Table 1.
Averaged interaction free energies between Eph and ephrin reflect their tendencies to form complexes. Complexes with available crystal structures are indicated with their PDB codes.
| Eph-ephrin complex |
Interaction based on classification |
Interaction energies* (kcal/mol) |
Results from simulations |
|---|---|---|---|
| 2wo2(EphA4 ephrin-B2) |
√, promiscuous | −77.5 ± 10.4 | √ |
| 2wo3(EphA4 ephrin-A2) |
√, promiscuous | −33.2 ± 9.3 | √ |
| 3hei(EphA2 ephrin-A1) |
√, specific | −42.7 ± 8.2 | √ |
| 2hle(EphB4 ephrin-B2) |
√, specific | −40.1 ± 9.4 | √ |
| 1kgy(EphB2 ephrin-B2) |
√, promiscuous | −28.0 1± 0.7 | √ |
| 3mx0(EphA2 ephrin-A5) |
√, specific | −4.0 ± 6.8 | √? |
| 1shw(EphB2 ephrin-A5) |
√, promiscuous | −10.4 ± 4.7 | √ |
| 4BKA(EphA4 ephrin-A5) |
√, promiscuous | −7.0 ± 7.9 | √ |
|
EphA4 ephrin-A1 |
√, promiscuous | −30.7 ± 7.9 | √ |
|
EphA2 ephrin-A2 |
√, specific | −14.7 ± 6.2 | √ |
| EphB4 ephrin-A5 | X | 18.3 ± 12.2 | X |
| EphB2 ephrin-A2 | X | 0.4 ± 7.0 | X? |
| EphA2 ephrin-B2 | X | 39.4 ± 9.9 | X |
| EphB2 ephrin-A1 | X | 11.0 ± 6.2 | X |
| EphB4 ephrin-A2 | X | 11.9 ± 11.3 | X |
| EphB4 ephrin-A1 | X | 11.5 ± 3.4 | X |
•
Based on the trajctories from 300 ps to 500 ps after RMSDs are stablized.