Molecular recognition and information gain.

Molecular recognition is considered as an information transduction process, and information theory is applied to analyze the efficiency of the information transduction during molecular recognition. It is shown that a certain amount of information is gained in the recognition process, and it can be expressed in terms of thermodynamic quantities in the binding process of molecules. The information gain, which can be interpreted as the amount of information extracted from the sequence or structure by a molecule, represents the intrinsic ability of a molecule to recognize specific sequence or structure out of large ambient ensemble based on physical interactions. In contrast with thermodynamic quantities themselves, the information gain is a normalized quantity, and thus serves as a good measure of specificity in the molecular recognition. The information gain, which can be evaluated experimentally, enables us to identify the specific interactions and compare the specificity among different molecules quantitatively. In contrast with macroscopic recognition, specificity of molecular recognition may be severely restricted by the thermodynamic nature of molecular interactions. The thermodynamic meaning of the information gain and its biological implications to molecular recognition are discussed.