Molecular Mechanism of ATP Hydrolysis in an ABC Transporter.
Molecular Mechanism of ATP Hydrolysis in an ABC Transporter.
复制标题
DOI：
10.1021/acscentsci.8b00369
复制
发表时间：
2018-10-24
影响因子：
18.2
通讯作者：
Schäfer LV
中科院分区：
文献类型：
--
作者：
Prieß M;Göddeke H;Groenhof G;Schäfer LV
核苷三磷酸(NTP)的水解在许多生物分子系统的功能中起着关键作用。然而，从原子水平上理解与其相关的结构、动力学和自由能变化的催化反应的化学往往仍然未知。在这里，我们报道了三磷酸腺苷(ATP)在三磷酸腺苷结合盒(ABC)转运体BtuCD-F中水解的分子机制。由混合量子力学/分子力学(QM/MM)分子动力学(MD)模拟得到的自由能分布表明，水解反应是逐步进行的。首先，活化的裂解水分子在三磷酸腺苷γ-磷酸上的亲核攻击产生作为中间产物的二磷酸腺苷+磷酸二氢钾。一种保守的谷氨酸位于非常接近γ-磷酸的位置，瞬时地接受质子，从而起到催化碱的作用。在第二步中，质子从催化碱基转移回γ-磷酸，生成ADP+H_2PO_4-。这两个化学反应步骤之后是氢键网络的重排和镁离子的配位。由计算的自由能垒估算的速率常数与实验符合得很好。反应的总自由能变化接近于零，这表明磷酸键断裂本身并不为构象变化提供动力。相反，ATP结合对于核苷酸结合区的紧密二聚化和跨膜区从内向外的转变是必不可少的，而ATP水解会重置构象周期。这一机制可能与所有ABC转运蛋白相关，也可能对其他NTPase有影响，因为参与核苷酸结合和水解的许多残基是严格保守的。ABC转运蛋白BtuCD中的ATP水解遵循三步机制。蛋白质中的反应自由能接近于零，因此不能为构象转变提供动力。
Hydrolysis of nucleoside triphosphate (NTP) plays a key role for the function of many biomolecular systems. However, the chemistry of the catalytic reaction in terms of an atomic-level understanding of the structural, dynamic, and free energy changes associated with it often remains unknown. Here, we report the molecular mechanism of adenosine triphosphate (ATP) hydrolysis in the ATP-binding cassette (ABC) transporter BtuCD-F. Free energy profiles obtained from hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations show that the hydrolysis reaction proceeds in a stepwise manner. First, nucleophilic attack of an activated lytic water molecule at the ATP γ-phosphate yields ADP + HPO42– as intermediate product. A conserved glutamate that is located very close to the γ-phosphate transiently accepts a proton and thus acts as catalytic base. In the second step, the proton is transferred back from the catalytic base to the γ-phosphate, yielding ADP + H2PO4–. These two chemical reaction steps are followed by rearrangements of the hydrogen bond network and the coordination of the Mg2+ ion. The rate constant estimated from the computed free energy barriers is in very good agreement with experiments. The overall free energy change of the reaction is close to zero, suggesting that phosphate bond cleavage itself does not provide a power stroke for conformational changes. Instead, ATP binding is essential for tight dimerization of the nucleotide-binding domains and the transition of the transmembrane domains from inward- to outward-facing, whereas ATP hydrolysis resets the conformational cycle. The mechanism is likely relevant for all ABC transporters and might have implications also for other NTPases, as many residues involved in nucleotide binding and hydrolysis are strictly conserved. ATP hydrolysis in ABC transporter BtuCD follows a three-step mechanism. The reaction free energy in the protein is close to zero and thus cannot provide a power stroke for conformational transitions.
登录
查看更多内容
影响因子：
5.5
作者：
Hess, Berk;Kutzner, Carsten;Lindahl, Erik
通讯作者：
Lindahl, Erik
影响因子：
3.4
作者：
Dittrich, M;Hayashi, S;Schulten, K
通讯作者：
Schulten, K
DOI：
10.1073/pnas.0800191105
发表时间：
2008-04-01
影响因子：
11.1
作者：
Ernst, Robert;Kueppers, Petra;Schmitt, Lutz
通讯作者：
Schmitt, Lutz
影响因子：
5.5
作者：
Hess, Berk
通讯作者：
Hess, Berk
影响因子：
4.4
作者：
Horn, HW;Swope, WC;Head-Gordon, T
通讯作者：
Head-Gordon, T