Opuu Vaitea, Simonson Thomas
Institut Chimie Biologie Innovation (CNRS UMR8231), Ecole Supérieure de Physique et Chimie de Paris (ESPCI), 75005 Paris, France.
Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, Institut Polytechnique de Paris, 91128 Palaiseau, France.
Protein Eng Des Sel. 2023 Jan 21;36. doi: 10.1093/protein/gzad017.
Enzyme design is an important application of computational protein design (CPD). It can benefit enormously from the additional chemistries provided by noncanonical amino acids (ncAAs). These can be incorporated into an 'expanded' genetic code, and introduced in vivo into target proteins. The key step for genetic code expansion is to engineer an aminoacyl-transfer RNA (tRNA) synthetase (aaRS) and an associated tRNA that handles the ncAA. Experimental directed evolution has been successfully used to engineer aaRSs and incorporate over 200 ncAAs into expanded codes. But directed evolution has severe limits, and is not yet applicable to noncanonical AA backbones. CPD can help address several of its limitations, and has begun to be applied to this problem. We review efforts to redesign aaRSs, studies that designed new proteins and functionalities with the help of ncAAs, and some of the method developments that have been used, such as adaptive landscape flattening Monte Carlo, which allows an enzyme to be redesigned with substrate or transition state binding as the design target.
酶设计是计算蛋白质设计（CPD）的一个重要应用。它能从非天然氨基酸（ncAA）提供的额外化学性质中极大受益。这些非天然氨基酸可被整合到“扩展”的遗传密码中，并在体内引入到目标蛋白质中。遗传密码扩展的关键步骤是改造一种氨酰 - 转移RNA（tRNA）合成酶（aaRS）以及一种处理非天然氨基酸的相关tRNA。实验性定向进化已成功用于改造aaRS，并将200多种非天然氨基酸整合到扩展密码中。但定向进化有严重局限性，且尚未适用于非天然氨基酸骨架。CPD有助于解决其一些局限性，并且已开始应用于这个问题。我们综述了重新设计aaRS的努力、借助非天然氨基酸设计新蛋白质和功能的研究，以及所使用的一些方法进展，如适应性景观扁平化蒙特卡罗方法，该方法允许以底物或过渡态结合作为设计目标来重新设计酶。
