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10 results for “TRP channel”
Role of TRP channels in dinoflagellate mechanotransduction
<p>This repository contains several files associated with the publication:</p> <p><strong>Transcriptome:</strong> <em>Lingulodinium polyedra </em>transcriptome assembled from 100 bp paired-end Illumina RNA sequences available at http://www.ebi.ac.uk/ (run accession SRR1184657) using the assembly and annotation pipeline “MakeMyTranscriptome” (https://github.com/bluegenes/MakeMyTranscriptome), which leverages the Trinity <em>de novo</em> assembler (v2.1.1; Grabherr 2011). The transcriptome contains 183,451 transcripts, with an N50 of 1161, and 66.5% GC (guanine-cytosine) content. Annotation-based assessment using BUSCO showed that this transcriptome contained 62% of eukaryotic genes predicted to be present in all eukaryotic assemblies. Open reading frames (ORFs) predicted using transDecoder are also provided as a second file (ends with .pep).</p> <p><strong>TRP-like polypeptide sequences: </strong>Transient Potential Receptor (TRP)-like polypeptide sequences identified in transcriptomic data from the dinoflagellate <em>Lingulodinium polyedra</em>.</p> <p><strong>Video: </strong>Video of luminescence from the dinoflagellate <em>Lingulodinium polyedra</em> in response to capsaicin treatment. Samples consisted of 1 ml volumes of <em>L. polyedra</em> culture containing approximately 7000 cells, kept in two separate glass vials. The injection of 0.1 ml volumes of control solution (left vial) and capsaicin (30 µM final concentration, right vial) at a rate of 1ml min<sup>-1</sup> caused some light response due to stimulation of cells by the fluid addition. However, following fluid addition the capsaicin treatment clearly stimulated luminescence in the <em>L. polyedra</em> cells, seen as individual sources of light, while the cells in the control treatment produced essentially no light.</p>
Underlying data for "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms"
<p><strong>Output Files from Structural Alignment of TRP Channels</strong><br> The archive contains the key output files resulting from the structural alignment of members of the TRP channel family described in "Global alignment and assessment of TRP channel transmembrane domain structures to explore functional mechanisms", Huffer et al., (2020), eLife.</p> <p><strong>Contents of trp_struct_align_outputs.tar.gz</strong><br> <em>Aligned_structures</em><br> For each alignment where the transmembrane (TM) domain of the mobile structure was aligned to the TM domain of the stationary/reference structure (6co7):<br> 1) mobile_stationary_full_align.pdb: aligned based on Fr-TM-Align output matrix, contains all residues<br> 2) mobile_stationary_tmem_align.pdb: aligned based on Fr-TM-Align output matrix, contains only TM residues used for alignment<br> 3) mobile_stationary_hole.pdb: aligned based on Fr-TM-Align output matrix, contains HOLE profile of mobile structure</p> <p><em>Alignments</em><br> Multiple sequence alignments constructed using the TM domain of each structure as the stationary/reference structure, with all other structures aligned pairwise.<br> 1) stationary_full.ali: Full multiple sequence alignment containing all TM residues from all stationary and mobile structures.<br> 2) stationary_nogap.ali: Multiple sequence alignment containing all TM residues from the stationary structure. Any gaps in the stationary structure removed, which removes any residue in any mobile structure that does not align to the stationary/reference structure.</p> <p><em>Fr-TM-Align_outputs</em><br> - frtmalign_output.csv: contains all information from Fr-TM-Align output files for each pairwise alignment of TM domains, including PDB IDs of mobile and stationary structures, lengths of mobile and stationary structures, length of pairwise alignment sequence, RMSD of alignment, TM-score of alignment, and sequence identity of alignment.<br> - aligned_length.csv, RMSD.csv, sequence_identity.csv, and TM_score.csv: csv files containing the specified values for all pairwise alignments of TM domains, with the mobile structure in rows and stationary structure in columns</p> <p><strong>Reproducibility</strong><br> Code to reproduce this alignment and analysis is available on GitHub at: <a href="https://github.com/kehuffer/TRP_Structural_Alignment">https://github.com/kehuffer/TRP_Structural_Alignment</a></p>
Sequence conservation and structural features that are common within TRP channels
<p class="MsoNormal"><span>TRP proteins are a large family of cation-selective channels, surpassed in variety only by voltage-gated potassium channels. Detailed molecular mechanisms governing how membrane voltage, ligand binding, or temperature can induce conformational changes promoting the open state in TRP channels are still a matter of debate. Aiming to unveil distinctive structural features common to the transmembrane domains within the TRP family, we performed phylogenetic reconstruction, sequence statistics, and structural analysis over a large set of TRP channel genes. Here we report an exceptionally conserved set of residues. This fingerprint is composed of twelve residues localized at equivalent three-dimensional positions in TRP channels from the different subtypes. Moreover, these amino acids are arranged in three groups, connected by a set of aromatics located at the core of the transmembrane structure. We hypothesize that differences in the connectivity between these different groups of residues harbors the apparent differences in coupling strategies used by TRP subgroups.</span></p>
Sequence conservation and structural features that are common within TRP channels
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Data from: Diethylcarbamazine elicits calcium signals in HEK293 cells by activation of heterologously expressed <em>Brugia malayi</em> TRP-2b channels
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Data from: Compensatory growth in C. elegans is regulated by a thermosensitive TRP channel and increases reproductive fitness
<p>Animals are often not growing at the maximum rate, but can compensate for a bad start of life by further increasing growth rate. While this compensatory growth is widespread, its direct fitness consequences are seldom investigated and its genetic basis is unknown. We investigated the genetic regulation, as well as fitness and lifespan consequences of compensatory growth in response to temperature, using <i>C. elegans</i> knockout of the thermo-sensitive TRP ion channel TRPA-1, involved in temperature recognition. We exposed juvenile worms to cold, normal or warm temperatures in order to delay or speed up development. After returning to normal temperature, we found that wild-type worms where early development was delayed, expressed compensatory growth and catched up in size, while juvenile exposure to warm temperatures expressed slowed-down growth and small size. Compensatory growth also altered the reproductive schedule towards early reproduction, so that rate-sensitive individual fitness increased even though total reproduction was unaffected. Surprisingly, no lifespan cost of compensatory growth was found. In contrast, juvenile temperature did not induce compensatory or slowed-down growth in the <i>trpa-1</i> knockout mutants, and consequently did not affect fitness. We show that temperature-induced compensatory growth in <i>C. elegans</i> is regulated by the <i>trpa-1</i> and can increase fitness.</p>
Identification of TRP Channels as New Potential Therapeutic Targets in Primary and Secondary Raynaud's Phenomenon.
ClinicalTrials.gov study NCT03211325. IPD Sharing: UNDECIDED. Countries: 1. Publications: 25.
Data from: Compensatory growth in C. elegans is regulated by a thermosensitive TRP channel and increases reproductive fitness
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The Role of TRP Channels in CIPN
ClinicalTrials.gov study NCT04415892. IPD Sharing: NO. Countries: 1. Publications: 0.
The Role of TRP Channels in DPN
ClinicalTrials.gov study NCT07237022. IPD Sharing: Not stated. Countries: 1. Publications: 0.
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