Intrinsic dynamics of an enzyme underlies catalysis
Intrinsic dynamics of an enzyme underlies catalysis
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DOI：
10.1038/nature04105
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发表时间：
2005-11-03
期刊：
影响因子：
64.8
通讯作者：
Kern, D
中科院分区：
文献类型：
--
作者：
Eisenmesser, EZ;Millet, O;Kern, D
由酶介导的化学催化的一个独特特征是催化活性原子嵌入折叠的蛋白质中。虽然目前对酶功能的理解集中在化学反应和静态三维结构上，但蛋白质的动态性质已被提出具有催化功能（1-5）。构象亚态的概念已经被描述（6）;然而，挑战在于解开蛋白质柔性和酶功能之间的密切联系。在这里，我们表明，蛋白质的内在可塑性是催化的一个关键特征。用核磁共振弛豫实验研究了脯氨酰顺反异构酶亲环素A（CypA）在无底物状态和催化过程中的动力学。在催化过程中检测到的特征酶运动已经存在于游离酶中，其频率对应于催化周转率。这种相关性表明，催化所需的蛋白质运动是酶的内在特性，甚至可能限制总周转率。运动不仅局限于活动位点，而且局限于更广泛的动态网络。鉴于蛋白质中的耦合网络以前已经提出（3，7 -10），我们实验测量的集体性质的运动与突变形式的CypA的使用。我们提出，在催化之前的酶的集体动力学的预先存在是生物催化剂的一个共同特征，蛋白质的结构和动力学之间的协同压力下进化。
A unique feature of chemical catalysis mediated by enzymes is that the catalytically reactive atoms are embedded within a folded protein. Although current understanding of enzyme function has been focused on the chemical reactions and static three-dimensional structures, the dynamic nature of proteins has been proposed to have a function in catalysis(1-5). The concept of conformational substates has been described(6); however, the challenge is to unravel the intimate linkage between protein flexibility and enzymatic function. Here we show that the intrinsic plasticity of the protein is a key characteristic of catalysis. The dynamics of the prolyl cis - trans isomerase cyclophilin A ( CypA) in its substrate-free state and during catalysis were characterized with NMR relaxation experiments. The characteristic enzyme motions detected during catalysis are already present in the free enzyme with frequencies corresponding to the catalytic turnover rates. This correlation suggests that the protein motions necessary for catalysis are an intrinsic property of the enzyme and may even limit the overall turnover rate. Motion is localized not only to the active site but also to a wider dynamic network. Whereas coupled networks in proteins have been proposed previously(3,7-10), we experimentally measured the collective nature of motions with the use of mutant forms of CypA. We propose that the pre-existence of collective dynamics in enzymes before catalysis is a common feature of biocatalysts and that proteins have evolved under synergistic pressure between structure and dynamics.