Dihydrofolate reductase (DHFR) is an important enzyme and drug target because it maintains intracellular pools of 5,6,7,8-tetrahydrofolate, a cofactor in the synthesis of several metabolites. Structural studies of the E. coli enzyme indicate that significant conformational changes occur during the catalytic cycle. However, the relationship between these conformational changes and catalytic processing is not well understood. To investigate this, molecular dynamics simulations will be performed on various complexes of DHFR. Analysis of the results will provide information on how protein fluctuations are correlated and related to ligand binding. In addition, the catalytic pathway for DHFR will be explored using trajectory generation techniques which determine the minimum energy pathway between a reactant and product state. Structures of different intermediates taken from NMR, crystallography and mutational analysis will provide the starting points for these calculations. The application of these techniques to large systems such as DHFR and its substrates will provide a novel method for calculating the catalytic pathways of enzymes. The free energy changes along this pathway will be determined using biased umbrella sampling calculations and provide a better understanding of the catalytic process energetics. The results will elucidate the conformational changes necessary for catalysis and the atomic interactions that control these processes and they will be used to interpret DHFR kinetic and thermodynamic data.
