Liu Ye, Yu Zhengfei, Zhu Jingxuan, Wang Song, Xu Dong, Han Weiwei
Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, Changchun, China.
State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, China.
Front Chem. 2018 Jun 14;6:223. doi: 10.3389/fchem.2018.00223. eCollection 2018.
Argonaute (TtAgo) is a complex, which is consisted of 5'-phosphorylated guide DNA and a series of target DNA with catalytic activities at high temperatures. To understand why high temperatures are needed for the catalytic activities, three molecular dynamics simulations and binding free energy calculations at 310, 324, and 338K were performed for the TtAgo-DNA complex to explore the conformational changes between 16-mer guide DNA/15-mer target DNA and TtAgo at different temperatures. The simulation results indicate that a collapse of a small β-strand (residues 507-509) at 310 K caused Glu512 to move away from the catalytic residues Asp546 and Asp478, resulting in a decrease in catalytic activity, which was not observed in the simulations at 324 and 338 K. The nucleic acid binding channel became enlarged at 324 and 338K, thereby facilitating the DNA to slide in. Binding free energy calculations and hydrogen bond occupancy indicated that the interaction between TtAgo and the DNA was more stable at 324K and 338K than at 310 K. The DNA binding pocket residues Lys575 and Asn590 became less solvent accessible at 324 and 338K than at 310 K to influence hydrophilic interaction with DNA. Our simulation studies shed some light on the mechanism of TtAgo and explained why a high temperature was needed by TtAgo during gene editing of CRISPR.
嗜热栖热菌 Argonaute（TtAgo）是一种复合物，它由 5'-磷酸化引导 DNA 和一系列在高温下具有催化活性的靶 DNA 组成。为了理解催化活性为何需要高温，我们对 TtAgo-DNA 复合物在 310K、324K 和 338K 下进行了三次分子动力学模拟和结合自由能计算，以探究 16 聚体引导 DNA/15 聚体靶 DNA 与 TtAgo 在不同温度下的构象变化。模拟结果表明，在 310K 时，一小段β链（残基 507 - 509）的塌陷导致 Glu512 远离催化残基 Asp546 和 Asp478，从而导致催化活性降低，而在 324K 和 338K 的模拟中未观察到这种情况。在 324K 和 338K 时，核酸结合通道变大，从而便于 DNA 滑入。结合自由能计算和氢键占有率表明，TtAgo 与 DNA 之间的相互作用在 324K 和 338K 时比在 310K 时更稳定。与 310K 相比，在 324K 和 338K 时，DNA 结合口袋残基 Lys575 和 Asn590 的溶剂可及性降低，从而影响与 DNA 的亲水相互作用。我们的模拟研究为 TtAgo 的作用机制提供了一些线索，并解释了 TtAgo 在 CRISPR 基因编辑过程中为何需要高温。
