User:Steven J. Koch/Notebook/Kochlab/2010/09/05/Cell (2008) Yildiz, Tomishige, Gennerich, Vale strain coordinates stepping

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Yildiz, A., Tomishige, M., Gennerich, A., & Vale, R. D. (2008). Intramolecular strain coordinates kinesin stepping behavior along microtubules. Cell, 134(6), 1030-41.

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  • Very important is that they use 12 mM PIPES buffer for their experiments (they call it BRB12), instead of what I think is much more common BRB80 (80 mM PIPES). Hancock point this out as a potential reason (along with the added lysines they put in the neck linker) for the high processivity even with longer neck linker. See: User:Steven J. Koch/Notebook/Kochlab/2010/09/04/Curr Bio (2010) Shastry, Hancock neck linker kinesin1,2
    • After reading both this paper, and the Hancock paper, and the Hackney papers, my opinion is that the use of extra lysines in the Yildiz work and the low ionic strength buffer makes it difficult to interpret any processivity results.
  • They say that introducing a cystein rescues the speed by shortening the neck linker. However, the speed only goes from 100-ish to 250-ish nm/s. 250 nm / s is not full "rescue," so I don't know why they seem to imply that it is.
  • The optical trapping work, I think is easier to interpret, because probably ionic interactions are not as important at the high forces used (>1pN).
  • Deficiencies of any one-dimensional models are evident from this work, because side-stepping plays a factor, even for wild-type kinesin. There is something about the geometry of the neck linker and heads that still biases kinesin to stay on one protofilament, even with long neck-linkers, though for sure side-stepping is common in their assays.
  • Supplementary information / neck-linker modeling.
    • Yildiz et al. have extensive supplementary information, including some physics-based modeling of the neck linker. I'm hoping to summarize this later today.

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