA subunit is also possible (see Supplementary Note 1). This was named “alternative” (a) configuration, as opposed to the “original” (o), thus producing 4 starting models: a24-aly, o24-aly, a24-lys and o24-lys (Supplementary Data 5). All these configurations were subjected to a first round of production consisting of 125 ns in duplicate to define the stable configuration for further extension of the simulation time to 500 ns.</p> <p>The main stages of the simulation can be summarized as follows:1) solvent and side-chain relaxation by 2 stages of 20’000 steps of energy minimization, imposing positional restraints of 1000 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the whole protein (stage 1) and only on backbone beads (GN and GO, stage 2); 2) solvent NVT ensemble equilibration with a first stage where the temperature was slowly increased from 303K to 363K in 7 steps of 4 ns each, and a second stage to equilibrate the protein by gradually releasing the positional restraints from 1000 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the backbone beads (GN and GO) to 100 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the C-terminus to compensate for the missing stabilization effect of the Met799-Fe cluster; 3) production simulation of an additional 80 ns in NPT ensemble at 363 K and 1 bar imposing positional restraints of 100 kJ mol<sup>-1</sup> nm<sup>-2 </sup>on the C-terminus. Non-bonded interactions were treated with a 1.2 nm cutoff and PME for long-range electrostatics. An integration time-step of 15 fs was used during MD production runs. The system pressure was controlled by the Parrinello-Rahman barostat (Parrinello and Rahman, 1981) with a coupling time of 4 ps. The positional restraints during the production simulation were necessary to maintain the overall system at the high energy of the particles at 363 K (90 ˚C), the temperature mimicking the near-optimum temperature for PPSA catalytic activity. All simulations were run in duplicate. Although the simulations do not accurately reflect the possible dynamics of the protein in native conditions, the computational challenges of simulating >350000 atoms for the protein only drove us to use a CG representation of the system. To analyze the trajectories, every functional module (tetramer) was extracted from the simulation of the full 24-mer for each replicate, resulting in two sets of 12 independent trajectories (6 for each 24-mer) either with and without acetylated Lysine residues. To produce morphed movies and analyze secondary structure and interfaces, the CG tetramers trajectories were back mapped to atomistic detail using SIRAH tools via VMD. A back mapped atomistic model was produced every 35.7 ns, and subjected to 100 cycles of energy minimization in AMBER, resulting in 14 atomistic models describing each trajectory of a given tetramer over the 500 ns of simulation, further interpolated in ChimeraX using the morph command to produce the atomistic representation of the dynamics (Supplementary Data 5). RMSD calculation and trajectory analysis were done with the MDanalysis suite(Michaud-Agrawal et al., 2011).</p> <p>Each probability density in Figure 5B and 5C is calculated over two independent coarse-grained molecular dynamics simulations of the last 250 ns of production of the PPSA 24-mer in the acetylated and non-acetylated form, using a snapshot frequency of 5 ns. In Figure 5B, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) of the NBD region (residues 1-365) in the tetramer form was calculated with respect to their conformation in the tetramer PPSA resting state. The six trajectories of all six tetramers included in the simulated PPSA complex, resulting in 3 μs ([250ns*6]*2) of accumulated tetramer simulation, were used in the probability density calculation. In Figure 5C, the RMSD of the Cα atoms (equivalent to backbone GC beads in CG MD) was calculated over the CD (residues 379-481) and PBD (residues 510-790) regions with respect to the modelled CD-PBD state of PPSA in the monomer form. All 24 PPSA monomers of which the simulated PPSA complex was composed were included in the probability density calculation, resulting in 12 μs ([250ns*24]*2) of accumulated PPSA monomer simulation.</p> <p> </p>
Data from: Ecosystem engineers shape ecological network structure and stability: a framework and literature review
<p>Ecosystem engineering is a ubiquitous process where species influence the physical environment and thereby structure ecological communities. However, there has been little effort to synthesise or predict how ecosystem engineering may impact the structure and stability of interaction networks. To assess the current scientific understanding of ecosystem engineering impacts via habitat forming, habitat modification, and bioturbation on interaction networks/food webs, we reviewed the literature covering marine, freshwater, and terrestrial food webs, plant-pollinator networks, and theory. We provide a conceptual framework and identify three major pathways of engineering impact on networks through changes in resource availability and energy flow, habitat heterogeneity, and environmental filtering. These three processes often work in concert and most studies report that engineering increases species richness. This is particularly marked for engineers that increase habitat heterogeneity and thereby the number of available niches. The response of network structure to ecosystem engineering varies, however some patterns emerge from this review. Engineered habitat heterogeneity leads to a higher number of links between species in the networks and increases link density. Connectance can be negatively or positively affected by ecosystem engineer impact, depending on the engineering pathway and the engineer impact of species richness. We discuss how ecosystem engineers can stabilize or destabilize communities through the changes in niche space, diversity, network structure, and the dependency on the engineering impact. Theory and empirical evidence need to inform each other to better integrate ecosystem engineering and ecological networks. A mechanistic understanding how ecosystem engineering traits shape interactions networks and their stability will be important to predict species extinctions and can provide crucial information for conservation and ecosystem restoration.</p>
Research Data for "Evaluating the electronic structure and stability of epitaxially grown Sr-doped LaFeO3 perovskite alkaline O2 evolution model electrocatalysts"
<p>This is the research data supporting figures and tables for the paper "Evaluating the electronic structure and stability of epitaxially grown Sr-doped LaFeO3 perovskite alkaline O2 evolution model electrocatalysts" appearing in <em>RSC Applied Interfaces </em>under DOI <a title="Link to landing page via DOI" href="https://doi.org/10.1039/D4LF00260A">https://doi.org/10.1039/D4LF00260A</a>.</p>
Research Data for "Electronic structure and stability of the active surface phase of NixCo3-xO4 spinel alkaline O2 evolution electrocatalysts: from an epitaxial model catalyst perspective"
<p>These datasets support main text and supplementary figures and tables of the paper "Electronic structure and stability of the active surface phase of NixCo3-xO4 spinel alkaline O2 evolution electrocatalysts: from an epitaxial model catalyst perspective" appearing in <em>ACS Applied Energy Materials </em>under DOI: <a href="https://doi.org/10.1021/acsaem.4c01688">https://doi.org/10.1021/acsaem.4c01688 </a></p>
VASP data for Structure and Stability of Copper Nanoclusters on Monolayer Tungsten Dichalcogenides
<p>VASP INCAR and CONTCAR files</p>
Data from: Limited gene dispersal and spatial genetic structure as stabilizing factors in an ant-plant mutualism
Comparative studies of the population genetics of closely associated species are necessary to properly understand the evolution of these relationships because gene flow between populations affects the partners' evolutionary potential at the local scale. As a consequence (at least for antagonistic interactions), asymmetries in the strength of the genetic structures of the partner populations can result in one partner having a co-evolutionary advantage. Here, we assess the population genetic structure of partners engaged in a species-specific and obligatory mutualism: the Neotropical ant-plant, Hirtella physophora, and its ant associate, Allomerus decemarticulatus. Although the ant cannot complete its life cycle elsewhere than on H. physophora and the plant cannot live for long without the protection provided by A. decemarticulatus, these species also have antagonistic interactions: the ants have been shown to benefit from castrating their host plant and the plant is able to retaliate against too virulent ant colonies. We found similar short dispersal distances for both partners, resulting in the local transmission of the association and, thus, inbred populations in which too virulent castrating ants face the risk of local extinction due to the absence of H. physophora offspring. On the other hand, we show that the plant populations probably experienced greater gene flow than did the ant populations, thus enhancing the evolutionary potential of the plants. We conclude that such levels of spatial structure in the partners' populations can increase the stability of the mutualistic relationship. Indeed, the local transmission of the association enables partial alignments of the partners' interests, and population connectivity allows the plant retaliation mechanisms to be locally adapted to the castration behaviour of their symbionts.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.