Table 1. Calculated Thermodynamic Properties of X-Ray Crystallographic Water Molecules and Corresponding Hydration Sites in the Binding Site of Closed Form Hsp90a.
| X-ray
crystallographic hydration sites |
clustered hydration Sites | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| water | D | ΔG kcal/mol | ΔGbind kcal/mol | ΔE kcal/mol | ΔEbind kcal/mol | –TΔS kcal/mol | –TΔSbind kcal/mol | Esw kcal/mol | ΔG kcal/mol |
| W301 | 0.05 | –11.81 | –5.57 | –13.46 | –3.74 | 1.65 | –1.83 | –23.19 | –11.78 |
| W323 | 0.27 | –9.07 | –9.30 | –8.59 | –4.13 | –0.48 | –5.17 | –14.41 | –10.10 |
| W324 | 0.57 | –3.95 | –3.10 | –3.88 | –0.13 | –0.07 | –2.97 | –7.65 | –3.98 |
| W325 | 0.30 | –6.55 | –2.05 | –6.70 | 1.08 | 0.15 | –3.13 | –14.44 | –6.68 |
| W328 | 0.09 | –5.92 | –6.17 | –6.42 | –2.90 | 0.50 | –3.27 | –10.36 | –6.64 |
| W336 | 0.99 | –8.28 | –6.47 | –8.85 | –3.16 | 0.57 | –3.31 | –14.58 | –8.46 |
| W338 | 0.92 | –1.47 | –0.95 | –1.21 | 2.33 | –0.25 | –3.28 | –3.32 | –1.57 |
| W346 | 0.18 | –6.75 | –3.69 | –6.93 | –0.43 | 0.18 | –3.27 | –13.45 | –6.84 |
| W357 | 1.00 | –0.50 | –0.71 | –0.22 | 3.54 | –0.27 | –4.25 | –1.14 | –1.26 |
| W379 | 0.95 | –1.79 | –2.86 | –1.55 | –0.52 | –0.24 | –2.34 | –2.89 | –1.68 |
| W381 | 0.96 | –1.81 | –5.30 | –1.46 | –1.05 | –0.34 | –4.25 | –2.71 | |
| W385 | 0.64 | –2.37 | –1.59 | –2.37 | 1.03 | 0.00 | –2.63 | –5.29 | –3.00 |
| W405 | 0.97 | –2.23 | –1.88 | –2.11 | 1.06 | –0.12 | –2.94 | –4.82 | –2.42 |
| W412 | 0.70 | –5.97 | –5.94 | –5.64 | –2.70 | –0.33 | –3.24 | –9.67 | –7.03 |
| W435 | 0.97 | –2.43 | –4.26 | –1.91 | 0.10 | –0.52 | –4.36 | –3.86 | –3.55 |
| W476 | 0.99 | –1.27 | –3.76 | –0.91 | 0.04 | –0.36 | –3.80 | –1.83 | –4.84 |
| W529 | 0.42 | –6.62 | –5.95 | –6.11 | –1.50 | –0.51 | –4.45 | –11.11 | –7.27 |
| W536 | 0.89 | –0.73 | –1.54 | –0.84 | –0.90 | 0.11 | –0.63 | –1.41 | |
| W547 | 0.92 | –1.40 | –3.40 | –1.06 | –0.45 | –0.34 | –2.95 | –1.96 | –1.59 |
| W598 | 0.81 | –5.49 | –7.92 | –4.84 | –3.34 | –0.65 | –4.58 | –8.03 | –5.51 |
| R2 against D | 0.57 | 0.13 | 0.58 | 0.19 | 0.27 | 0.00 | 0.62 | 0.50 | |
a
The water molecules are identified by their numbering in 1YER. D is the observed displacement fraction calculated using eq 2. Seven different IFST predictions are reported for hydration sites determined from crystallographic water molecule locations and the IFST free energy prediction is reported for hydration sites determined by clustering of water molecules from the MD trajectory. Not all crystallographic water molecules are identified by clustering.