User:TheLarry/Notebook/Larrys Notebook/2009/08/01

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2nd iteration

I haven't edited this thing for a while but i might as well update what is going on.

I am trying to make a kinetic monte carlo simulation of kinesin walking. For this i'll need to know rate constants and states for this process.

I have read a shit load to find rate constants, and i should rummage through the papers and make a table of the many diff't constants. Later

For now i am gonna write down what I think the states are:

Let's start with nomenclature i've been using.
F1 means foot one while F2 means foot two
ATP means that an ATP molecule is bound to the foot
ADP means that an ADP molecule is bound to the foot
ADP-P means an ADP plus P is attached to the foot
0 means that neither ADP nor ATP is attached b means that the Foot is behind the other foot
f means that the foot is in front of the other foot
and i'll separate the information from each foot with a |

i.e. F1-ATP-f | F2-ADP-b
this means that F1 ATP attached (thus is bound to the MT); and is in front. F2 meanwhile is hooked up to an ADP; and is behind

So let's pick a state to start in:

  1. F1-ATP-f | F2-ADP-b
  2. F1-ATP-b | F2-ADP-f
    • F2 took a step to the front
    • there is a small chance that the foot will diffuse backwards according to Block. I don't know how to deal with this as far as the monte carlo goes
    • this is a step of 8.2 nm
    • a short amount of time is taken for this step something like 10 microseconds
  3. F1-ATP-b | F2-0-f
    • ADP has been released from Foot 2
  4. F1-ADP-P-b | F2-0-f
    • ATP is turning into ADP
  5. F1-ADP-b | F2-0-f
    • Released the phosphate group
  6. F1-ADP-b | F2-ATP-f
    • ATP has bound

I need to add in the ability for a foot to unbind from the MT and rebind at the same spot--so not diffusing. I wonder if there is anything else i missed.

I read some shit about a pause too. If that really is a state i would have missed that too.

Questions

  1. I don't know when kinesin detaches. i assume it does it while there is no ATP hooked up since ATP causes the kinesin to bind tightly to the MT
    • I also haven't seen any rate constants for detachment. All I know is that it usually occurs in 100 steps

Rate Constants

so right now i have an arrow to and from each of these states except the detachment where it is only a one way street.

also i know that some rate constants are load (force) dependant, but i am gonna ignore this for now.

ok right now the table is in google docs but i'll embed it here soon


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