Table 1.
Five p53REs and possible p53 binding modes examined by sequence analysis, molecular dynamics simulations, and molecular free energy evaluations (GBMV)
| Gene | Sequence | Q1234 | T13 | T24 | H14 | |
|---|---|---|---|---|---|---|
| P21-5′ | CTATGAG GAACATGTCC CAACATGTTG AGCTC | Probability (sequence) % | 21.2 | 25.4 | 29.4 | 24.0 |
| Probability (GBMV) % | 24.9 (25.4) | 25.3 (25.5) | 22.6 (23.1) | 27.2 (26.0) | ||
| Gadd45 | TGTACA GAACATGTCT AAGCATGCTG GGGTC | Probability (sequence) % | 21.5 | 25.7 | 23.8 | 29.0 |
| Probability (GBMV) % | 24.5 (26.2) | 28.0 (25.3) | 19.4 (19.6) | 27.8 (28.9) | ||
| pDINP1 | TTTATA GAACTTGGGG GAACATGTTT ACCAA | Probability (sequence) % | 19.6 | 30.2 | 20.8 | 29.4 |
| Probability (GBMV) % | 23.4 (23.4) | 28.7 (28.5) | 21.5 (20.5) | 27.5 (27.6) | ||
| P53Aip1 | TCCTCC TCTCTTGCCC GGGCTTGTCG AGATG | Probability (sequence) % | 19.9 | 21.5 | 32.7 | 26.0 |
| Probability (GBMV) % | 19.7 (18.9) | 24.3 (24.0) | 27.1 (28.1) | 28.9 (29.1) | ||
| Puma-BS2 | CGCGC CTGCAAGTCC TGACTTGTCC GCGGCA | Probability (sequence) % | 16.6 | 25.8 | 18.3 | 39.3 |
| Probability (GBMV) % | 23.1 (24.2) | 27.1 (27.0) | 20.3 (19.2) | 29.5 (29.5) |
The probabilities (sequence) were evaluated based on quarter-site couplings, and the probabilities (GBMV) were evaluated using 2000 molecular dynamics-refined structures. The numbers in parenthesis were evaluated using 1200 molecular dynamics-refined structures.