Molecular dynamics free-energy simulations of the binding contribution to the fidelity of T7 DNA polymerase
Molecular dynamics free-energy simulations of the binding contribution to the fidelity of T7 DNA polymerase
复制标题
DOI：
10.1021/jp020791m
复制
发表时间：
2002-06-06
影响因子：
3.3
通讯作者：
Goodman, MF
中科院分区：
文献类型：
--
作者：
Florián, J;Warshel, A;Goodman, MF
使用线性响应 (LRA) 分子动力学模拟检查了 T7 DNA 聚合酶 (pol T7) 活性位点中 Watson-Crick 和错配 dNTP 模板碱基对的相对稳定性。 LRA 方法通过评估平均静电能和范德华能来近似相对结合自由能。将这些计算机模拟的结果与之前在相同理论水平上进行的人类 DNA 聚合酶 P (pol) 三元复合物（Florian, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B, 2002, 106, 5739）的模拟结果进行了比较。结果发现，pol T7 通过更有效地区分最有可能发生在中性抗抗构型中的错配，比 pol 0 对复制保真度提供了更大的结合贡献。 pol T7 在结合步骤中的选择性很大程度上取决于模板-dNTP 相互作用。这些相互作用通过预组织的蛋白质活性位点和位于新形成的碱基对的小沟中的结晶水分子的贡献而得到加强。 pol T7 活性位点比 pol 3 活性位点更有效地限制 dNTP 碱基相对于碱基对平面的垂直位移。另一方面，pol T7活性位点为dNTP碱基在主沟方向上的位移提供了更大的灵活性。
The relative stability of Watson-Crick and mismatched dNTP-template base pairs in the active site of T7 DNA polymerase (pol T7) was examined using linear-response (LRA) molecular dynamics simulations. The LRA method approximates the relative binding free energies by evaluating average electrostatic and van der Waals energies. The results of these computer simulations and the previous simulations of the human DNA polymerase P (pol) ternary complex (Florian, J.; Goodman, M. F.; Warshel, A. J. Phys. Chem. B, 2002, 106, 5739) carried out at the same theoretical level were compared. It was found that pol T7 provides a larger binding contribution to the replication fidelity than pol 0 by discriminating more effectively against mismatches that are most probable to occur in the neutral anti-anti configurations. The selectivity of the pol T7 in the binding step is largely determined by the template-dNTP interactions. These interactions are strengthened by the preorganized protein active site and the contribution of the crystallographic water molecule positioned in the minor groove of the newly forming base pair. The pol T7 active site limits the vertical displacements of dNTP base relative to the base-pair plane more effectively than the pol 3 active site. On the other hand, the pol T7 active site provides greater flexibility for the dNTP base to be displaced in the major-groove direction.