Table 2.
Number of binding modes found in MD simulation for ibuprofen, either in charged or neutral form, complexed with albumin. Selection from first to second stage was performed on the basis of coarse binding free energy estimates from the Zwanzig relationship,45 the number of the binding modes, and the observed population of each binding mode in our simulations.
| Subdomain | Site | Binding modes | |||
|---|---|---|---|---|---|
| Charged form | Neutral form | ||||
| 1st stage | 2nd stage | 1st stage | 2nd stage | ||
| IA-IIA | FA2 | 1 | 1 | 1 | 1 |
| IB | FA1 | 2 | 2 | 3 | 1 |
| IIA | DS1 | 23 | 4 | 28 | 3 |
| IIA-IIB | FA6 | 25 | 2 | 22 | 2 |
| IIA-IIIA | PCdown | 5 | 2 | 15 | 2 |
| IIIA | DS2 | 11 | 3 | 8 | 3 |
| IIIA-IB | PCup | 6 | 3 | 4 | 0 |
| IIIB | FA5 | 1 | 1 | 1 | 1 |
| 74 | 18 | 82 | 13 | ||