Amino acid usage

Protein Variations, Codon, and Amino Acid Usage... 

Codon usage and the related amino acid usage data have been correlated with a number of genomic features mostly related to evolution (17) and more... 

Lobry J.R. and Gautier C. (1994). Hydrophobicity, expressivity and aromaticity are the major trends of amino-acid usage in 999 Escherichia coli chromosome-encoded genes. Nucleic Acids Res. 22 3174-3180. 

Estrogen stimulates the penetration of amino acid into the cell. This could result from a modification in the cell permeability or from an acceleration of amino acid usage. McCorquodale and Mueller demonstrated that the administration of estradiol to ovariec-tomized rats stimulates amino acid activation in the... 

In the previous section, we have examined peptides composed of nonpro-teinogenic amino acids, namely artificial, D-, f3-, and y-amino acids. In this section, we move even further afield from natural peptides. Given inconsistent usage in the literature, we begin by specifying the definitions used here [7][11][139][181][182][184-188][229]. 

G. D Onolno, D. Mouchiroud, B. Aiissani, C. Gautier, and G. Bernardi, Correlations between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J. Mol. Evol. 32, 504—510 (1991). 

Unhappily, there is another, older convention for designating chiral molecules here the labels are D and L. The R S system is more systematic and more generally useful but old usages die hard. We shall encounter D and L when we talk about amino acids in chapter 10. 

Masuda, M., Kakushima, N., Wilt, S., Ruscetti, S., Hoffman, P., Iwamoto, A. and Masuda, M. (1999) Analysis of receptor usage hy ecotropic murine retroviruses, using green fluorescent protein-tagged cationic amino acid transporters. J Vlron3, 8623-8629. 

The computer program presented here can generate very different relative frequencies of occurrence of all amino acids (and stop codons) within a target set. One-pot, two-pot, and three-pot syntheses can be simulated. Optionally, correction factors can be included to compensate for the (possible) differences in chemical coupling efficiencies of the nucleotide synthons. Finally, the codon usage of three major expression microorganisms can be considered, treating rare codons as pseudo stop codons. 

Fig. 10.2. Screenshots of die GUI after obtaining results for die problem of equimolar mixtures of amino acids, i. e., 5% of each amino acid and 0% of stop codons, (a) Standard one-pot syndiesis (b) two-pot syndiesis (c) diree-pot syndiesis (d) one-pot syndiesis using E. coli codon usage. Input fields are white and inactive fields are light gray. Computed fields are light blue and stop codons are light green (in die copy of diis figure on die CD diat accompanies diis book).

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