Enriching productive mutational paths accelerates enzyme evolution

IF 12.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Nature chemical biology Pub Date : 2024-09-11 DOI:10.1038/s41589-024-01712-3
David Patsch, Thomas Schwander, Moritz Voss, Daniela Schaub, Sean Hüppi, Michael Eichenberger, Peter Stockinger, Lisa Schelbert, Sandro Giger, Francesca Peccati, Gonzalo Jiménez-Osés, Mojmír Mutný, Andreas Krause, Uwe T. Bornscheuer, Donald Hilvert, Rebecca M. Buller
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Abstract

Darwinian evolution has given rise to all the enzymes that enable life on Earth. Mimicking natural selection, scientists have learned to tailor these biocatalysts through recursive cycles of mutation, selection and amplification, often relying on screening large protein libraries to productively modulate the complex interplay between protein structure, dynamics and function. Here we show that by removing destabilizing mutations at the library design stage and taking advantage of recent advances in gene synthesis, we can accelerate the evolution of a computationally designed enzyme. In only five rounds of evolution, we generated a Kemp eliminase—an enzymatic model system for proton transfer from carbon—that accelerates the proton abstraction step >108-fold over the uncatalyzed reaction. Recombining the resulting variant with a previously evolved Kemp eliminase HG3.17, which exhibits similar activity but differs by 29 substitutions, allowed us to chart the topography of the designer enzyme’s fitness landscape, highlighting that a given protein scaffold can accommodate several, equally viable solutions to a specific catalytic problem. By enriching productive mutational paths, a Kemp eliminase that speeds up proton abstraction >108-fold was developed in only five evolution rounds. Recombining it with a variant differing by 29 substitutions revealed the underlying fitness landscape.

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丰富富有成效的突变途径可加速酶的进化
达尔文进化论催生了地球上所有的酶。模仿自然选择,科学家们学会了通过突变、选择和放大的递归循环来定制这些生物催化剂,通常依靠筛选大型蛋白质库来有效调节蛋白质结构、动力学和功能之间复杂的相互作用。在这里,我们展示了通过在文库设计阶段去除不稳定突变,并利用基因合成的最新进展,我们可以加速计算设计酶的进化。仅经过五轮进化,我们就生成了一种坎普消除酶--一种从碳中转移质子的酶模型系统--与未催化反应相比,它能将质子抽取步骤加速 108 倍。我们将产生的变体与之前进化的肯普消除酶 HG3.17 进行重组,后者具有相似的活性,但有 29 个取代位点,这使我们能够绘制出设计酶的适应性地形图,突出表明特定的蛋白质支架可以容纳几种同样可行的解决方案来解决特定的催化问题。
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来源期刊
Nature chemical biology
Nature chemical biology 生物-生化与分子生物学
CiteScore
23.90
自引率
1.40%
发文量
238
审稿时长
12 months
期刊介绍: Nature Chemical Biology stands as an esteemed international monthly journal, offering a prominent platform for the chemical biology community to showcase top-tier original research and commentary. Operating at the crossroads of chemistry, biology, and related disciplines, chemical biology utilizes scientific ideas and approaches to comprehend and manipulate biological systems with molecular precision. The journal embraces contributions from the growing community of chemical biologists, encompassing insights from chemists applying principles and tools to biological inquiries and biologists striving to comprehend and control molecular-level biological processes. We prioritize studies unveiling significant conceptual or practical advancements in areas where chemistry and biology intersect, emphasizing basic research, especially those reporting novel chemical or biological tools and offering profound molecular-level insights into underlying biological mechanisms. Nature Chemical Biology also welcomes manuscripts describing applied molecular studies at the chemistry-biology interface due to the broad utility of chemical biology approaches in manipulating or engineering biological systems. Irrespective of scientific focus, we actively seek submissions that creatively blend chemistry and biology, particularly those providing substantial conceptual or methodological breakthroughs with the potential to open innovative research avenues. The journal maintains a robust and impartial review process, emphasizing thorough chemical and biological characterization.
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