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Sequence conservation and structural features that are common within TRP channels

Citation

Cabezas-Bratesco, Deny et al. (2022), Sequence conservation and structural features that are common within TRP channels, Dryad, Dataset, https://doi.org/10.5061/dryad.k6djh9w75

Abstract

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.

Methods

Please see Materials and Methods in published paper.

Usage Notes

Amino_acid_sequences_fig1.fasta contains the sequences aligned in Amino_acid_alignment_Fig1_FFT-NS-i.fasta, used for generation of the phylogenetic reconstruction depicted in Figure 1. Phylogenetic reconstruction parameters are detailed in Tree_file_fig1.treefile. 

Amino_acid_sequences_Fig1_FigSupl1.fasta contains the sequences aligned in Amino_acid_alignment_Fig1_FigSupl1_FFT-NS-i.fasta, used for generation of the phylogenetic reconstruction depicted in Figure 1 supplement 1. Phylogenetic reconstruction parameters are detailed in Tree_file_Fig1_FigSupl1.treefile. 

Supplementary_TableS1.xlsx contains the data of the sequences used in Figure 1, and Figure 1 supplement 1.

Primary MSA.fasta is the massive sequences alignment, containing the final set of sequences used for the analysis of highly conserved features described on the manuscript (Fig.2 to 6).

Funding

Fondo Nacional de Desarrollo Científico y Tecnológico from Chile, Award: FONDECYT 1191868

Fondo Nacional de Desarrollo Científico y Tecnológico from Chile, Award: FONDECYT 1210471

ANID-Millennium Science Initiative Program, Award: NC160011