Amino acid composition
From Proteopedia
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**Arg peaks in middle-sized proteins. | **Arg peaks in middle-sized proteins. | ||
**Trp is constant at about 1.4% for lengths 75-200. | **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<ref name="linkers">PMID: 29426365</ref>. | ||
==References== | ==References== | ||
<references /> | <references /> | ||
Revision as of 23:53, 23 April 2020
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; 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[3].
References
- ↑ 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
- ↑ 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
- ↑ 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
