Investigating role of conformational changes of microtubule in regulating its binding affinity to kinesin by all‐atom molecular dynamics simulation

Abstract

Changes of affinity of kinesin head to microtubule regulated by changes in the nucleotide state are essential to processive movement of kinesin on microtubule. Here, using all-atom molecular dynamics simulations we show that besides the nucleotide state, large conformational changes of microtubule-tubulin heterodimers induced by strong interaction with the head in strongly binding state are also indispensable to regulate the affinity of the head to the tubulin. In strongly binding state the high affinity of the head to microtubule arises largely from mutual conformational changes of the microtubule and head induced by the specific interaction between them via an induced-fit mechanism. Moreover, the ADP-head has a much weaker affinity to the local microtubule-tubulin, whose conformation is largely altered by the interaction with the head in strongly binding state, than to other unperturbed tubulins. This indicates that upon Pi release the ADP-head temporarily has a much weaker affinity to the local tubulin than to other tubulins.

All‐atom molecular dynamics simulations reveal how kinesin transits from one‐head‐bound to two‐heads‐bound state

“…Indeed, the experimental data showed such dependence of the bias magnitude on particle size . Furthermore, because the binding energy between the two heads in 1HB state before ATP binding (about 27 k B T ) is weaker than the binding energy between the nucleotide‐free head and MT (more than 40 k B T ), the detached ADP‐head would have a much larger fluctuation than the MT‐bound nucleotide‐free head (see earlier). Additionally, due to the linker that connects the head and particle having a certain persistent length, it is noted that at the intermediate state, where the linker is nearly perpendicular to the xoy plane (Figure S6), the fluctuation of the particle should be larger in the xoy plane than that at the MT‐bound state, where the linker is nearly in the xoy plane.…”

“…Note that although the binding energy between the two heads is high (about 27 k B T ), it is much weaker than the binding energy between the nucleotide‐free head and MT (more than 40 k B T ). Thus, the detached ADP‐head would have a larger fluctuation relative to the MT‐bound head than the MT‐bound nucleotide‐free head relative to MT (see Discussion), consistent with available experimental data showing that the detached head exhibits much more mobile than the MT‐bound nucleotide‐free head …”

“…In our previous work, using MD simulations we showed that the ADP‐head has a much weaker affinity (denoted by E w1 ) to the α/β‐tubulin heterodimer with large conformational changes induced by the strong interaction with the nucleotide‐free or ATP‐head than that (denoted by E w2 ) to the unperturbed α/β‐tubulin heterodimers. Based on these MD simulation results together with the results in the current work, the following model for a mechanical stepping of the kinesin by hydrolyzing an ATP in the trailing head can be proposed (Figure ).…”

“…The spring constant was set to be 1000 kJ mol −1 nm −2 and the pulling rate was 0.001 nm/ps. We have checked that decreasing the pulling rate produced similar initial configurations, thereby ensuring that the pulling rate of 0.001 nm/ps to be sufficiently slow, as done in our previous works . From the pulling trajectory, snapshots were taken to generate the starting umbrella sampling windows.…”

“…Detailed structural and dynamic pictures of a kinesin head in nucleotide‐free, ADP and ATP states bound to MT tubulin were studied . The interactions between MT tubulin and a kinesin head in different nucleotide states were analyzed and the binding energies were calculated . The conformational changes of MT tubulin induced by the strong interaction with the nucleotide‐free or ATP‐head and their effects on the binding energy of the ADP‐head to the tubulin were investigated …”