Computer simulations of protein dynamics and thermodynamics

The computational challenges of producing realistic biomedical simulations are reviewed. Techniques for applying classical mechanics simulation methods to proteins and ways to solve Newton´s equations are discussed. Two recent applications of these methods are examined. The first considers the rate at which molecular oxygen binds to myoglobin, an oxygen-storage protein found in muscle. The second application involves the thermodynamics of the binding of oxygen to hemoglobin, a protein that is the major component of red blood cells. The comparison of this biochemical event to one in which oxygen is bound to an unusual variant of hemoglobin illustrates many of the simulation methods commonly used in the pharmaceutical industry to aid in the drug discovery process.<>