Title :
Molecular recognition as an information channel: The role of conformational changes
Author :
Savir, Yonatan ; Tlusty, Tsvi
Author_Institution :
Dept. of Phys. of Complex Syst., Weizmann Inst. of Sci., Rehovot
Abstract :
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar competing molecules. We consider molecular recognition as a transmission of information via a noisy channel and use this analogy to gain insights on the optimal, or fittest, molecular recognizer. We focus on the optimal structural properties of the molecules such as flexibility and conformation. We show that conformational changes upon binding, which often occur during molecular recognition, may optimize the detection performance of the recognizer. We thus suggest a generic design principle termed dasiaconformational proofreadingpsila in which deformation enhances detection. We evaluate the optimal flexibility of the molecular recognizer, which is analogous to the stochasticity in a decision unit. In some scenarios, a flexible recognizer, i.e., a stochastic decision unit, performs better than a rigid, deterministic one. As a biological example, we discuss conformational changes during homologous recombination, the process of genetic exchange between two DNA strands.
Keywords :
biochemistry; biocomputing; molecular biophysics; stochastic processes; DNA strands; biological systems; conformational changes; conformational proofreading; flexible recognizer; generic design principle; genetic exchange; information channel; information processing; molecular recognition; optimal structural properties; Biochemistry; Biological information theory; Biological system modeling; Biological systems; Biology; DNA; Physics; Stochastic processes; Target recognition; Working environment noise; Molecular information channels; conformational proofreading; molecular recognition;
Conference_Titel :
Information Sciences and Systems, 2009. CISS 2009. 43rd Annual Conference on
Conference_Location :
Baltimore, MD
Print_ISBN :
978-1-4244-2733-8
Electronic_ISBN :
978-1-4244-2734-5
DOI :
10.1109/CISS.2009.5054833