Table 1.
Reactions for scaffold with 3 binding sites. A complete mechanistic model of a scaffold protein with 3 binding domains (1,2,3), where each domain can bind one effector protein (E1, E2, E3), has to consider the following 12 reactions. The kinetic parameters for each reaction can be denoted with k+i for the association and k-i for the dissociation reaction
| Binding of E1 | Binding of E2 | Binding of E3 |
| R[0, 0, 0]+E1 ⇋ R[1, 0, 0] (49a) | R[0, 0, 0]+E2 ⇋ R[0, 1, 0] (50a) | R[0, 0, 0]+E3 ⇋ R[0, 0, 1] (51a) |
| R[0, 1, 0]+E1 ⇋ R[1, 1, 0] (49b) | R[0, 0, 1]+E2 ⇋ R[0, 1, 1] (50b) | R[0, 1, 0]+E3 ⇋ R[0, 1, 1] (51b) |
| R[0, 0, 1]+E1 ⇋ R[1, 0, 1] (49c) | R[1, 0, 0]+E2 ⇋ R[1, 1, 0] (50c) | R[1, 0, 0]+E3 ⇋ R[1, 0, 1] (51c) |
| R[0, 1, 1]+E1 ⇋ R[1, 1, 1] (49d) | R[1, 0, 1]+E2 ⇋ R[1, 1, 1] (50d) | R[1, 1, 0]+E3 ⇋ R[1, 1, 1] (51d) |