Table 1.
Reaction scheme and rate constants in phage lambda epigenetic switch mode. We use CORn denotes Cro2 bound operator site ORn, RORn denotes CI2 bound ORn, where n can be 1, 2, and 3. Note that molecular species enclosed in parenthesis are those whose presence is required for the specific reactions to occur, but their copy numbers do not influence the transition rates between microstates.
| Reactions | Rate constants |
|---|---|
| Synthesis reactions [50, 55, 56, 57] | |
|
| |
| ∅ + (OR3 + OR2) → CI2 + (OR3 + OR2) | ksCI2 = 0.0069/s |
| ∅ + (OR3 + COR2) → CI2 + (OR3 + COR2) | ksCI2 = 0.0069/s |
| ∅ + (OR3 + ROR2) → CI2 + (OR3 + ROR2) | ks1CI2 = 0.069/s |
| ∅ + (OR1 + OR2) → Cro2 + (OR1+ OR2) | ksCro2 = 0.0929/s |
|
| |
| Degradation reactions [58, 50] | |
|
| |
| CI2 → ∅ | kdCI2 = 0.0026/s |
| Cro2 → ∅ | kdCro2 = 0.0025/s |
|
| |
| Association rate of binding reactions [59] | |
|
| |
| CI2 + OR1 → ROR1 | kbOR1CI2 = 0.021/s |
| CI2 + OR2 → ROR2 | kbOR2CI2 = 0.021/s |
| CI2 + OR3 → ROR3 | kbOR3CI2 = 0.021/s |
| Cro2 + OR1 → COR1 | kbOR1Cro2 = 0.021/s |
| Cro2 + OR2 → COR2 | kbOR2Cro2 = 0.021/s |
| Cro2 + OR3 → COR3 | kbOR3Cro2 = 0.021/s |
|
| |
| Dissociation reactions - CI2 dissociation from OR1 | |
|
| |
| ROR1 + (OR2) → CI2 + OR1 + (OR2) | 0.00898/s |
| ROR1 + (ROR2 + OR3) → CI2 + OR1 + (ROR2 + OR3) | 0.00011/s |
| ROR1 + (ROR2 + ROR3) → CI2 + OR1 + (ROR2 + ROR3) | 0.01242/s |
| ROR1 + (ROR2 + COR3) → CI2 + OR1+ (ROR2 + COR3) | 0.00011/s |
| ROR1 + (COR2) → CI2 + OR1 + (COR2) | 0.00898/s |
|
| |
| Dissociation reactions - CI2 dissociation from OR2 | |
|
| |
| ROR2 + (OR1 + OR3) → CI2 + OR2 + (OR1 + OR3) | 0.2297/s |
| ROR2 + (ROR1 + OR3) → CI2 + OR2 + (ROR1 + OR3) | 0.0029/s |
| ROR2 + (OR1 + ROR3) → CI2 + OR2 + (OR1+ ROR3) | 0.0021/s |
| ROR2 + (ROR1 + ROR3) → CI2 + OR2 + (ROR1 + ROR3) | 0.0029/s |
| ROR2 + (COR1 + OR3) → CI2 + OR2 + (COR1 + OR3) | 0.2297/s |
| ROR2 + (OR1 + COR3) → CI2 + OR2 + (OR1 + COR3) | 0.2297/s |
| ROR2 + (COR1 + COR3) → CI2 + OR2 + (COR1 + COR3) | 0.2297/s |
| ROR2 + (ROR1 + COR3) → CI2 + OR2+ (ROR1 + COR3) | 0.0029/s |
| ROR2 + (COR1 + ROR3) → CI2 + OR2+ (COR1 + ROR3) | 0.0021/s |
|
| |
| Dissociation reactions - CI dissociation from OR3 | |
|
| |
| ROR3 + (OR2) → CI2 + OR3 + (OR2) | 1.13/s |
| ROR3 + (ROR2 + OR1) → CI2 + OR3 + (ROR2 + OR1) | 0.0106/s |
| ROR3 + (ROR2 + ROR1) → CI2 + OR3 + (ROR2 + ROR1) | 0.0106/s |
| ROR3 + (ROR2 + COR1) → CI2 + OR3+ (ROR2 + COR1) | 0.0106/s |
| ROR3 + (COR2) → CI2 + OR3 + (COR2) | 1.13/s |
|
| |
| Dissociation reactions - Cro dissociation from OR1 | |
|
| |
| COR1 + (OR2) → Cro2 + OR1 + (OR2) | 0.0202/s |
| COR1 + (ROR2) → Cro2 + OR1+ (ROR2) | 0.0202/s |
| COR1 + (COR2 + OR3) → Cro2 + OR1 + (COR2 + OR3) | 0.0040/s |
| COR1 + (COR2 + ROR3) → Cro2 + OR1+ (COR2 + ROR3) | 0.0040/s |
| COR1 + (COR2 + COR3) → Cro2 + OR1 + (COR2 + COR3) | 0.0040/s |
|
| |
| Dissociation reactions - Cro dissociation from OR2 | |
|
| |
| COR2 + (OR1 + OR3) → Cro2 + OR2 + (OR1+ OR3) | 0.1413/s |
| COR2 + (ROR1 + OR3) → Cro2 + OR2 + (ROR1 + OR3) | 0.1413/s |
| COR2 + (OR1 + ROR3) → Cro2 + OR2 + (OR1 + ROR3) | 0.1413/s |
| COR2 + (ROR1 + ROR3) → Cro2 + OR2 + (ROR1 + ROR3) | 0.1413/s |
| COR2 + (COR1 + OR3) → Cro2 + OR2 + (COR1 + OR3) | 0.0279/s |
| COR2 + (OR1 + COR3) → Cro2 + OR2 + (OR1 + COR3) | 0.053/s |
| COR2 + (COR1 + COR3) → Cro2 + OR2 + (COR1 + COR3) | 0.0328/s |
| COR2 + (ROR1 + COR3) → Cro2 + OR2+ (ROR1 + COR3) | 0.053/s |
| COR2 + (COR1 + ROR3) → Cro2 + OR2+ (COR1 + ROR3) | 0.0279/s |
|
| |
| Dissociation reactions - Cro dissociation from OR3 | |
|
| |
| COR3 + (OR2) → Cro2 + OR3 + (OR2) | 0.0022/s |
| COR3 + (ROR2) → Cro2 + OR3+ (ROR2) | 0.0022/s |
| COR3 + (COR2 + OR1) → Cro2 + OR3 + (COR2 + OR1) | 0.0008/s |
| COR3 + (COR2 + ROR1) → Cro2 + OR3+ (COR2 + ROR1) | 0.0008/s |
| COR3 + (COR2 + COR1) → Cro2 + OR3 + (COR2 + COR1) | 0.003/s |