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)


Conzelmann et al. BMC Bioinformatics 2006 7:34   doi:10.1186/1471-2105-7-34

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