Abstract
The amino acid composition of α and β structural class of proteins from five species, Escherichia coli, Thermotoga maritima, Thermus thermophilus, yeast, and humans were investigated. Amino acid residues of proteins were classified into interior or surface residues based on the relative accessible surface area. The hydrophobic Leu, Ala, Val, and Ile residues were rich in interior residues, and hydrophilic Glu, Lys, Asp, and Arg were rich in surface residues both in α and β proteins. The amino acid composition of α proteins was different from that of β proteins in five species, and the difference was derived from the different contents of their interior residues between α and β proteins. α-helix content of α proteins was rich in interior residues than surface ones. Similarly, β-sheet content of β proteins was rich in interior residues than surface ones. The content of Leu residues was very high, approximately 20%, in interior residues of α proteins. This result suggested that the Leu residue plays an important role in the folding of α proteins.
Highlights
30 years ago, Nakashima et al [1] reported that the amino acid composition of proteins is different among the four structural classes: α, β, α/β and α + β
The hydrophobic Leu, Ala, Ile, and Val residues were rich in interior residues, and hydrophilic Glu, Lys, Asp, and Arg were rich in surface residues, both in α and β proteins
The ratios of the interior residues against surface residues clearly indicated that Cys, Phe, Ile, Trp, and Leu were favored as interior residues, and Lys, Glu, Asp, Arg, and Gln were favored as surface residues both in α and β proteins
Summary
30 years ago, Nakashima et al [1] reported that the amino acid composition of proteins is different among the four structural classes: α, β, α/β and α + β. (2014) Differences in Amino Acid Composition between α and β Structural Classes of Proteins. It is known that bacteria have species-specific nucleotide compositions in their protein-coding genes [9]-[11]. We compared the amino acid composition of proteins form five species; Escherichia coli, Thermotoga maritima, Thermus thermophilus, yeast (Saccharomyces cerevisiae), and humans (Homo sapiens), because these species have relatively large numbers of structural proteins. The species-specific nucleotide composition is largely dependent on G + C content. The G + C content in the whole genome is 50.8% in E. coli, 46.2% in T. maritima, 69.5% in T. thermophilus, and 38.3% in yeast. It is reported that proteins of thermophiles have a different amino acid composition compared to that of mesophiles [13]-[17]
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