QM/MM calculations suggest a novel intermediate following the proton abstraction catalyzed by thymidylate synthase.
QM/MM calculations suggest a novel intermediate following the proton abstraction catalyzed by thymidylate synthase.
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DOI：
10.1021/bi400267q
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发表时间：
2013-04-02
期刊：
影响因子：
2.9
通讯作者：
Kohen, Amnon
中科院分区：
文献类型：
--
作者：
Wang, Zhen;Ferrer, Silvia;Moliner, Vicent;Kohen, Amnon
共价C-H键的断裂是能量要求最高的化学转化之一，但生物学上是必需的。胸苷酸合成酶（TSase）催化的反应中涉及两个C-H键裂解，TSase为大多数生物体提供唯一的从头胸苷酸来源（即DNA碱基T）。我们的QM/MM自由能计算表明，C-H→O质子转移有三个能量相似但结构不同的过渡态。这些特征与我们以前关于C-H→C氢化物转移的计算结果不同，解释了这两个C-H键活化步骤的KIE随温度变化的差异.计算还表明，传统上提出的蛋白质和底物之间的共价键（C6-S键）在多步催化反应过程中非常不稳定。集体蛋白质运动不仅有助于裂解C6-S键以稳定质子转移步骤的过渡态，而且还在该步骤结束时重排H-键网络以准备后续化学步骤的活性位点。这些计算结果说明了特定蛋白质残基的功能，调和许多以前的实验观察，并为未来的实验研究所提出的机制提供指导。在我们的模拟中观察到的蛋白质和配体的同步构象变化表明蛋白质运动参与酶促反应的反应坐标。我们的计算结果表明，存在新的反应中间体不共价结合TSase，这可能会导致一类新的药物靶向DNA生物合成。
The cleavage of covalent C-H bonds is one of the most energetically demanding, yet biologically essential, chemical transformations. Two C-H bond cleavages are involved in the reaction catalyzed by thymidylate synthase (TSase), which provides the sole de novo source of thymidylate (i.e. the DNA base T) for most organisms. Our QM/MM free energy calculations show that the C-H→O proton transfer has three transition states that are energetically similar but structurally diverse. These characteristics are different from our previous calculation results on the C-H→C hydride transfer, providing an explanation for differences in temperature dependences of KIEs on these two C-H bond activation steps. The calculations also suggest that the traditionally-proposed covalent bond between the protein and substrate (the C6-S bond) is very labile during the multi-step catalytic reaction. Collective protein motions not only assist cleavage of the C6-S bond to stabilize the transition state of the proton transfer step, but also rearrange the H-bond network at the end of this step to prepare the active site for subsequent chemical steps. These computational results illustrate functionalities of specific protein residues that reconcile many previous experimental observations, and provide guidance for future experiments to examine the proposed mechanisms. The synchronized conformational changes in the protein and ligands observed in our simulations demonstrate participation of protein motions in the reaction coordinate of enzymatic reactions. Our computational findings suggest the existence of new reaction intermediates not covalently bound to TSase, which may lead to a new class of drugs targeting DNA biosynthesis.
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影响因子：
2.9
作者：
Hyatt, DC;Maley, F;Montfort, WR
通讯作者：
Montfort, WR
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
4.4
作者：
BECKE, AD
通讯作者：
BECKE, AD
影响因子：
4.4
作者：
JORGENSEN, WL;CHANDRASEKHAR, J;KLEIN, ML
通讯作者：
KLEIN, ML
DOI：
10.1016/s0925-4439(02)00083-2
发表时间：
2002-07-18
影响因子：
6.2
作者：
Costi, MP;Tondi, D;Stroud, RM
通讯作者：
Stroud, RM