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Proteome-wide comparison between the amino acid composition of domains and linkers.

ABSTRACT: Amino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns.The amino acid composition in the 38 proteomes studied showcase the greater variability found in archaea and bacteria species compared to eukaryotes. When focusing on domains and linkers, we describe the preferential use of polar residues in linkers and hydrophobic residues in domains. To let any user perform this analysis on a given domain (or set of them), we developed a dedicated R script called RACCOON, which can be easily used and can provide interesting insights into the compositional differences between a domain and its surrounding linkers.

SUBMITTER: Brune D

PROVIDER: S-EPMC5807739 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Proteome-wide comparison between the amino acid composition of domains and linkers.

Brüne Daniel D Andrade-Navarro Miguel A MA Mier Pablo P

BMC research notes 20180209 1

<h4>Objective</h4>Amino acid composition is a sequence feature that has been extensively used to characterize proteomes of many species and protein families. Yet the analysis of amino acid composition of protein domains and the linkers connecting them has received less attention. Here, we perform both a comprehensive full-proteome amino acid composition analysis and a similar analysis focusing on domains and linkers, to uncover domain- or linker-specific differential amino acid usage patterns.<h ...[more]

PMID: 29426365

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Project description:This study determined the effect of temperament on antioxidant capacity and the relationship between antioxidant capacity and the contents of amino acids (AA) and fatty acids (FA) in muscle of Hu sheep. Organ and muscle samples of five calm and five nervous Hu sheep were collected to determine the antioxidant capacity and the contents of AA and FA in muscle tissue. The concentrations of malondialdehyde (MDA) and superoxide excretion enzyme (SOD) in muscle and intestinal tissue of calm Hu sheep were lower than those of nervous Hu sheep (p < 0.01), and the activity of glutathione peroxidase (GSH-Px) in liver of calm Hu sheep was significantly higher than that of nervous Hu sheep (p = 0.050). The content of AA of calm Hu sheep was higher than that of nervous Hu sheep, especially the content of reductive amino acids, which was significantly higher than that of nervous Hu sheep (p = 0.029). Fatty acid content of nervous Hu sheep was higher than that of calm type, and saturated fatty acid content was significantly higher than that of calm type (p = 0.001). The SOD content in muscle tissue was positively correlated with the contents of aspartic acid (Asp), alanine (Ala) and lysine (Lys). Catalase (CAT) activity was positively correlated with Ala content. There was a significant positive correlation between total antioxidants (T-AOC) and glutamate (Glu) (p < 0.05). MDA concentration was positively correlated with lauric acid (C12:0), triseconic acid (C13:0), myristic acid (C14:0) content (p < 0.01), and ginkgo acid (C15:0) content. The total antioxidants (T-AOC) was negatively correlated with stearic acid (C18:0) (p < 0.05). Our conclusion is that the antioxidant capacity of calm Hu sheep is superior to that of nervous Hu sheep, which may be due to the higher AA (especially reductive amino acids (Arg, Lys, Ala and Glu)) content in the muscle and the lower FA (especially SFA) content, which improve the antioxidant capacity of the organism and allow for further exploration of the mechanisms by which animal temperament affects antioxidant performance.

Dataset Information

Proteome-wide comparison between the amino acid composition of domains and linkers.

Publications

Proteome-wide comparison between the amino acid composition of domains and linkers.

Similar Datasets

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