Department of Chemical Engineering, The Pennsylvania State University, University Park, State College, PA 16802, U.S.A.
Biochem Soc Trans. 2018 Jun 19;46(3):513-522. doi: 10.1042/BST20170272. Epub 2018 Apr 6.
Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors. The procedure then identifies the minimum number of intervening reactions to connect the source and sink metabolites. We also further the pathway design procedure by expanding the search space to include both known and hypothetical reactions, represented by reaction rules, in a new tool termed novoStoic. Reaction rules are derived based on a mixed-integer linear programming (MILP) compatible reaction operator, which allow us to explore natural promiscuous enzymes, engineer candidate enzymes that are not already promiscuous as well as design enzymes. The identified biochemical reaction rules then guide novoStoic to design routes that expand the currently known biotransformation space using a single MILP modeling procedure. We demonstrate the use of the two computational tools in pathway elucidation by designing novel synthetic routes for isobutanol.
计算途径设计工具通常面临平衡共代谢物和辅因子的化学计量以及在单个工作流程中处理反应规则利用的挑战。为此，我们提供了我们小组开发的两种基于化学计量的途径设计工具 optStoic 和 novoStoic 的概述，以解决这些挑战。optStoic 旨在首先确定整体转化的化学计量，优化性能标准（例如高碳/能量效率），并确保对共代谢物和辅因子进行全面搜索。然后，该程序确定连接源和汇代谢物的最小中间反应数。我们还通过在新工具 novoStoic 中扩展搜索空间来包括已知和假设反应（由反应规则表示），进一步扩展了途径设计过程。反应规则是基于混合整数线性规划 (MILP) 兼容的反应算子推导出来的，这使我们能够探索天然的混杂酶，设计候选酶，而候选酶本身并不混杂，以及设计酶。然后，所确定的生化反应规则指导 novoStoic 使用单个 MILP 建模过程设计扩展当前已知生物转化空间的路线。我们通过设计异丁醇的新合成路线来展示这两种计算工具在途径阐明中的用途。
