National Institute of Standards and Technology, Gaithersburg, MD, USA.
SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
Mol Syst Biol. 2021 Mar;17(3):e10179. doi: 10.15252/msb.202010179.
Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli, LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.
变构作用是一种基本的生物物理机制，它是细胞感应、信号传递和代谢的基础。然而，对于变构基因型-表型关系的定量理解仍然难以捉摸。在这里，我们报告了一种变构蛋白（大肠杆菌的 lac 阻遏物 LacI）的基因型-表型景观的大规模测量。我们使用一种结合了长读和短读 DNA 测序的方法，定量测量了近 10 种 LacI 遗传传感器变体的剂量反应曲线。由此产生的数据提供了 LacI 变构作用中氨基酸取代对其影响的定量图谱，并揭示了系统的序列-结构-功能关系。我们发现，在许多情况下，变构表型可以用加性或神经网络模型进行定量预测，但也会出现不可预测的变化。例如，我们惊讶地发现了一种新的带阻表型，它挑战了变构作用的传统模型，而且这种表型是由几乎沉默的氨基酸取代组合产生的。
