题目：

Comparing mutagenesis and simulations as tools for identifying functionally important sequence changes for protein thermal adaptation
比较突变和模拟这两种方法在确定蛋白质热适应过程中重要功能序列的改变的应用

作者：

Ming-ling Liao, George N. Somero, and Yun-wei Dong 

 董云伟，研究方向，全球变化背景下潮间带海洋无脊椎动物生理生态学

单位：

厦门大学 海洋与地球科学学院 海洋环境科学国家重点实验室

时间

2018-12

期刊：

PNAS

摘要：

背景:

Comparative studies of orthologous proteins of species evolved at different temperatures have revealed consistent patterns of temperature-related variation in thermal stabilities of structure and function.
   关于比较物种间因为进化在不同温度产生的不同直系同源蛋白的研究，揭示了一些在结构和功能的热稳定性上一致的模式。

问题1：

However, the precise mechanisms by which interspecific variations in sequence foster these adaptive changes remain largely unknown.
   然而，种间序列变异促进这些自适应变化的精确机制在很大程度上仍是未知的。

方法1：

Here, we compare orthologs of cytosolic malate dehydrogenase (cMDH) from marine molluscs adapted to temperatures ranging from −1.9 °C (Antarctica) to ～55 °C (South China coast) and show how amino acid usage in different regions of the enzyme (surface, intermediate depth, and protein core) varies with adaptation temperature.
   这里，我们比较了来自于海洋软体动物的胞质苹果酸脱氢酶，它们能够适应从-1.9摄氏度（南极洲）到~55摄氏度的温度变化。然后展示了随着适应温度的过程，氨基酸在酶不同区域（表层，中层和内部）中的使用差异。

结论1：

This eukaryotic enzyme follows some but not all of the rules established in comparisons of archaeal and bacterial proteins.
   这个真核细胞的酶遵循了一些但不是所有的，已经在古菌和细菌蛋白比较中建立的一些规则。

问题2：

To link the effects of specific amino acid substitutions with adaptive variations in enzyme thermal stability,
    为了连接特定氨基酸替代的作用和酶热稳定性的适应差异，

方法2：

we combined site-directed mutagenesis (SDM) and in vitro protein experimentation with in silico mutagenesis using molecular dynamics simulation (MDS) techniques.
  我们结合了定点诱变（SDM）和采用分子动力学模拟技术（MDS）产生硅诱变的体外蛋白实验。

结论2：

SDM and MDS methods generally but not invariably yielded common effects on protein stability. MDS analysis is shown to provide insights into how specific amino acid substitutions affect the conformational flexibilities of mobile regions (MRs) of the enzyme that are essential for binding and catalysis. Whereas these substitutions invariably lie outside of the MRs, they effectively transmit their flexibility-modulating effects to the MRs through linked interactions among surface residues.
   定点突变和分子动力学模拟通常但不是总是对蛋白稳定性产生共同效果。MDS提供了一个视角来深入分析特定氨基酸替换是如何影响酶中对结合和催化必需的可变区域（MRs）的构象变化。虽然这些替换总是位于可变区域的之外，但它们通过连接表面残基间的相互作用，将它们的柔性调节作用有效的传递给可变区域。

意义：

This discovery illustrates that regions of the protein surface lying outside of the site of catalysis can help establish an enzyme’s thermal responses and foster evolutionary adaptation of function.
   这项发现揭示了蛋白位于催化点外的表面区域能够帮助酶建立热反应，促进功能上的进化性适应。

​