Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
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DOI：
10.1073/pnas.0706443104
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发表时间：
2007-11-20
影响因子：
11.1
通讯作者：
Brooks, Charles L., III
中科院分区：
文献类型：
--
作者：
Arora, Karunesh;Brooks, Charles L., III
蛋白质的大规模构象变化通常与底物的结合有关。由于构象变化可能与酶的功能有关，因此了解这些运动的动力学和能量学非常重要。我们已经描绘了磷酸转移酶腺苷酸激酶（AdK）的抑制剂的存在和不存在下的原子详细的构象转换途径。计算的自由能曲线与构象转变提供了详细的机制的见解，以及动力学信息，配体结合机制。具体而言，潜在的平均力计算表明，在无配体的状态下，没有显着的障碍分开的开放和封闭的构象的AdK。酶样品接近封闭构象，即使在没有其底物的情况下。配体结合事件发生较晚，朝向封闭状态，并改变自由能景观。在配体结合状态下，闭合构象在能量上最有利，具有大的打开势垒。这些结果强调了酶的基本动力学性质，并表明AdK的构象转变比晶体结合和非结合状态之间的仅仅两个状态的跳跃更复杂。基于酶在开放和封闭状态下存在多种构象，提出了配体结合的不同观点。我们估算的构象转变活化能也与实验结果雅阁。
Large-scale conformational changes in proteins are often associated with the binding of a substrate. Because conformational changes may be related to the function of an enzyme, understanding the kinetics and energetics of these motions is very important. We have delineated the atomically detailed conformational transition pathway of the phosphotransferase enzyme adenylate kinase (AdK) in the absence and presence of an inhibitor. The computed free energy profiles associated with conformational transitions offer detailed mechanistic insights into, as well as kinetic information on, the ligand binding mechanism. Specifically, potential of mean force calculations reveal that in the ligand-free state, there is no significant barrier separating the open and closed conformations of AdK. The enzyme samples near closed conformations, even in the absence of its substrate. The ligand binding event occurs late, toward the closed state, and transforms the free energy landscape. In the ligand-bound state, the closed conformation is energetically most favored with a large barrier to opening. These results emphasize the underlying dynamic nature of the enzyme and indicate that the conformational transitions in AdK are more intricate than a mere two-state jump between the crystal-bound and -unbound states. Based on the existence of the multiple conformations of the enzyme in the open and closed states, a different viewpoint of ligand binding is presented. Our estimated activation energy barrier for the conformational transition is also in reasonable accord with the experimental findings.