Mathematical Models of Protease-Based Enzymatic Biosensors
Mathematical Models of Protease-Based Enzymatic Biosensors
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DOI：
10.1021/acssynbio.9b00279
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发表时间：
2020-02-01
影响因子：
4.7
通讯作者：
Sontag, Eduardo D.
中科院分区：
文献类型：
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作者：
Agrawal, Deepak K.;Dolan, Elliott M.;Sontag, Eduardo D.
合成生物学的一个重要目标是建造具有明确输入输出关系的生物传感器和电路，这些传感器和电路以自然生物系统中的速度运行。然而，对于分子计算，最常用的遗传电路元件通常涉及从输入检测到输出信号产生的几个步骤：转录、翻译和翻译后修饰。这些多个步骤加在一起需要长达几个小时才能对单个刺激做出反应，这限制了基因电路的整体速度和复杂性。为了解决这一差距，已经提出了完全依赖翻译后步骤来实现反应网络的分子框架，该反应网络可以在几秒到几分钟的时间尺度上处理输入。在这里，我们建立了能够产生布尔逻辑功能的快速生物传感器的数学模型。我们使用了基于蛋白酶的化学和光诱导开关，研究了它们的操作，并提供了它们作为开关使用的选择指南。作为概念验证，我们在体外实现了雷帕霉素诱导的开关，并证明其响应与我们模型的预测定性一致。然后，我们使用这些开关作为基本模块，开发生物传感器的模型，这些模型可以执行OR和XOR布尔逻辑计算，同时使用反应条件作为调整参数。我们使用敏感性分析来确定输出对蛋白质分解和蛋白质结合反应参数的依赖时间的敏感性。这些基于快速蛋白酶的生物传感器可以用来实现复杂的分子电路，具有可控和算法处理多个输入的能力。我们的评估和优化电路性能的框架也可以应用于其他分子逻辑电路。
An important goal of synthetic biology is to build biosensors and circuits with well-defined input-output relationships that operate at speeds found in natural biological systems. However, for molecular computation, most commonly used genetic circuit elements typically involve several steps from input detection to output signal production: transcription, translation, and post-translational modifications. These multiple steps together require up to several hours to respond to a single stimulus, and this limits the overall speed and complexity of genetic circuits. To address this gap, molecular frameworks that rely exclusively on post-translational steps to realize reaction networks that can process inputs at a time scale of seconds to minutes have been proposed. Here, we build mathematical models of fast biosensors capable of producing Boolean logic functionality. We employ protease-based chemical and light-induced switches, investigate their operation, and provide selection guidelines for their use as on-off switches. As a proof of concept, we implement a rapamycin-induced switch in vitro and demonstrate that its response qualitatively agrees with the predictions from our models. We then use these switches as elementary blocks, developing models for biosensors that can perform OR and XOR Boolean logic computation while using reaction conditions as tuning parameters. We use sensitivity analysis to determine the time-dependent sensitivity of the output to proteolytic and protein-protein binding reaction parameters. These fast protease-based biosensors can be used to implement complex molecular circuits with a capability of processing multiple inputs controllably and algorithmically. Our framework for evaluating and optimizing circuit performance can be applied to other molecular logic circuits.