The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Table 1 KcsA amino acid (aa) composition (N = 160 aa, plus one-stop codon)

aa	Acronym	No. of codons in a genetic code^a	Observed no. of aa (percent) in KcsA	Expected^b no. of aa (percent) in KcsA
G	gly	4	14 (8.69)	10 (6.25)
S	ser	6	6 (3.73)	15 (9.37)
T	thr	4	12 (7.45)	10 (6.25)
C	cys	2	0 (0.00)	5 (3.12)
Y	tyr	2	5 (3.10)	5 (3.12)
N	asn	2	1 (0.62)	5 (3.12)
Q	gln	2	2 (1.24)	5 (3.12)
K	lys	2	2 (1.24)	5 (3.12)
R	arg	6	17 (10.56)	15 (9.37)
H	his	2	5 (3.10)	5 (3.12)
D	asp	2	4 (2.48)	5 (3.12)
E	Glu	2	9 (5.59)	5 (3.12)
A	ala	4	22 (13.66)	10 (6.25)
V	val	4	16 (9.94)	10 (6.25)
L	leu	6	24 (14.91)	15 (9.37)
I	ile	3	3 (1.86)	7 (4.68)
P	pro	4	5 (3.10)	10 (6.25)
M	met	1	4 (2.48)	3 (1.56)
F	phe	2	4 (2.48)	5 (3.12)
W	trp	1	5 (3.10)	3 (1.56)
Stop		3	1 (0.62)	7 (4.68)
Total		64	161 (≈100)	≈161 (≈100)

The observed composition of amino acids in KcsA differs from what would be expected by chance (Chi-square = 52.91; df = 19; p ≤ 0.001; the stop codon was excluded), which suggests that directional selection has favored and retained adaptive peptide sequence in KcsA for optimal function. Protein sequence available at NCBI (GenBank Z37969; Swiss-Prot P0A334)
^aCorresponds to the number of codons coding for a specific amino acid
^bExpected values were estimated from the percentile differential allocation of codons coding for each amino acid or stop signal in the genetic code

ISSN: 1936-6434