Zheng Yuqing, Cui Qiang
Graduate Program in Biophysics and Department of Chemistry , University of Wisconsin-Madison , 1101 University Avenue , Madison , Wisconsin 53706 , United States.
J Chem Theory Comput. 2018 Mar 13;14(3):1716-1726. doi: 10.1021/acs.jctc.7b01064. Epub 2018 Feb 12.
The open/close transition in adenylate kinase (AK) is regarded as a representative example for large-scale conformational transition in proteins, yet its mechanism remains unclear despite numerous experimental and computational studies. Using extensive (∼50 μs) explicit solvent atomistic simulations and Markov state analysis, we shed new lights on the mechanism of this transition in the apo form of AK. The closed basin of apo AK features an open NMP domain while the LID domain closes and rotates toward it. Therefore, although the computed structural properties of the closed ensemble are consistent with previously reported FRET and PRE measurements, our simulations suggest that NMP closure is likely to follow AMP binding, in contrast to the previous interpretation of FRET and PRE data that the apo state was able to sample the fully closed conformation for "ligand selection". The closed state ensemble is found to be kinetically heterogeneous; multiple pathways and time scales are associated with the open/close transition, providing new clues to the disparate time scales observed in different experiments. Besides interdomain interactions, a novel mutual information analysis identifies specific intradomain interactions that correlate strongly to transition kinetics, supporting observations from previous chimera experiments. While our results underscore the role of internal domain properties in determining the kinetics of open/close transition in apo AK, no evidence is observed for any significant degree of local unfolding during the transition. These observations about AK have general implications to our view of conformational states, transition pathways, and time scales of conformational changes in proteins. The key features and time scales of observed transition pathways are robust and similar from simulations using two popular fixed charge force fields.
腺苷酸激酶（AK）的开放/关闭转变被视为蛋白质大规模构象转变的一个典型例子，尽管有大量实验和计算研究，但该转变的机制仍不清楚。通过广泛的（约50微秒）显式溶剂原子模拟和马尔可夫状态分析，我们对脱辅基形式的AK的这种转变机制有了新的认识。脱辅基AK闭合态的特征是NMP结构域开放，而LID结构域闭合并向其旋转。因此，尽管计算得到的闭合态集合的结构性质与先前报道的FRET和PRE测量结果一致，但我们的模拟表明，与先前对FRET和PRE数据的解释相反，NMP闭合可能在AMP结合之后发生，先前认为脱辅基状态能够采样完全闭合构象以进行“配体选择”。发现闭合态集合在动力学上是异质的；开放/关闭转变涉及多条途径和多个时间尺度，这为不同实验中观察到的不同时间尺度提供了新线索。除了结构域间相互作用外，一种新的互信息分析识别出与转变动力学强烈相关的特定结构域内相互作用，支持了先前嵌合体实验的观察结果。虽然我们的结果强调了内部结构域性质在决定脱辅基AK开放/关闭转变动力学中的作用，但在转变过程中未观察到任何显著程度的局部解折叠的证据。这些关于AK的观察结果对我们关于蛋白质构象状态、转变途径和构象变化时间尺度的观点具有普遍意义。从使用两种流行的固定电荷力场进行的模拟中观察到的转变途径的关键特征和时间尺度是稳健且相似的。
