Amino acid composition

From Proteopedia

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].

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.
• 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^[2] concluded:
  • Increased with length, reaching a plateau: Ala, Asp, Glu, Gly, Pro, Val.
  • 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.

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. ↑ 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