Snow Catherine, Qi Guoying, Hayward Steven
School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom.
Proteins. 2007 May 1;67(2):325-37. doi: 10.1002/prot.21280.
Essential dynamics sampling simulations of the domain conformations of unliganded Escherichia coli adenylate kinase have been performed to determine whether the ligand-induced closed-domain conformation is accessible to the open unliganded enzyme. Adenylate kinase is a three- domain protein with a central CORE domain and twoflanking domains, the LID and the NMPbind domains. The sampling simulations were applied to the CORE and NMPbind domain pair and the CORE and LID domain pair separately. One aim is to compare the results to those of a similar study on the enzyme citrate synthase to determine whether a similar domain-locking mechanism operates in adenylate kinase. Although for adenylate kinase the simulations suggest that the closed-domain conformation of the unliganded enzyme is at a slightly higher free energy than the open for both domain pairs, the results are radically different to those found for citrate synthase. In adenylate kinase the targeted domain conformations could always be achieved, whereas this was not the case in citrate synthase due to an apparent free-energy barrier between the open and closed conformations. Adenylate kinase has been classified as a protein that undergoes closure through a hinge mechanism, whereas citrate synthase has been assigned to the shear mechanism. This was quantified here in terms of the change in the number of interdomain contacting atoms upon closure which showed a considerable increase in adenylate kinase. For citrate synthase this number remained largely the same, suggesting that the domain faces slide over each other during closure. This suggests that shear and hinge mechanisms of domain closure may relate to the existence or absence of an appreciable barrier to closure for the unliganded protein, as the latter can hinge comparatively freely, whereas the former must follow a more constrained path. In general though it appears a bias toward keeping the unliganded enzyme in the open-domain conformation may be a common feature of domain enzymes.
已对未结合配体的大肠杆菌腺苷酸激酶结构域构象进行了必要动力学采样模拟，以确定开放的未结合配体酶是否可转变为配体诱导的闭合结构域构象。腺苷酸激酶是一种三结构域蛋白，有一个中央核心结构域以及两个侧翼结构域，即LID结构域和NMP结合结构域。采样模拟分别应用于核心结构域与NMP结合结构域对以及核心结构域与LID结构域对。一个目的是将结果与对柠檬酸合酶的类似研究结果进行比较，以确定腺苷酸激酶中是否存在类似的结构域锁定机制。尽管对于腺苷酸激酶，模拟表明未结合配体的酶的闭合结构域构象对于这两个结构域对而言，其自由能略高于开放构象，但结果与柠檬酸合酶的结果截然不同。在腺苷酸激酶中，目标结构域构象总能实现，而在柠檬酸合酶中却并非如此，因为开放构象与闭合构象之间存在明显的自由能障碍。腺苷酸激酶已被归类为通过铰链机制发生闭合的蛋白质，而柠檬酸合酶则被归为剪切机制。此处根据闭合时结构域间接触原子数量的变化对其进行了量化，结果显示腺苷酸激酶中该数量有显著增加。对于柠檬酸合酶，该数量基本保持不变，这表明在闭合过程中结构域表面相互滑动。这表明结构域闭合的剪切和铰链机制可能与未结合配体的蛋白质闭合时是否存在明显障碍有关，因为后者可以相对自由地铰链转动，而前者必须遵循更受限制的路径。不过总体而言，使未结合配体的酶保持在开放结构域构象的倾向似乎是结构域酶的一个共同特征。
