Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA.
Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.
Nucleic Acids Res. 2018 Jan 4;46(D1):D509-D515. doi: 10.1093/nar/gkx893.
ClusterCAD is a web-based toolkit designed to leverage the collinear structure and deterministic logic of type I modular polyketide synthases (PKSs) for synthetic biology applications. The unique organization of these megasynthases, combined with the diversity of their catalytic domain building blocks, has fueled an interest in harnessing the biosynthetic potential of PKSs for the microbial production of both novel natural product analogs and industrially relevant small molecules. However, a limited theoretical understanding of the determinants of PKS fold and function poses a substantial barrier to the design of active variants, and identifying strategies to reliably construct functional PKS chimeras remains an active area of research. In this work, we formalize a paradigm for the design of PKS chimeras and introduce ClusterCAD as a computational platform to streamline and simplify the process of designing experiments to test strategies for engineering PKS variants. ClusterCAD provides chemical structures with stereochemistry for the intermediates generated by each PKS module, as well as sequence- and structure-based search tools that allow users to identify modules based either on amino acid sequence or on the chemical structure of the cognate polyketide intermediate. ClusterCAD can be accessed at https://clustercad.jbei.org and at http://clustercad.igb.uci.edu.
ClusterCAD 是一个基于网络的工具包，旨在利用 I 型模块化聚酮合酶 (PKS) 的共线结构和确定性逻辑，应用于合成生物学领域。这些大型合酶的独特组织，加上其催化结构域构建块的多样性，激发了人们利用 PKS 的生物合成潜力，用于微生物生产新型天然产物类似物和工业相关的小分子。然而，对 PKS 折叠和功能的决定因素的理论认识有限，这对设计活性变体构成了实质性的障碍，并且确定可靠构建功能性 PKS 嵌合体的策略仍然是一个活跃的研究领域。在这项工作中，我们为 PKS 嵌合体的设计制定了一个范例，并引入了 ClusterCAD 作为一个计算平台，以简化和简化设计实验的过程，以测试用于工程 PKS 变体的策略。ClusterCAD 为每个 PKS 模块生成的中间体提供了具有立体化学的化学结构，以及基于序列和结构的搜索工具，允许用户根据氨基酸序列或同源聚酮中间物的化学结构来识别模块。ClusterCAD 可在 https://clustercad.jbei.org 和 http://clustercad.igb.uci.edu 访问。
