驱动蛋白自由能景观的格子模型研究
Free-Energy Landscape of Kinesin by a Realistic Lattice Model
摘要：
在热平衡的驱动蛋白马达域的结构波动进行了研究，使用晶格蛋白模型与围棋相互作用。利用多重自重叠系综（MSOE）蒙特卡罗方法和主成分分析（PCA）方法，得到了自由能谱的自由能景观。结果表明，驱动蛋白有两个亚结构域，表现出部分折叠/解折叠的功能重要的区域：一个是位于周围的核苷酸结合位点，另一个包括主要的微管结合位点。这些子域是一致的结构变异性，最近报道的基础上实验获得的结构。另一方面，这种大的结构性波动还没有被B因子或正常模式分析所捕获。因此，它们超出了弹性范围，并且对于研究驱动蛋白的功能来说，考虑链连接性是必要的。
英文摘要：
Structural fluctuations in the thermal equilibrium of the kinesin motor domain are studied using a lattice protein model with Go interactions. By means of the multi-self-overlap ensemble (MSOE) Monte Carlo method and the principal component analysis (PCA), the free-energy landscape is obtained. It is shown that kinesins have two subdomains that exhibit partial folding/unfolding at functionally important regions: one is located around the nucleotide binding site and the other includes the main microtubule binding site. These subdomains are consistent with structural variability that was reported recently based on experimentally-obtained structures. On the other hand, such large structural fluctuations have not been captured by B-factor or normal mode analyses. Thus, they are beyond the elastic regime, and it is essential to take into account chain connectivity for studying the function of kinesins.
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