cdp mechanism Kd parameter

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tcp

cdp mechanism Kd parameter

Post by tcp »

Dear All,

According to Yamada et al. 1989 at the paragraph about Calcium buffers (in Methods in Neuronal Modelling book), K_D equals to:
K_D=backward_rate/forward_rate (K_D=1 microMolar).

In the cdp.mod [1] file K_D is defined as k1buf/k2buf, that is forward_rate/backward rate giving a result in (microMolar)^-1.
I would appreciate any suggestions on this.

Regards,
Eleftheria

[1] http://www.neuron.yale.edu/neuron/stati ... 00/cdp.mod
ted
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Re: cdp mechanism Kd parameter

Post by ted »

In standard usage, KD means "dissociation constant" and is defined as kr/kf for reactions of the form
xA + yB <-> AxBy
where the forward rate is kf and the backward rate is kr. This is the usage applied by Yamada et al.. Note that the units of KD depend on the units of kf and kr, which in turn depend on the units of A and B and the numerical values of x and y.

cdp.mod uses a term Kd which is defined in that file as kf/kr.* Since Kd is just the inverse of KD, its units will be the inverse of the units of KD.

*--There's no particularly good reason for this--it's just the way that file is. If you like, feel free to define KD and replace every occurrence of Kd in cdp.mod with 1/KD--won't affect simulation results.
tcp

Re: cdp mechanism Kd parameter

Post by tcp »

Thank you Ted, it is clear now.
Eleftheria
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Re: cdp mechanism Kd parameter

Post by ted »

Yep. It's a bit of a wart, but even warty code can work properly.
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