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Computational modeling of a new fluorescent biosensor for caspase proteolytic activity improves dynamic range

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2 Author(s)
J. J. -H. Chiang ; Dept. of Electr. & Comput. Eng., Toronto Univ., Ont., Canada ; Kevin Truong

The class of fluorescence resonance energy transfer (FRET) protein biosensors that are useful for measuring protease activity is composed of a tandem fusion of yellow fluorescent protein (YFP), a cleavage recognition sequence, and cyan fluorescent protein (CFP). The dynamic range of these FRET-based protein biosensors is often weak, but applications such as high throughput drug screening require stronger dynamic ranges. Using the biosensor for the caspase-3 protease as an example, here we showed a computational approach to improve the FRET dynamic range based on the atomic structure of caspase-3 bound to its inhibitor. This result was verified from our experiments where the FRET dynamic range improved by at least 60% on average in both in vitro and in vivo contexts. In concept, the same strategy can be applied to improve dynamic range of other FRET-based protein biosensors for protease activity where there exist solved atomic structures for protein complexes

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IEEE Transactions on NanoBioscience  (Volume:5 ,  Issue: 1 )