Department of Biomedical Engineering, Texas A&M University, College Station, Texas, USA.
Biophys J. 2011 Sep 7;101(5):1105-13. doi: 10.1016/j.bpj.2011.07.017.
Ncd is a Kinesin-14 family protein that walks to the microtubule's minus end. Although available structures show its α-helical neck in either pre- or post-stroke orientations, little is known about the transition between these two states. Using a combination of molecular dynamics simulations and structural analyses, we find that the neck sequentially makes intermediate contacts with the motor head along its mostly longitudinal path, and it develops a 24° twist in the post-stroke orientation. The forward (pre-stroke to post-stroke) motion has an ∼4.5 k(B)T (where k(B) is the Boltzmann constant, and T=300 K) free-energy barrier and is a diffusion guided by the intermediate contacts. The post-stroke free-energy minimum is higher and is formed ∼10° before reaching the orientation in the post-stroke crystal structure, consistent with previous structural data. The importance of intermediate contacts correlates with the existing motility data, including those for mutant Ncds. Unlike the forward motion, the recovery stroke goes nearly downhill in free energy, powered in part by torsional relaxation of the neck. The hysteresis in the energetics of the neck motion arises from the mechanical compliance of the protein, and together with guided diffusion, it may be key to the directed motility of Ncd.
Ncd 是一种驱动蛋白-14 家族蛋白，它向微管的负端行走。虽然现有的结构显示其α-螺旋颈处于前向或后向构象，但对这两种构象之间的转变知之甚少。本研究采用分子动力学模拟和结构分析相结合的方法，发现颈链沿着其主要的纵向路径与马达头部依次形成中间接触，并在后向构象中形成 24°的扭转。前向（前向到后向）运动具有约 4.5 k(B)T（其中 k(B)是玻尔兹曼常数，T=300 K）的自由能势垒，并且由中间接触引导扩散。后向的自由能最小势能更高，并且在达到后向晶体结构的取向之前形成约 10°，与先前的结构数据一致。中间接触的重要性与现有的运动学数据相关，包括突变体 Ncd 的运动学数据。与前向运动不同，后向恢复运动在自由能上几乎呈下坡趋势，部分由颈链的扭转松弛提供动力。颈链运动的能量滞后源于蛋白质的机械顺应性，与引导扩散一起，可能是 Ncd 定向运动的关键。
