User:TheLarry/Notebook/Larrys Notebook/2009/08/02

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KMC of KP
I think my states from yesterday might be a bit too simple. After talking to Koch, he reminded me there has to be a step where the ADP Foot combo unbinds from the MT. As well as the ability to step forward or remind at the same spot. Also there maybe some kind of wait state or something.


 * Actually if I put in a state of unbinding in general from MT. If that state has a double arrow, then the arrow back will mean that the Kinesin can rebind at the same spot.

Also there is a cooperation between each foot.
 * 1) Both feet can be combined to ATP
 * 2) a foot can't detach until ATP is bound to the other foot
 * 3) ATP can't bind to the other foot until the other foot's ATP is hyrolized
 * Kinesin: world’s tiniest biped by Charles L Asbury

OK This is getting ridiculous. I found a Cross Review where he has like an 8 state diagram of one head binding to MT. Including open, closed, tight configurations. Now i get there is a closed state of the foot where the salt bridge closes that mother fucker down, but i am getting bogged down here. Do i want to use such a large diagram or should i go with a simpler diagram where the foot binds and releases P and all that jazz. I don't know any more. I can make the larger more complex version. I just need some one to say yeah do it this way that is right go just fucking do it. I am definitely up to that point where there is nothing left to it but to do it. OK i'll grab some lunch and make a kinetic monte carlo of cross' more complex version. the only problem is he just looks at one head so he ends the cycle with the foot hanging in the air. after that though is diffusion, and then weak attachment to the MT. I can do this fucking shit.
 * Robert A cross The kinetic mechanism of kinesin



Next
Ok I made the above diagram. Now shoul i try to implement into a stepping mechanism. I don't think it'll be too tough. I have to add in the constraints. So basically i gotta make it impossible for certain steps before the other head has done some stuff. But then do I want to make it that complicated or should I use a simpler model and not worry about closed/open/trapped states. I don't want to do this any more today. Tomorrow i'll talk to Koch about it and see what he says.

For the record here is my simpler model. of course i don't have the drawing skills ant has.

I can make a quick program in like half an hour so if i get the chemistry/biology down i can have this done before the end of the week.

I don't like working on the weekend without a sweet looking program to show for the work.

Questions
I still don't know how the whole ATPase will detach from the MT. There seems to be an ATP or ADP induced detachment but i don't know what states this occurs in. I'll ask Koch about it tomorrow.


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