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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.