Synthsys Centre for Systems and Synthetic Biology, Deanery of Biomedical Science, University of Edinburgh, Edinburgh, UK.
Protein Sci. 2021 Jan;30(1):160-167. doi: 10.1002/pro.3971. Epub 2020 Nov 2.
Optimizing synthetic biological systems, for example novel metabolic pathways, becomes more complicated with more protein components. One method of taming the complexity and allowing more rapid optimization is engineering external control into components. Pharmacology is essentially the science of controlling proteins using (mainly) small molecules, and a great deal of information, spread between different databases, is known about structural interactions between these ligands and their target proteins. In principle, protein engineers can use an inverse pharmacological approach to include drug response in their design, by identifying ligand-binding domains from natural proteins that are amenable to being included in a designed protein. In this context, "amenable" means that the ligand-binding domain is in a relatively self-contained subsequence of the parent protein, structurally independent of the rest of the molecule so that its function should be retained in another context. The SynPharm database is a tool, built on to the Guide to Pharmacology database and connected to various structural databases, to help protein engineers identify ligand-binding domains suitable for transfer. This article describes the tool, and illustrates its use in seeking candidate domains for transfer. It also briefly describes already-published proof-of-concept studies in which the CRISPR effectors Cas9 and Cpf1 were placed separately under the control of tamoxifen and mefipristone, by including ligand-binding domains of the Estrogen Receptor and Progesterone Receptor in modified versions of Cas9 and Cpf1. The advantages of drug control or the rival protein-control technology of optogenetics, for different purposes and in different situations, are also briefly discussed.
优化合成生物系统，例如新型代谢途径，随着蛋白质组件的增加变得更加复杂。一种驾驭这种复杂性并允许更快速优化的方法是在组件中引入外部控制工程。药理学本质上是使用（主要）小分子控制蛋白质的科学，并且关于这些配体与其靶蛋白之间的结构相互作用的大量信息，散布在不同的数据库之间。原则上，蛋白质工程师可以通过从天然蛋白质中识别可用于设计蛋白质的配体结合域，将药物反应纳入其设计中。在这种情况下，“可接受”是指配体结合域位于母体蛋白的相对自成一体的子序列中，在结构上与分子的其余部分独立，因此其功能应该在另一个上下文中保留。SynPharm 数据库是一种工具，建立在药理学指南数据库之上，并与各种结构数据库连接，以帮助蛋白质工程师识别适合转移的配体结合域。本文介绍了该工具，并说明了其在寻找候选转移域中的用途。它还简要描述了已经发表的概念验证研究，其中 Cas9 和 Cpf1 的 CRISPR 效应物分别在他莫昔芬和米非司酮的控制下，通过在 Cas9 和 Cpf1 的修饰版本中包含雌激素受体和孕激素受体的配体结合域。还简要讨论了药物控制或光遗传学的竞争蛋白控制技术的优点，用于不同的目的和不同的情况。
