Journal of Physical Chemistry B, Vol.121, No.1, 118-128, 2017
Ligand Binding Swaps between Soft Internal Modes of alpha,beta-Tubulin and Alters Its Accessible Conformational Space
The dynamic instability of the microtubule originates from the conformational switching of its building block, that is, the alpha, beta-tubulin dimer. Ligands occupying the interface of the alpha-beta dimer bias the switch toward the disintegration of the microtubule, which in turn controls the cell division. A little loop of tubulin is structurally encoded as a biophysical gear that works by changing its structural packing. The consequence of such change propagates to the quaternary level to alter the global dynamics and is reflected as a swapping between the relative contributions of dominating internal modes. Simulation shows that there is an appreciable separation between the conformational space accessed by the liganded and unliganded systems; the clusters of conformations differ in their intrinsic tendencies to "bend" and "twist". The correlation between the altered breathing modes and conformational space rationally hypothesizes a mechanism of straight-bent interconversion of the system. In this mechanism, a ligand is understood to bias the state of the gear that detours the conformational equilibrium away from its native preference. Thus, a fundamental biophysical insight into the mechanism of the conformational switching of tubulin is presented as a multiscale process that also shows promise to yield newer concept of ligand design.