Table 2.
Loop | α | β | Lk | Ψ | Φ | GLacR | GDNA | ΔGDNA |
---|---|---|---|---|---|---|---|---|
A1c | 34 | 33 | 9 | 38.2 | 71.2 | – | 121.9 | 42.2 |
A1d | 34 | 33 | 10 | 50.1 | 70.0 | – | 132.1 | 52.4 |
A2c | 34 | 33 | 8 | 76.5 | 73.7 | – | 162.6 | 82.9 |
A2d | 34 | 33 | 9 | 80.6 | 73.6 | – | 167.0 | 87.3 |
P1c | 34 | 33 | 9 | 44.5 | 72.9 | – | 128.2 | 48.5 |
P1d | 34 | 33 | 10 | 82.8 | 73.9 | – | 167.7 | 88.0 |
Ec | 110 | 18 | 8 | 35.6 | 68.9 | 2.8±1 | 120.1±1 | 40.4±1 |
Ed | 108 | −50 | 9 | 24.3 | 67.2 | 2.8±1 | 105.9±1 | 26.2±1 |
Free | – | – | – | 0 | 67.0 | – | 79.7 |
Loops denoted by labels in Figure 4; α, β, Lk, Ψ, Φ, GLacR, GDNA are as in Table 1. ΔGDNA: free energy difference between loop and “free” DNA with bound CAP and LacR dimers. Sequence: GGCAGTGAGCGCAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAATTGTGAGCGGATAACAATT. Here the O3 and O1 sequences are shown in boldface and the CAP binding site is underlined.