We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.
Amino acid composition
From Proteopedia
(Difference between revisions)
| Line 4: | Line 4: | ||
Other, weaker influences are: | Other, weaker influences are: | ||
| - | *'''Growth temperatures''' (mesophily/thermophily/hyperthermophily). Thermophiles have more glutamic acid (with reduction in glutamine), and more lysine and arginine<ref name="tekala-genomes" />. This likely relates to the larger number of [[salt bridges]] in proteins of thermophiles, believe to contribute to thermostability. | + | *'''Growth temperatures''' (mesophily/thermophily/hyperthermophily). Thermophiles have more glutamic acid (with reduction in glutamine), and more lysine and arginine<ref name="tekala-genomes" />. This likely relates to the larger number of [[salt bridges]] in proteins of thermophiles, believe to contribute to thermostability<ref name="saltbridges">PMID:21720566</ref>. |
*'''Chain length'''. Proteins of thermophiles are, on average, shorter than those of mesophiles. Average lengths are 283 and 340, respectively<ref name="tekala-genomes" />. A study of ~550,000 proteins with lengths 50-200 amino acids<ref name="length">PMID:18780815</ref> concluded: | *'''Chain length'''. Proteins of thermophiles are, on average, shorter than those of mesophiles. Average lengths are 283 and 340, respectively<ref name="tekala-genomes" />. A study of ~550,000 proteins with lengths 50-200 amino acids<ref name="length">PMID:18780815</ref> concluded: | ||
**Increased with length, reaching a plateau: Ala, Asp, Glu, Gly, Pro, Val; less increase for Gln and Thr. | **Increased with length, reaching a plateau: Ala, Asp, Glu, Gly, Pro, Val; less increase for Gln and Thr. | ||
Revision as of 00:05, 24 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][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
- ↑ 1.0 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
- ↑ 2.0 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
- ↑ 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
- ↑ 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
- ↑ 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
