Table 1 Summary of MD simulation trajectories and open pocket occurrences.
From: Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
wt p53 | R175H | G245S | R273H | C124A | |
|---|---|---|---|---|---|
Total number of clusters in trajectory | 28 | 39 | 74 | 41 | 50 |
Open pocket as % of total trajectory by geometric criteria | 6.3 | 7.3 | 6.7 | 5.0 | 5.4 |
Open pocket as % of total trajectory by Fpocket43 | 27.3 | 29.9 | 22.9 | 7.3 | 35.3 |
Avg. SASA Å2±s.d. of Cys124 side chain in MD | 10.93±4.81 | 9.58±4.45 | 6.94±4.71 | 8.38±5.84 | (124Ala value) 4.45±2.99 |
Cys124 exposure as % of MD frames with SASA>5 Å2 | 90.80 | 86.97 | 60.70 | 64.97 | (124Ala value) 34.20 |
Avg. SASA Å2±s.d. of Cys141 side chain in MD | 0.51±0.84 | 1.03±1.27 | 0.56±0.86 | 0.78±1.32 | 1.56±1.54 |
Cys141 exposure as % of MD frames with SASA>5 Å2 | 0.33 | 1.53 | 0.43 | 2.06 | 3.00 |
Avg. SASA Å2±s.d. of Cys135 side chain in MD | 0.17±0.48 | 0.41±0.91 | 0.09±0.27 | 0.09±0.34 | 0.20±0.44 |
Cys135 exposure as % of MD frames with SASA>5 Å2 | 0.06 | 0.50 | 0.00 | 0.00 | 0.03 |
