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Jul 27, 2018, 10:11:57 AM7/27/18

to kappa-users

Hi,

I was wondering how we can translate the following statements into Kappa rules:

Statment 1: A Gene agent 'G' has two transcription factor binding sites 'a' and 'b', and T is the transcription factor. Now, when the site 'a' is occupied by one molecule of T then the other site 'b' will be occupied by another T molecule.

Statement 2: When all the transcription factors are bound to the promoter region or all the sites of 'G' is bounded to the transcription factors, the transcriptional process is initiated and one molecule of mRNA is produced. Let's consider 'M' as the agent for mRNA.

Sincerely

Debdas

Jul 27, 2018, 11:23:05 AM7/27/18

to kappa-users

Le vendredi 27 juillet 2018 16:11:57 UTC+2, debdaspaul a écrit :

Hi,I was wondering how we can translate the following statements into Kappa rules:Statment 1: A Gene agent 'G' has two transcription factor binding sites 'a' and 'b', and T is the transcription factor. Now, when the site 'a' is occupied by one molecule of T then the other site 'b' will be occupied by another T molecule.

This sounds as a property about the reachable species.

It has to be a consequence of the mechanistic interactions (not an assumption about the rule).

The simplest mechanistic assumptions to entail this are:

a) a can by to T only if b if bound to T

b) b can release a bond with T only if a is not bound to T.

assuming that a and b may only bind with T I get:

G(a[•],b[1]),T(x[.]),T(x[1]) -> G(a[2],b[1]),T(x[2]),T(x[1])

G(a[1]),T(x[1]) -> G(a[.]),T(x[.])

G(b[.]),T(x[.]) -> G(b[1]),T(x[1])

G(a[.],b[1]),T(x[1]) -> G(a[.],b[.]),T(x[.])

KaSa will tell you that:

------------------------------------------------------------

* Relational properties:

------------------------------------------------------------

G(a[x.T]) => G(a[x.T],b[x.T])

(If a is bound, then b is bound as well).

Statement 2: When all the transcription factors are bound to the promoter region or all the sites of 'G' is bounded to the transcription factors, the transcriptional process is initiated and one molecule of mRNA is produced. Let's consider 'M' as the agent for mRNA.

(I assume that G has only two sites to be bound to the transcription factor)

G(a[1],b[2]),T(x[1]),T(x[2]),. -> G(a[1],b[2]),T(x[1]),T(x[2]),M()

Cheers.

Jérôme.

SincerelyDebdas

Jul 27, 2018, 5:47:59 PM7/27/18

to kappa-users

Many thanks, Jérôme!

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