| |
Protocol
|
Mean ΔG
|
P
|
Mean Z(ΔG)
|
Mean %pairs
|
|---|
|
Real (mouse)
| |
-737.98 ± 55.52
| | |
60.96 ± 0.28
|
|
Modification
|
Swap G4C4
|
-734.10 ± 55.08
|
0.0169
| |
62.11 ± 0.33
|
|
Randomization
|
Sh.4-fold
|
-725.76 ± 54.71
|
9e-15
|
-1.41 ± 0.14
|
60.77 ± 0.23
|
| |
Sh.codon
|
-728.49 ± 55.01
|
6e-10
|
-1.04 ± 0.14
|
60.61 ± 0.23
|
| |
Re-sub.K
|
-733.28 ± 55.15
|
4e-05
|
-0.64 ± 0.15
|
61.06 ± 0.24
|
| |
Re-sub.N3
|
-734.14 ± 55.20
|
4e-04
|
-0.51 ± 0.14
|
61.09 ± 0.24
|
- Means ± SEM are shown, N = 70. P-values for modifications were determined by paired t-tests (μ = Real < Modification) on ΔG. P-values for randomizations were by one-sample t-tests (expected mean (μ) = 0) on Z(ΔG). %Pairs is the proportion of the coding sequence involved in base-pairing interactions. Artificial sequences generated by the first five protocols encode the same protein as the mouse sequence. A brief description of each protocol follows (see Results for details). 'Sh.4-fold': nucleotides at all 4-fold degenerate sites are shuffled. 'Sh.codon': for each amino acid, the synonymous codons are permuted. 'Re-sub.K': synonymous substitutions are reverted back to the rat-mouse common ancestor (rat-mouse common ancestor) state, followed by reallocation of the same number of synonymous point mutations. 'Re-sub.N3': like the previous protocol, except that the nucleotide replacement is also selected at random from the nucleotide distribution at third sites observed in the mouse sequence. 'Swap G4C4': all guanine bases at 4-fold sites are replaced by cytosine, and vice versa.
