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Table 3 Model parameter values

From: Exploring the rate-limiting steps in visual phototransduction recovery by bottom-up kinetic modeling

Param. Unit Description Reaction no. Dell’Orco & Koch[19] Present model Present source
kG10 s-1 Rate of binding of Gt to unphosphorylated R* DO-13 3.28e-5 2.416e-2 Optimized
k RK10 s-1 Rate of binding of RK to unphosphorylated R* DO-2 7.543e-3 5.198e-2 Optimized
m RK   Slope of the rate of decrease in RK affinity for R* with increasing phosphorylation events DO-2   0.1 Manually tuned
k Arr s-1 Rate of binding of Arr to R* with a single phosphate attached DO-5 6.092e-10 6.204e-8 Optimized
m Arr   Slope of t The rate of increase of Arr-R* affinity with additional R* phosphorylations DO-5   1.14e-8 Optimized
k A2 s -1 Rate constant of dissociation of R* from Arr · R* without R* deactivation DO-5 3.232e-3 2.754e-4 Optimized
k A3 s-1 Rate constant of dissociation of R* from Arr · R* after R* deactivation DO-6 4.451e-2 2.649e-2 Optimized
k A4 s -1 Rate constant of Arr self-association 3, 4   1.787e-8 Optimized
k A5 s -1 Rate constant of Arr self-dissociation 3, 4   0.646 Manually tuned
k RGS1 s -1 Rate of binding RGS to an effector complex DO-22, DO-24 1.57e-7 1.86e-7 Optimized
k PDEshutoff s -1 Rate constant of PDE-induced shutoff of an effector complex DO-26, DO-27 3.3e-2 2e-2 Manually tuned
k Rec1 μM-1 s-1 Ca2+−dependent rate of Rec conformational change from “tense” to “relaxed” form 1   0.011 [43]
k Rec2 s -1 Rate of Rec conformational change from “relaxed” to “tense” form 1   0.05 [43]
  1. Changes in parameter values relative to the model of Dell’Orco and Koch [19]. Reaction numbers prefixed with “DO-” refer to reaction numbers listed in the Additional file 1 of ref. [15]; otherwise they refer to reactions in the present work.