User:TheLarry/Notebook/Larrys Notebook/2010/07/28

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 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Neck Linker Docking
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Amino Acid Binding to Catalytic Core
After searching for what feels like 2 days, i think i finally found the amount of amino acids that bind to the catalytic core: 4.

In "Controlling Kinesin by Reversible Disulfide Cross-linking: Identifying the Motility-producing Conformational Change" by Michio Tomishige and Ronald D. Vale where they purport that unwinding of the neck coiled-coil is not part of the processivity. They say:

The program SSBOND identified only two pairs of residues in the neck linker whose Ca–Ca and calculated Cb–Cb distances are capable of forming energetically favorable disulfide bonds (Fig. 1 a): (a) between residue 334 at the end of the neck linker and residue 222 at the tip of the catalytic core; and (b) between residue 330 (located between b9 and b10) and residue 4 at the NH 2 terminus. A disulfide bond between residues 334 and 222 would be expected to totally immobilize the ATP-dependent neck linker movement, while a disulfide bond between residues 330 and 4 should partially immobilize the neck linker movement.

So i think from 330-334 the neck linker is bonded to the catalytic core via disulfide bonds. I thought it was something like gamma bonds but 1) i don't remember where reading that and 2) i don't know what that means. So hopefully that is the bonding.

Ahh crap did i forget what i was trying to do again. lemme restate

Restatement
Koch and I want to figure out the force on the 30 amino acid neck linker by modeling it like a worm-like chain. So in a normal state docked/undocked there is a contour length L_0. But when the status is docked/docked there is a shorter contour length L_-1. From this binding of possibly 4 less amino acids. Likewise for undocked/undocked there is a larger contour length L_1. And for these three configurations there is a a distance the neck linker covers. For the normal configuration it is 8.2 nm. For docked/docked it is greater than 8.2 since the neck linker binds to the opposite side of the neck linker. So it is possible 4 nm farther since the dimension of the neck linker is 4.5x4.5x7.5 nm. For the undocked/undocked configuration this distance should be shorter by maybe 4 nm. So that is what i am thinking.


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