Predictive shifts in free energy couple mutations to their phenotypic consequences
Predictive shifts in free energy couple mutations to their phenotypic consequences
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DOI：
10.1073/pnas.1907869116
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发表时间：
2019-09-10
影响因子：
11.1
通讯作者：
Phillips, Rob
中科院分区：
文献类型：
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作者：
Chure, Griffin;Razo-Mejia, Manuel;Phillips, Rob
突变是进化探索蛋白质功能景观的关键机制。尽管我们有能力在实验上随意施加突变，但仍然很难将序列水平的扰动与系统水平的反应联系起来。在这里，我们提出了一个框架，集中在测量系统的自由能的变化，以连接个别突变的变构转录抑制因子的参数，管理其响应。我们发现，充满活力的突变的影响可以分为几类，具有特征曲线作为诱导剂浓度的函数。我们实验测试这些诊断预测使用的特点是LacI阻遏大肠杆菌，探测几个突变的DNA结合和诱导剂结合域。我们发现，由于点突变的基因表达的变化，可以通过修改仅描述野生型蛋白质的相应域的模型参数来捕获。这些参数似乎是绝缘的，在DNA结合结构域中的突变只改变DNA亲和力和那些在诱导剂结合结构域只改变变构参数。改变这些参数的子集以与理论预期一致的方式调整系统的自由能。最后，我们表明，诱导配置文件和由此产生的自由能与成对双突变体可以预测与定量的准确性给定的知识的单突变体，识别和定量上位相互作用提供了一种途径。
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level responses. Here, we present a framework centered on measuring changes in the free energy of the system to link individual mutations in an allosteric transcriptional repressor to the parameters which govern its response. We find that the energetic effects of the mutations can be categorized into several classes which have characteristic curves as a function of the inducer concentration. We experimentally test these diagnostic predictions using the well-characterized LacI repressor of Escherichia coli, probing several mutations in the DNA binding and inducer binding domains. We find that the change in gene expression due to a point mutation can be captured by modifying only the model parameters that describe the respective domain of the wild-type protein. These parameters appear to be insulated, with mutations in the DNA binding domain altering only the DNA affinity and those in the inducer binding domain altering only the allosteric parameters. Changing these subsets of parameters tunes the free energy of the system in a way that is concordant with theoretical expectations. Finally, we show that the induction profiles and resulting free energies associated with pairwise double mutants can be predicted with quantitative accuracy given knowledge of the single mutants, providing an avenue for identifying and quantifying epistatic interactions.