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

From OpenWetWare
Jump to navigationJump to search
Owwnotebook icon.png Neck Linker Docking Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

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.