Research Projects

Molecular recognition in enzymes is crucial for controlling biomolecular reactions and preventing spurious reactions and diseases. During a catalytic cycle, an enzyme binds to a substrate, and if the substrate is recognized, the reaction occurs and the product is formed. The deformation of enzymes is essential to gain information about the substrate, helping them lower the activation barrier. Deformation costs energy but also gains better information about the substrate in a noisy environment. This results in a tradeoff between the cost of deformation and the mutual information between the enzyme and substrate shapes. Longer enzyme cycles allow the enzyme to fit the substrate better but slow down life processes. The optimal time scales for recognition will be found, with specific enzymes binding only to certain substrates and promiscuous enzymes having low recognition ability binding to many. The phase diagram will be analyzed to understand differences in recognition ability from deformation energy, activation energy, and the enzyme cycle period. The enzyme reaction will be modeled as an information erasure based on Landauer's principle, with the barrier being lowered and restored periodically to mimic the enzyme cycle. The second law of information thermodynamics will be used to describe the thermodynamics and determine the phase diagram of recognition ability with deformation and enzyme cycle time. In the induced fit model, more deformation leads to higher mutual information, leading to a tradeoff between the cost of deformation energy and mutual information.