Nuclear Quantum Effects and Enzyme Dynamics in Dihydrofolate Reductase Catalysis

Abstract

Mixed quantum/classical molecular dynamics simulations of the hydride transfer reaction catalyzed by dihydrofolate reductase are presented. The nuclear quantum effects such as zero point energy and hydrogen tunneling, as well as the motion of the entire solvated enzyme, are included during the generation of the free energy profiles and the real-time dynamical trajectories. The calculated deuterium kinetic isotope effect agrees with the experimental value. The simulations elucidate the fundamental nature of the nuclear quantum effects and provide evidence of hydrogen tunneling in the direction along the donor−acceptor axis. The transmission coefficient was found to be 0.80 for hydrogen and 0.85 for deuterium, indicating the significance of dynamical barrier recrossings. Nonadiabatic transitions among the vibrational states were observed but did not strongly affect the transmission coefficient. A study of motions involving residues conserved over 36 diverse species from Escherichia coli to human implies that motions of residues both in the active site and distal to the active site impact the free energy of activation and the degree of barrier recrossing. This analysis resulted in the characterization of a network of coupled promoting motions that extends throughout the protein and involves motions spanning femtosecond to millisecond time scales. This type of network has broad implications for protein engineering and drug design.

Allosteric Communication in Dihydrofolate Reductase: Signaling Network and Pathways for Closed to Occluded Transition and Back

“…It was also found that motions of residues W22, D27, M42, I60, L62, and T113 which forms hydrogen bond network with DHF in the active site might also be involved in coupled promoting motions [6,7]. Taken together, the present and previous studies show that the allostery wiring diagram, that represents the network of signaling residues in DHFR, is spread throughout the structure (Fig.…”

“…Similar conclusions were obtained using all atom simulations of the WT DHFR [13]. The present simulations and previous MD studies [6,7,8,9,13,15] …”

“…Hammes-Schiffer used sequence conservation of a small dataset of DHFR sequences to identify a network of residues whose coordinated motion is apparently linked to catalysis [6,7]. Among them, I14 is found to be in the allostery wiring diagram that we have identified using SCA.…”

“…While it is difficult to unambiguously demonstrate whether collective dynamics involving a network of residues facilitates catalysis [17], it is clear that enzymes sample a number of distinct states during a reaction cycle. In the best studied example of E. coli dihydrofolate reductase (DHFR) the role of the conformational motions in the enzyme in facilitating the hydride transfer has been linked using mutational studies [10,18,19], NMR relaxation dispersion measurements [20,21,22] that probe the dynamics on µs to ms time scale, molecular dynamics simulations [6,7,13], and sequence analysis [6].…”

“…DHFR catalyzes the reduction of 7,8 dihydrofolate (DHF) to 5,6,7,8 tetrahydrofolate (THF) [1]. By binding the co-factor, nicotinamide adenine dinucleotide phosphate (NADPH), hydride transfer from NADPH to protonated DHF leads to production of NADP + and THF [27].…”