Using Molecular Dynamics Simulations to Study the Dynamic and Catalytic Properties of R67 Dihydrofolate Reductase

Dihydrofolate reductase (DHFR) catalyzes the reduction of dihydrofolate (DHF) to tetrahydrofolate (THF) using NADPH as a cofactor. Since THF is an essential factor for nucleotide biosynthesis, inhibition of this enzyme in bacteria with folate analogs such as trimethoprim results in bacterial cell death. Plasmid encoded R67 DHFR confers resistance to trimethoprim and is both sequentially and structurally unrelated to any known chromosomal version of the enzyme. R67 DHFR is a 34,000 Da. homo-tetramer containing a rare 222 axis of symmetry in the center of its active site pore. The active site pore is contacted by residues belonging to each of the four subunits. The enzyme can nonspecifically bind 2 NADPH’s, 2 DHF’s, or, in the case of the productive complex, 1 NADPH and 1 DHF. R67 DHFR employs the endo transition state as opposed to the exo transition state used by E. coli DHFR. In this study molecular dynamics approach using the CHARMM program is employed to study the dynamics of the enzyme and energetics of the hydride transfer step catalyzed by R67 DHFR in silico. Structural and dynamic properties of four different mutants are also examined.