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934 results for “Amino acids”
Supplementary data for structure-conditioned amino-acid couplings
<p>This dataset contains supplementary data for the work "Structure-conditioned amino-acid couplings: how contact geometry affects pairwise sequence preferences" and includes two files: a spreadsheet listing the CASP models used for structure evaluation and an archived directory containing the structure and energy files that make up "DB200K", the main dataset of interaction motifs and their structure-conditioned energies used in the published work.</p> <p>The spreadsheet, "CASP-models.xlsx", lists the CASP round (9, 10, etc.), target name, model ID, and GDT_TS score for each model included in the structure evaluation experiment (see Fig. 7 in the published work). All information was collected from the CASP website, predictioncenter.org. See the "CASP model evaluation" section in the Methods section of the published work for more information.</p> <p>The archived directory, "DB200K.tar.gz", contains the structures and structure-conditioned energies of 200,002 inter-residue contact motifs. Each motif has a structure and set of structure-conditioned energies for each of the three motif sizes considered in the published work: 1x1, 3x3, and 5x5. For each motif of each size, there are two corresponding files, both indexed by the motif size, PDB ID, and position pair (chain and residue numbers according to the PDB file). One file is a PDB file containing the motif's structure and the other is a text-based file listing the 400 structure-conditioned energies of the motif's interacting residue pair. Each of the 400 energies is indexed by the pair of three-letter amino-acid codes it corresponds to. The residue positions in the PDB file match those listed in the energy file. For details on how this database's contacts were selected, see the "Contact database creation" section in the Methods section of the published work; for details on how these energies were computed, see the "Structure-conditioned potentials" section.</p>
The Surface Composition of Amino Acid - Halide Salt Solutions is pH-Dependent
<p>Set of raw data which has been used for the publication. In short, it's about how the pH of a mixed solution of an amino acid and an inorganic halogen salt impacts the surface propensity of the inorganic ions.</p>
Amino acid sequences of RWP-RK domain containing proteins used for the construction of phylogenetic tree shown in Fig. 1
<p><span>The RWP-RK protein family is a group</span><span> of transcription factors containing </span><span>the RWP-RK DNA-binding domain. The RWP-RK DNA-binding domain is an ancient motif that emerged before the establishment of the Viridiplantae (green plants), which consist of green algae and land plants. This domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which</span><span> </span><span>are seemingly unrelated phenomena but possible interdependent processes</span><span> </span><span>in autotrophs. Consistent with</span><span> related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Therefore, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge about the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and </span><span>procurement</span><span> of sophisticated mechanisms for adaptation to the terrestrial environment.</span></p>
Oxidation of L-leucine amino acid initiated by HO● radical - Are transition metal ions an enhancement factor?
<p class="MsoNormal"><span><span>Hydroxyl radical (HO<sup>●</sup>) formation initiated by the Fenton-type reactions of Fe and Cu complexes of L-leucine (Leu) amino acid, as well as its oxidation reaction by HO<sup>●</sup> were computationally investigated by using the density functional theory (DFT) method at the M05-2X/6-311++G(3df,2pd)//M05-2X/6-311++G(d,p) level of theory in the aqueous phase. The results showed that dipole-salt is the main form of Leu in the physiological condition. Leu exhibits high chelating potential towards both Fe(III)/Fe(II) and Cu(II)/Cu(I) ions with the most favorable coordinating positions at two oxygen atoms of the –COO functional groups. Furthermore, the Leu-ions complexes show a high risk of HO<sup>●</sup> formation <em><span>via</span></em> Fenton-like reactions, especially when ascorbate anion exists in the environment as a reducing agent. Finally, the oxidation reaction of L-leucine by HO<sup>●</sup> demonstrated a relatively high overall apparent reaction rate – </span><em><span>k<sub>overall</sub></span></em><span><span> being 1.18 × 10<sup>9</sup> M<sup>-1</sup>s<sup>-1</sup>,</span><span> </span><span>in which</span><span> </span><span>formal hydrogen transfer (FHT) reactions of the dipole-salt form occur as the primary mechanism. Consequently, the Leu oxidation by HO<sup>●</sup> radical can be promoted by the Fenton-reaction enhancement of its transition metal complexes.</span></span></span></p>
Concatenated amino acid (AA) phylogenetic dataset of nuclear gene orthologs for Ephydroidea (Diptera)
<p>The schizophoran superfamily Ephydroidea (Diptera: Cyclorrhapha) includes eight families, ranging from the well-known vinegar flies (Drosophilidae) and shore flies (Ephydridae), to several small, relatively unusual groups, the phylogenetic placement of which has been particularly challenging for systematists. Extraordinary diversity in life histories, feeding habits, and morphology are hallmarks of fly biology, and the Ephydroidea are no exception. Extreme specialization can lead to "orphaned" taxa with no clear evidence for their phylogenetic position. To resolve relationships among a diverse sample of Ephydroidea, including the highly modified flies in the families Braulidae and Mormotomyiidae, we conducted phylogenomic sampling. Using exon capture from Anchored Hybrid Enrichment and transcriptomics to obtain 320 orthologous nuclear genes sampled for 32 species of Ephydroidea and 11 outgroups, we evaluate a new phylogenetic hypothesis for representatives of the superfamily. These data strongly support monophyly of Ephydroidea with Ephydridae as an early branching radiation and the placement of Mormotomyiidae as a family-level lineage sister to all remaining families. We confirm the placement of Cryptochetidae as a sister taxon to a large clade containing both Drosophilidae and Braulidae – the latter a family of honeybee ectoparasites. Our results reaffirm that sampling of both taxa and characters is critical in hyperdiverse clades and that these factors have a major influence on phylogenomic reconstruction of the history of the schizophoran fly radiation.</p>
Data from: Dietary plasticity and broad North Atlantic origins inferred from bulk and amino acid-specific δ15N and δ13C favor killer whale range expansions into Arctic waters
<p>Killer whales (<em>Orcinus orca</em>) occur seasonally in the eastern Canadian Arctic (ECA), where their range expansion associated with declining sea ice have raised questions about the impacts of increasing killer whale predation pressure on Arctic-endemic prey. We assessed diet and distribution of ECA killer whales using bulk and compound specific stable isotope analysis (CSIA) of amino acids (AA) of 54 skin biopsies collected from 2009-2020 around Baffin Island, Canada. Bulk ECA killer whale skin δ15N and δ13C values did not overlap with potential Arctic prey after adjustment for trophic discrimination, and instead reflected foraging history in the North Atlantic prior to their arrival in the ECA. Adjusted killer whale stable isotope (SI) values primarily overlapped with several species of North Atlantic baleen whales or tuna. Amino acid (AA)-specific δ15N values indicated the ECA killer whales fed primarily on marine mammals, having similar glutamic acid δ15N – phenylalanine δ15N (δ15NGlx-Phe) and threonine δ15N (δ15NThr) as mammal-eating killer whales from the eastern North Pacific (ENP) that served as a comparative framework. However, one ECA whale grouped with the fish-eating ENP ecotype based δ15NThr. Distinctive essential AA δ13C of ECA killer whale groups, along with bulk SI similarity to killer whales from different regions of the North Atlantic, indicate different populations converge in Arctic waters from a broad source area. Generalist diet and long-distance dispersal capacity favor range expansions, and integration of these insights will be critical for assessing ecological impacts of increasing killer whale predation pressure on Arctic-endemic species.</p>
Files for MD simulation of adsorption of amino acids onto the PVC surface
<p>Input files, parameter files and forcefield parameters for 50 ns MD simulation of AA acid adsorption onto the PVC surface.</p>
Lipid extraction alters amino acid composition and bulk, but not amino acid, carbon and nitrogen isotope values
<p>Rationale: Concerns exist over observed shifts in value and variance of nitrogen isotopes following physicochemical extraction of lipids from organic matter. The mechanisms behind these apparent changes in bulk tissue δ15N values are not fully understood yet have major implications for analytical costs and integrity of data interpretations.</p> <p>Methods: Changes in proximate analysis, amino acid composition, C:N ratios, bulk tissue and amino acid δ13C and δ15N values, and resulting isotope‐based food web metrics were compared between lipid‐intact and lipid‐extracted muscle tissue of fishes spanning <1% to >20% muscle fat content to identify mechanisms of nitrogen isotope fractionation associated with physicochemical lipid extraction.</p> <p>Results: Bulk δ13C and δ15N values increased and %N, C:N ratios and crude protein content decreased following lipid extraction. Resulting bulk isotope niche spacing and overlap varied significantly between lipid‐intact and lipid‐extracted tissues. While amino acid composition significantly changed during lipid extraction, particularly for lipid‐associated amino acids (e.g., Glu, Lys, Ser), individual amino acid δ13C and δ15N values, and their associated compound‐specific isotope analysis of amino acids (CSIA‐AA)‐based food web metrics, did not.</p> <p>Conclusions: Physicochemical lipid extraction caused significant tissue composition changes (e.g., leaching of amino acids and 15N‐deplete nitrogenous waste) that affected δ13C and δ15N values and tissue %C and %N beyond simply removing lipids. However, lipid extraction did not alter individual amino acid δ13C or δ15N values or their associated CSIA‐AA‐based food web metrics.</p>
Does the processing of black soldier fly larvae meal affect the amino acid solubility in Atlantic salmon (Salmo salar)?
Open the record for dataset details and reuse information.
Amino acid sequences of the proteins predicted from the whole genome of hilsa shad (Tenualosa ilisha) of the Bay of Bengal
<p>Gene prediction was performed by AUGUSTUS (Stanke et al., 2006) from the whole genome sequence of <em>T. ilisha</em> (<a href="https://www.ncbi.nlm.nih.gov/bioproject/400122">PRJNA400122</a>). The data contain amino acid sequences of 37,450 predicted protein coding genes.</p>
A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction - buil and Analysis
<p><strong>Title publication: </strong><em>A Ceramide-Regulated Element in the Late Endosomal Protein LAPTM4B Controls Amino Acid Transporter Interaction</em></p> <p><strong><strong>Year publication:</strong></strong><strong> </strong>2018</p> <p><strong>DOI publication: </strong>10.1021/acscentsci.7b00582</p> <p><strong>Description:</strong> All scripts, jupyter notebooks, and data files used to building and analyzing systems in the presented in the paper. Also related experimental data.</p>
Multilinear regression results for the retention of amino acids of hydrolyzed peptide fractions and their properties - 5%Prolastin
<p>The data set is a part of the PhD thesis of Nattawan Chorhirankul, Wageningen University, The Netherlands.</p>
Data from: Detailed characterization of the UMAMITs proteins provides insight into their evolution, amino acid transport properties, and role in the plant
<p>Amino acid transporters play a critical role in distributing amino acids within the cell compartments and between the plant organs. Despite this importance, relatively few amino acid transporter genes have been characterized and their role elucidated with certainty. Two main families of proteins encode amino acid transporters in plants: the Amino Acid-Polyamine-Organocation superfamily, containing mostly importers, and the Usually Multiple Acids Move In and out Transporter family, apparently encoding exporters, totaling 63 and 44 genes in Arabidopsis, respectively. Knowledge on UMAMITs is scarce, based on six Arabidopsis genes and a handful of genes from other species. To get insight into the role of the members of this family and provide data to be used for future characterization, we studied the evolution of the UMAMITs in plants, and determined the functional properties, the structure, and the localization of the 47 Arabidopsis UMAMITs. Our analysis showed that the AtUMAMITs are essentially localized at the tonoplast or the plasma membrane, and that most of them are able to export amino acids from the cytosol, confirming a role in intra- and inter-cellular amino acid transport. As an example, this set of data was used to hypothesize the role of a few AtUMAMITs in the plant and the cell.</p>
Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state.
<p>Initial coordinates, molecular dynamics trajectories and representative snapshots resulting from the study "Structural determinants of ligands recognition by the human mitochondrial basic amino acids transporter SLC25A29. Insights from molecular dynamics simulations of the c-state." by Pasquadibisceglie and Polticelli.</p> <p>The MD folders contain the parameter/topology (parm7) and initial coordinates (rst7) for the molecular dynamics simulations. Moreover, a NetCDF trajectory "prod.nc" of the production phase is also included.<br> In detail:<br> - MD0 -> SLC25A29 in absence of ligands;<br> - MD1, MD3, MD4 -> SLC25A29-ARG complex;<br> - MD1-LYS, MD3-LYS, MD4-LYS -> SLC25A29-LYS complex.</p> <p>The folder PDB_figures contains the PDB files used to produce the figures presented in the manuscript.</p>
Seasonal dynamics of sinking organic matter in the Pacific Arctic Ocean revealed by nitrogen isotope ratios of amino acids
<p><span>The Pacific Arctic Ocean has experienced a rapidly changing climate, sea-ice retreat, and enhanced primary production over the past few decades. The export production generated by photoautotrophs and heterotrophs has been characterized in the Arctic Ocean, but their seasonal variations in relative proportion are largely unknown due to the limited access in the ice-covered season. We measured the concentration and nitrogen isotope ratio of individual amino acids from sinking particles in the northern east Siberian Sea (KAMS1), northern Chukchi Sea (KAMS2), and Northwind Ridge (KAMS4) from August 2017 to July 2019. </span><span>The average trophic position, based on differences in the nitrogen isotope ratios of glutamic acid and phenylalanine, can indicate the relative proportions of biogenic organic matters derived from photoautotrophs and heterotrophs in sinking particles. Decreasing values (close to 1.0) in summer at KAMS2 in 2018 suggest that primary producers are responsible for most of the downward flux of sinking particles. However, the average trophic position at KAMS1 in 2017 increased to > 1.5 in autumn and was maintained at approximately 1.7 during ice-covered winter periods, likely due to greater contributions from heterotrophic organisms. Exceptionally high average trophic positions (close to 2.0) of sinking particles in summer at KAMS1 in 2017 and KAMS4 in 2018 were likely due to small export of photoautotrophs due to the surface seawater stratification and limited pelagic production. </span><span>T</span><span>he average trophic position in sinking particles should reflect the spatiotemporal variation in export particle composition in the </span><span>Pacific Arctic Ocean</span><span>.</span></p>
Data for: Epistatic effects between amino acid insertions and substitutions mediate toxin-resistance of vertebrate Na+, K+-ATPases
<p>The recurrent evolution of resistance to cardiotonic steroids (CTS) across diverse animals most frequently involves convergent amino-acid substitutions in the H1-H2 extracellular loop of Na<sub>+</sub>, K<sub>+</sub>-ATPase (NKA). Previous work revealed that hystricognath rodents (e.g. chinchilla) and pterocliform birds (sandgrouse) have convergently evolved amino-acid insertions in the H1-H2 loop, but their functional significance was not known. Using protein engineering, we show that these insertions have distinct effects on CTS resistance in homologs of each of the two species that strongly depend on intramolecular interactions with other residues. Removing the insertion in the chinchilla NKA unexpectedly increases CTS resistance and decreases NKA activity. In the sandgrouse NKA, the amino acid insertion and substitution Q111R both contribute to an augmented CTS resistance without compromising ATPase activity levels. Molecular docking simulations provide additional insight into the biophysical mechanisms responsible for the context-specific mutational effects on CTS insensitivity of the enzyme. Our results highlight the diversity of genetic substrates that underlie CTS insensitivity in vertebrate NKA and reveal how amino-acid insertions can alter the phenotypic effects of point mutations at key sites in the same protein domain.</p>
Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis
<p>Raw data set for npj Bioflims and Microbiome article: “Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis”</p>
dSTORM imaging of Streptococcus pneumoniae using fluorescent d-amino acids
<p>Please see more details in the readme file.</p>
Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence
<p>Dataset for paper: Z. Qin, L. Wu, H. Sun, S. Huo, T. Ma, E. Lim, P.-Y. Chen, B. Marelli, M.J. Buehler, Artificial intelligence method to design and fold alpha-helical structural proteins from the primary amino acid sequence, Extreme Mechanics Letters, Vol. 36, 100652, 2020. <a href="https://doi.org/10.1016/j.eml.2020.100652">https://doi.org/10.1016/j.eml.2020.100652</a>.</p> <p>Code: https://github.com/lamm-mit/MNNN/ </p>
Supporting isotopic data for: Amino acid isotope analysis reveals variation in gut microbial contribution to host protein metabolism in a wild small mammal community
<p>Herbivory is a dominant feeding strategy among animals, yet herbivores are often protein limited. The gut microbiome is hypothesized to help maintain host protein balance by provisioning essential macromolecules, but this has never been tested in wild consumers. Using amino acid carbon (δ<sup>13</sup>C) and nitrogen (δ<sup>15</sup>N) isotope analysis, we estimated the proportional contributions of essential amino acids (AA<sub>ESS</sub>) synthesized by gut microbes to five co-occurring desert rodents representing herbivorous, omnivorous, and insectivorous functional groups. We found that herbivorous rodents occupying lower trophic positions (<em>Dipodomys </em>spp.) routed a substantial proportion (~40–50%) of their AA<sub>ESS</sub> from gut microbes, while higher trophic level omnivores (<em>Peromyscus </em>spp.) and insectivores (<em>Onychomys arenicola</em>) obtained most of their AA<sub>ESS</sub> (~58%) from plant-based energy channels but still received ~20% of their AA<sub>ESS</sub> from gut microbes. These findings empirically demonstrate that gut microbes play a key functional role in host protein metabolism in wild animals. </p>
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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.