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.

达尔文进化论产生了使地球上生命成为可能的所有酶。通过模拟自然选择，科学家们已经学会了通过突变、选择和扩增的递归循环来定制这些生物催化剂，通常依赖于筛选大型蛋白质文库来有效地调节蛋白质结构、动力学和功能之间的复杂相互作用。在这里，我们表明，通过在文库设计阶段去除不稳定的突变并利用基因合成的最新进展，我们可以加速计算设计的酶的进化。在短短五轮进化中，我们产生了一种 Kemp 消除酶——一种从碳中转移质子的酶促模型系统——它使质子提取步骤 >10 比未催化反应快⁸ 倍。将所得变体与先前进化的 Kemp 消除酶 HG3.17 重新组合，该酶表现出相似的活性，但相差 29 个取代，使我们能够绘制设计师酶适应度景观的地形图，强调给定的蛋白质支架可以容纳多个同样可行的解决方案来解决特定的催化问题。