Amino acid composition

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The amino acid composition of a protein refers to the percentages of each amino acid in the sequence of that protein. The percentage, sometimes called the Mole percentage, is calculated as the number of a given amino acid divided by the total number of amino acids in the protein chain or molecule.

GC-content of the organism's genome is the strongest genome-level determinant of amino acid composition.[1][2][3].

Other, weaker influences are:

  • Growth temperatures (mesophily/thermophily/hyperthermophily). Thermophiles have more glutamic acid (with reduction in glutamine), and more lysine and arginine[1]. This likely relates to the larger number of salt bridges in proteins of thermophiles, believe to contribute to thermostability[4].
  • Chain length. Proteins of thermophiles are, on average, shorter than those of mesophiles. Average lengths are 283 and 340, respectively[1]. A study of ~550,000 proteins with lengths 50-200 amino acids[5] concluded:
    • Increased with length, reaching a plateau: Ala, Asp, Glu, Gly, Pro, Val; less increase for Gln and Thr.
    • Decreased with length: Cys, Phe, His, Ile, Lys, Met, Asn, Ser.
    • Leu and Tyr are highest in short and long chains, and less frequent in middle-sized proteins.
    • Arg peaks in middle-sized proteins.
    • Trp is constant at about 1.4% for lengths 75-200.
  • Linkers vs. domains: Linkers between domains have more polar residues, while compact domains have more hydrophobic residues[2].
  • Compositional variability ranks archaea > baceteria > eukaryotes[2].

References

  1. ↑ 1.0 1.1 1.2 Tekaia F, Yeramian E, Dujon B. Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene. 2002 Sep 4;297(1-2):51-60. doi: 10.1016/s0378-1119(02)00871-5. PMID:12384285 doi:http://dx.doi.org/10.1016/s0378-1119(02)00871-5
  2. ↑ 2.0 2.1 2.2 Brune D, Andrade-Navarro MA, Mier P. Proteome-wide comparison between the amino acid composition of domains and linkers. BMC Res Notes. 2018 Feb 9;11(1):117. doi: 10.1186/s13104-018-3221-0. PMID:29426365 doi:http://dx.doi.org/10.1186/s13104-018-3221-0
  3. ↑ Moura A, Savageau MA, Alves R. Relative amino acid composition signatures of organisms and environments. PLoS One. 2013 Oct 25;8(10):e77319. doi: 10.1371/journal.pone.0077319., eCollection 2013. PMID:24204807 doi:http://dx.doi.org/10.1371/journal.pone.0077319
  4. ↑ Chan CH, Yu TH, Wong KB. Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. PLoS One. 2011;6(6):e21624. Epub 2011 Jun 24. PMID:21720566 doi:10.1371/journal.pone.0021624
  5. ↑ Carugo O. Amino acid composition and protein dimension. Protein Sci. 2008 Dec;17(12):2187-91. doi: 10.1110/ps.037762.108. Epub 2008 Sep, 9. PMID:18780815 doi:http://dx.doi.org/10.1110/ps.037762.108

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