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Optimal Design of a Molecular Recognizer: Molecular Recognition as a Bayesian Signal Detection Problem

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2 Author(s)
Yonatan Savir ; Dept. of Phys. of Complex Syst., Weiz-mann Inst. of Sci., Rehovot ; Tsvi Tlusty

Numerous biological functions-such as enzymatic catalysis, the immune response system, and the DNA-protein regulatory network-rely on the ability of molecules to specifically recognize target molecules within a large pool of similar competitors in a noisy biochemical environment. Using the basic framework of signal detection theory, we treat the molecular recognition process as a signal detection problem and examine its overall performance. Thus, we evaluate the optimal properties of a molecular recognizer in the presence of competition and noise. Our analysis reveals that the optimal design undergoes a ldquophase transitionrdquo as the structural properties of the molecules and interaction energies between them vary. In one phase, the recognizer should be complementary in structure to its target (like a lock and a key), while in the other, conformational changes upon binding, which often accompany molecular recognition, enhance recognition quality. Using this framework, the abundance of conformational changes may be explained as a result of increasing the fitness of the recognizer. Furthermore, this analysis may be used in future design of artificial signal processing devices based on biomolecules.

Published in:

IEEE Journal of Selected Topics in Signal Processing  (Volume:2 ,  Issue: 3 )