Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes.
Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes.
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自然进化为设计酶的实验室进化提供了强有力的线索。
DOI：
10.1073/pnas.2207904119
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发表时间：
2022-08-02
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
作者：
如何在实验室进化中优化非生物Kemp消除酶仍然是一个巨大的挑战。以往的机械研究只涵盖了很少的设计，导致对优化过程的部分理解。在这里，我们证明了从天然蛋白支架同源物中提取的进化信息与实验室进化中引入的各种突变体的Kemp消除活性相关。因此，即使活性位点被替换以催化新的反应，形成天然蛋白质支架的潜在进化压力仍然是相关的。目前的研究揭示了酶的结构，酶的进化，以及在酶设计中插入催化景观的力量。实验室进化与计算酶设计相结合，提供了产生新型生物催化剂的机会。然而，了解实验室进化如何通过引入看似随机的突变来优化设计酶一直是一项挑战。通过实验室进化优化的典型酶是非生物Kemp消除酶，最初通过将活性位点残基嫁接到天然蛋白质支架中来设计。在这里，我们使用最大熵模型将实验室进化的Kemp消去酶的催化能力与从其天然同源序列推断的统计能量（）联系起来。定向进化产生的设计与增强的活性和降低的稳定性相关，从而显示出稳定性-活性的权衡。相反，在催化活性的远端区域（其中远端残基对催化很重要）的突变体与活性呈强反相关。这些发现为蛋白质支架在适应新的酶功能中的作用提供了一个深入的见解。这也表明景观中的山谷可以指导非生物催化酶的设计。总的来说，实验室和自然进化之间的联系有助于理解实验室中优化了什么，以及自然界中如何出现新的酶功能，并为计算酶设计提供指导。
Rationalizing how the abiological Kemp eliminase is optimized in laboratory evolution remains a great challenge. Previous mechanistic studies only cover very few designs, leading to a partial understanding of the optimization process. Here, we demonstrate that the evolutionary information distilled from the homologs of natural protein scaffold correlates with the Kemp elimination activity of various mutants introduced in laboratory evolution. Therefore, even if an active site is replaced to catalyze a new reaction, the underlying evolutionary pressures that shaped the natural protein scaffold are still relevant. The present study sheds light on enzyme architecture, enzyme evolution, and the power of interpolating the catalytic landscape in enzyme design. Laboratory evolution combined with computational enzyme design provides the opportunity to generate novel biocatalysts. Nevertheless, it has been challenging to understand how laboratory evolution optimizes designer enzymes by introducing seemingly random mutations. A typical enzyme optimized with laboratory evolution is the abiological Kemp eliminase, initially designed by grafting active site residues into a natural protein scaffold. Here, we relate the catalytic power of laboratory-evolved Kemp eliminases to the statistical energy () inferred from their natural homologous sequences using the maximum entropy model. The of designs generated by directed evolution is correlated with enhanced activity and reduced stability, thus displaying a stability-activity trade-off. In contrast, the for mutants in catalytic-active remote regions (in which remote residues are important for catalysis) is strongly anticorrelated with the activity. These findings provide an insight into the role of protein scaffolds in the adaption to new enzymatic functions. It also indicates that the valley in the landscape can guide enzyme design for abiological catalysis. Overall, the connection between laboratory and natural evolution contributes to understanding what is optimized in the laboratory and how new enzymatic function emerges in nature, and provides guidance for computational enzyme design.
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影响因子：
6.8
作者：
Campbell, Eleanor C.;Correy, Galen J.;Jackson, Colin J.
通讯作者：
Jackson, Colin J.
影响因子：
3.3
作者：
Bhowmick, Asmit;Sharma, Sudhir C.;Head-Gordon, Teresa
通讯作者：
Head-Gordon, Teresa
DOI：
10.1073/pnas.0404387101
发表时间：
2004-08-10
影响因子：
11.1
作者：
Kaplan, J;DeGrado, WF
通讯作者：
DeGrado, WF
DOI：
10.1073/pnas.0901522106
发表时间：
2009-06-16
影响因子：
11.1
作者：
Bloom, Jesse D.;Arnold, Frances H.
通讯作者：
Arnold, Frances H.
影响因子：
5.6
作者：
Khersonsky, Olga;Rothlisberger, Daniela;Tawfik, Dan S.
通讯作者：
Tawfik, Dan S.