Table 2.
Oct4-DNA Contacts in Oct4-Nucleosome Complexes
| Binding Site | Oct4 Configuration | Simulation Step | # Stable Contactsb POUS-DNA Bases | # Stable Contactsb POUS-DNA Backbone | # Stable Contactsb POUHD-DNA Bases | # Stable Contactsb POUHD-DNA Backbone | % Time with Selected Contactc Present |
|---|---|---|---|---|---|---|---|
| POUS | MD | Eq01a | 67 | 38 | 0 | 0 | 92.40% |
| Eq02 | 14 | 43 | 0 | 0 | 0% | ||
| Eq03 | 30 | 51 | 0 | 0 | 0.52% | ||
| Prod | 61 | 50 | 0 | 0 | 95.32% | ||
| MORE | Eq01 | 69 | 47 | 4 | 23 | 85.80% | |
| Eq02 | 47 | 71 | 0 | 6 | 6.56% | ||
| Eq03a | 69 | 77 | 0 | 1 | 99.64% | ||
| Prod | 65 | 54 | 2 | 7 | 98.73% | ||
| POUHD 1 (3′-5′) | MD1 | Eq01 | 0 | 0 | 31 | 8 | 0% |
| Eq02 | 0 | 2 | 3 | 13 | 0% | ||
| Eq03 | 0 | 0 | 21 | 15 | 0% | ||
| Prod | – | – | – | – | – | ||
| MD2 | Eq01a | 1 | 5 | 41 | 44 | 65.52% | |
| Eq02 | 1 | 5 | 17 | 20 | 0% | ||
| Eq03 | 0 | 0 | 12 | 26 | 0% | ||
| Prod | 0 | 0 | 5 | 11 | 19.84% | ||
| POUHD 2 (5′-3′) | MD | Eq01 | 0 | 0 | 46 | 47 | 69.80% |
| Eq02 | 0 | 0 | 34 | 37 | 87.08% | ||
| Eq03a | 0 | 0 | 42 | 16 | 88.16% | ||
| Prod | 0 | 0 | 34 | 17 | 63.98% | ||
| MORE | Eq01a | 18 | 47 | 48 | 37 | 97.68% | |
| Eq02 | 23 | 51 | 50 | 50 | 88.68% | ||
| Eq03 | 16 | 50 | 42 | 51 | 95.84% | ||
| Prod | 2 | 35 | 31 | 27 | 85.43% |
Eq, Equilibration (last 5 ns); Prod, Production (100 ns).
a
Equilibration chosen for production.
b
Stable contact: atoms at a distance <4.5 Å for at least 75% of the simulation.
c
Selected contacts: Q44-A for the POUS and N143-A for the POUHD. Contact was considered present if donor-acceptor distance was smaller than 4 Å.