Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study.
Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study.
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DOI：
10.3389/fchem.2018.00223
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发表时间：
2018
影响因子：
5.5
通讯作者：
Han W
中科院分区：
文献类型：
--
作者：
Liu Y;Yu Z;Zhu J;Wang S;Xu D;Han W
热嗜热菌Argonaute （TtAgo）是一种由5 ' -磷酸化的引导DNA和一系列在高温下具有催化活性的靶DNA组成的复合物。为了解TtAgo-DNA络合物在310、324和338K下的分子动力学模拟和结合自由能计算，探究了16-mer引导DNA/15-mer靶DNA与TtAgo在不同温度下的构象变化。模拟结果表明，在310 K时，一个小的β-链（残基507-509）崩溃导致Glu512远离催化残基Asp546和Asp478，导致催化活性下降，而在324和338 K的模拟中没有观察到这一点。核酸结合通道在324和338K时扩大，从而有利于DNA的滑动。结合自由能计算和氢键占用率表明，TtAgo与DNA的相互作用在324K和338K时比在310 K时更稳定。DNA结合袋残基Lys575和Asn590在324和338K时比在310 K时溶剂可及性更低，从而影响与DNA的亲水性相互作用。我们的模拟研究揭示了TtAgo的作用机制，并解释了为什么TtAgo在CRISPR基因编辑过程中需要高温。
Thermus thermophiles 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.