Towards understanding the mechanisms of molecular recognition by computer simulations of ligand–protein interactions

The thermodynamic and kinetic aspects of molecular recognition for the methotrexate (MTX)–dihydrofolate reductase (DHFR) ligand–protein system are investigated by the binding energy landscape approach. The impact of ‘hot’ and ‘cold’ errors in ligand mutations on the thermodynamic stability of the native MTX–DHFR complex is analyzed, and relationships between the molecular recognition mechanism and the degree of ligand optimization are discussed. The nature and relative stability of intermediates and thermodynamic phases on the ligand–protein association pathway are studied, providing new insights into connections between protein folding and molecular recognition mechanisms, and cooperativity of ligand–protein binding. The results of kinetic docking simulations are rationalized based on the thermodynamic properties determined from equilibrium simulations and the shape of the underlying binding energy landscape. We show how evolutionary ligand selection for a receptor active site can produce well‐optimized ligand–protein systems such as MTX–DHFR complex with the thermodynamically stable native structure and a direct transition mechanism of binding from unbound conformations to the unique native structure. Copyright © 1999 John Wiley & Sons, Ltd.