Protein activation and deactivation is central to a variety of biological mechanisms, including cellular signaling and transport. Unimolecular fluorescent resonance energy transfer (FRET) probes are a class of fusion protein sensors that allow biologists to visualize using an optical microscope whether specific proteins are activated due to the presence nearby of small drug-like signaling molecules, ligands or analytes. Often such probes comprise a donor fluorescent protein attached to a ligand binding domain, a sensor or reporter domain attached to the acceptor fluorescent protein, with these ligand binding and sensor domains connected by a protein linker. Various choices of linker type are possible ranging from highly flexible proteins to hinge-like proteins. It is also possible to select donor and acceptor pairs according to their corresponding Föster radius, or even to mutate binding and sensor domains so as to change their binding energy in the activated or inactivated states. The focus of the present work is the exploration through simulation of the impact of such choices on sensor performance.

蛋白质激活和失活对于包括细胞信号传导和转运在内的多种生物学机制至关重要。单分子荧光共振能量转移（FRET）探针是一类融合蛋白传感器，可使生物学家使用光学显微镜观察是否由于小的药物样信号分子，配体或分析物的存在而激活了特定蛋白。通常，此类探针包含附接到配体结合结构域的供体荧光蛋白，附接到受体荧光蛋白的传感器或报道分子结构域，这些配体结合和传感器结构域通过蛋白质接头连接。接头类型的多种选择是可能的，范围从高度灵活的蛋白质到铰链样蛋白质。还可以根据它们对应的Föster半径选择供体和受体对，或者甚至突变结合域和传感器域，以在激活或灭活状态下改变它们的结合能。本工作的重点是通过模拟这些选择对传感器性能的影响进行探索。