Favorable and unfavorable amino acid residues in water-soluble and transmembrane proteins

Abstract

We analyzed the amino acid residues present in the water-soluble and transmembrane proteins of 6 thermophilic and 6 mesophilic species of the domains Archaea and Eubacteria, and characterized them as favorable or unfavorable. The characterization was performed by comparing the observed number of each amino acid residue to the expected number calculated from the percentage of nucleotides present in each gene. Amino acids that were more or less abundant than expected were considered as favorable or unfavorable, respectively. Comparisons of amino acid compositions indicated that the water-soluble proteins were rich in charged residues such as Glu, Asp, Lys, and His, whereas hydrophobic residues such as Trp, Phe, and Leu were abundant in transmembrane proteins. Interestingly, our results found that although the Trp residue was abundant in transmembrane proteins, it was not defined as favorable by our calculations, indicating that increased numbers of a particular amino acid does not necessary indicate it is a favorable residue. Amino acids with high G + C content such as Ala, Gly, and Pro were frequently observed as favorable in species with low G + C content. Comparatively, amino acids with low G + C content such as Phe, Tyr, Lys, Ile, and Met were frequently observed as favorable in species with high G + C content. These are the examples to increase the supply of amino acids than expected. Amino acids with neutral G + C content, i.e., Glu and Asp were favorable in water-soluble proteins from all species analyzed, and Cys was unfavorable both in water-soluble and transmembrane proteins. These results indicate that amino acid compositions are essentially determined by the nucleotide sequence of the genes, and the amino acid content is altered by a deviation from expectation.

Differences in Amino Acid Composition between <i>α</i> and <i>β</i> Structural Classes of Proteins

“…This result indicated that the increase or decrease of Ala content is compensated by the decrease or increase of Ile, and their contents were adjusted in the species with different G + C content. The variation in Ala and Ile contents was consistent with previous reports [25]- [29], which indicated that amino acids composed of G + C-rich or A + T-rich codons are related to the genomic G + C content of the species. The differences in the surface composition of α proteins are shown in Figure 5.…”

Principal Components of Genetic Sequences: Correlations and Significance

“…В литературе, посвященной гену SLC9A1, несмотря на огромное количество публикаций, ничего похожего найти не удалось. Однако обнаружилось несколько ранних работ, оставшихся практически неизвестными из-за крайне низкой цитируемости, в которых на других генах найдена статистическая связь между повышенным содержанием тимина в нуклеотидных последовательностях, пониженным, соответственно, аденина, и гидрофобностью / "трансмембранностью" кодируемых ими белков [38][39][40][41]. Весьма вероятно, что закономерность имеет более общий характер и заслуживает большего внимания.…”