Computational Methods for the Study of Enzymic Reaction Mechanisms. 1. Application to the Hydride Transfer Step in the Catalysis of Dihydrofolate Reductase

Exploring PfDHFR reaction surface: A combined molecular dynamics and QM/MM analysis

The substrate to the enzyme PfDHFR (Plasmodium falciparum Dihydrofolate Reductase) is a small molecule dihydrofolate (DHF), it gets converted to tetrahydrofolate (THF) in the active site of the enzyme. The PfDHFR reaction surface involves the protonation of DHF to DHFP as an initial step before the catalytic conversion. The binding affinities of all these species (DHF, DHFP and THF) contribute to the mechanism of DHFR catalytic action. Molecular dynamics (MD) simulations and Quantum Mechanics/Molecular Mechanics (QM/MM) analysis were performed to evaluate the binding affinity and molecular recognition interactions of the substrate DHF/DHFP and the product THF, in the active site of wild-type PfDHFR (wtPfDHFR). The binding affinities of the cofactor NADPH/NADP⁺ were also estimated in all the three complexes. The molecular dynamics (MD) simulations of the substrate, product and cofactor in the cavities of wtPfDHFR revealed the variation of the atomic level interactions during the course of the catalytic conversion. It was found that the DHFP binds very strongly to the PfDHFR active site and pulls the cofactor NADPH closer to itself. The QM/MM analysis revealed that the binding energy of DHFP (-59.82 kcal/mol) and NADPH (-100.24 kcal/mol) in DHFP-wtPfDHFR complex, is higher in comparison to the binding energy of DHF (-38.67 kcal/mol) and NADPH (-77.53 kcal/mol) in DHF-wtPfDHFR complex and the binding energy of THF (-30.72 kcal/mol) and NADP⁺ (-73.72 kcal/mol) in THF-wtPfDHFR complex. The hydride ion donor-acceptor distance (DAD) analysis was also carried out. This combined MD and QM/MM analysis revealed that the protonation of DHF increases the proximity between the substrate and the cofactor, thus facilitates the reaction profile of PfDHFR.

Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface

Dihydrofolate reductase (DHFR) catalyzes the reduction of 7,8-dihydrofolate by nicotinamide adenine dinucleotide phosphate hydride (NADPH) to form 5,6,7,8-tetrahydrofolate and oxidized nicotinamide. DHFR is a small, flexible, monomeric protein with no metals or SS bonds and serves as one of the enzymes commonly used to examine basic aspects in enzymology. In the current work, we present extensive benchmark calculations for several model reactions in the gas phase that are relevant to the DHFR catalyzed hydride transfer. To this end, we employ G4MP2 and CBS-QB3 ab initio calculations as well as numerous density functional theory methods. Using these results, we develop two specific reaction parameter (SRP) Hamiltonians based on the semiempirical AM1 method. The first generation SRP Hamiltonian does not account for dispersion, while the second generation SRP accounts for dispersion implicitly via the AM1 core-repulsion functions. These SRP semiempirical Hamiltonians are subsequently used in hybrid quantum mechanics/molecular mechanics simulations of the DHFR catalyzed reaction. Finally, kinetic isotope effects are computed using a mass-perturbation-based path-integral approach.

Computational approach for ranking mutant enzymes according to catalytic reaction rates

A computationally efficient approach for ranking mutant enzymes according to the catalytic reaction rates is presented. This procedure requires the generation and equilibration of the mutant structures, followed by the calculation of partial free energy curves using an empirical valence bond potential in conjunction with biased molecular dynamics simulations and umbrella integration. The individual steps are automated and optimized for computational efficiency. This approach is used to rank a series of 15 dihydrofolate reductase mutants according to the hydride transfer reaction rate. The agreement between the calculated and experimental changes in the free energy barrier upon mutation is encouraging. The computational approach predicts the correct direction of the change in free energy barrier for all mutants, and the correlation coefficient between the calculated and experimental data is 0.82. This general approach for ranking protein designs has implications for protein engineering and drug design.

Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate

We evaluate the pK(a) of dihydrofolate (H(2)F) at the N(5) position in three ternary complexes with Escherichia coli dihydrofolate reductase (ecDHFR), namely ecDHFR(NADP(+):H(2)F) in the closed form (1), and the Michaelis complexes ecDHFR(NADPH:H(2)F) in the closed (2) and occluded (3) forms, by performing free energy perturbation with molecular dynamics simulations (FEP/MD). Our simulations suggest that in the Michaelis complex the pK(a) is modulated by the Met20 loop fluctuations, providing the largest pK(a) shift in substates with a "tightly closed" loop conformation; in the "partially closed/open" substates, the pK(a) is similar to that in the occluded complex. Conducive to the protonation, tightly closing the Met20 loop enhances the interactions of the cofactor and the substrate with the Met20 side chain and aligns the nicotinamide ring of the cofactor coplanar with the pterin ring of the substrate. Overall, the present study favors the hypothesis that N(5) is protonated directly from solution and provides further insights into the mechanism of the substrate protonation.

Relating Protein Motion to Catalysis

This review examines the linkage between protein conformational motions and enzyme catalysis. The fundamental issues related to this linkage are probed in the context of two enzymes that catalyze hydride transfer, namely dihydrofolate reductase and liver alcohol dehydrogenase. The extensive experimental and theoretical studies addressing the role of protein conformational changes in these enzyme reactions are summarized. Evidence is presented for a network of coupled motions throughout the protein fold that facilitate the chemical reaction. This network is comprised of fast thermal motions that are in equilibrium as the reaction progresses along the reaction coordinate and that lead to slower equilibrium conformational changes conducive to the chemical reaction.

Hydrogen tunneling and protein motion in enzyme reactions

Theoretical perspectives on hydrogen transfer reactions in enzymes are presented. The proton-coupled electron transfer reaction catalyzed by soybean lipoxygenase and the hydride transfer reaction catalyzed by dihydrofolate reductase are discussed. The first reaction is nonadiabatic and involves two distinct electronic states, while the second reaction is predominantly adiabatic and occurs on the electronic ground state. Theoretical studies indicate that hydrogen tunneling and protein motion play significant roles in both reactions. In both cases, the proton donor-acceptor distance decreases relative to its equilibrium value to enable efficient hydrogen tunneling. Equilibrium thermal motions of the protein lead to conformational changes that facilitate hydrogen transfer, but the nonequilibrium dynamical aspects of these motions have negligible impact.

Quantum-classical simulation methods for hydrogen transfer in enzymes: a case study of dihydrofolate reductase

A variety of theoretical approaches have been used to investigate hydrogen transfer in enzymatic reactions. The free energy barriers for hydrogen transfer in enzymes have been calculated using classical molecular dynamics simulations in conjunction with quantum mechanical/molecular mechanical and empirical valence bond potentials. Nuclear quantum effects have been included with several different approaches. Applications of these approaches to hydride transfer in dihydrofolate reductase are consistent with experimental measurements and provide significant insight into the protein conformational changes that facilitate the hydride transfer reaction.

Computational methods for the study of enzymic reaction mechanisms III: A perturbation plus QM/MM approach for calculating relative free energies of protonation

We describe a coupling parameter, that is, perturbation, approach to effectively create and annihilate atoms in the quantum mechanical Hamiltonian within the closed shell restricted Hartree-Fock formalism. This perturbed quantum mechanical atom (PQA) method is combined with molecular mechanics (MM) methods (PQA/MM) within a molecular dynamics simulation, to model the protein environment (MM region) effects that also make a contribution to the overall free energy change. Using the semiempirical PM3 method to model the QM region, the application of this PQA/MM method is illustrated by calculation of the relative protonation free energy of the conserved OD2 (Asp27) and the N5 (dihydrofolate) proton acceptor sites in the active site of Escherichia coli dihydrofolate reductase (DHFR) with the bound nicotinamide adenine dinucleotide phosphate (NADPH) cofactor. For a number of choices for the QM region, the relative protonation free energy was calculated as the sum of contributions from the QM region and the interaction between the QM and MM regions via the thermodynamic integration (TI) method. The results demonstrate the importance of including the whole substrate molecule in the QM region, and the overall protein (MM) environment in determining the relative stabilities of protonation sites in the enzyme active site. The PQA/MM free energies obtained by TI were also compared with those estimated by a less computationally demanding nonperturbative method based on the linear response approximation (LRA). For some choices of QM region, the total free energies calculated using the LRA method were in very close agreement with the PQA/MM values. However, the QM and QM/MM component free energies were found to differ significantly between the two methods.

The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase

The energy barrier for hydride transfer in wild-type G121V and G121S variants of Escherichia coli dihydrofolate reductase (DHFR) fluctuates in a time-dependent manner. This fluctuation may be attributed to structural changes in the protein that modulate the site of chemistry. Despite being far from the active site, mutations at position 121 of DHFR reduce the hydride transfer rate of the enzyme. This occurrence has been suggested to arise from modifications to the conformational ensemble of the protein. We elucidate the effects of the G121S and G121V mutations on the hydride transfer barrier by identifying structural changes in the protein that correlate with lowered barriers. The effect of these structural parameters on the hydride transfer barrier may be rationalized by simple considerations of the geometric constraints of the hydride transfer reaction. Fluctuations of these properties are associated with specific backbone dihedral angles of residues within the Methione-20 (M20) loop. The dihedral angle preferences are mediated by interactions with the region of the enzyme in the vicinity of residue 121 and are translated into distinct ligand conformations. We predict mutations within the M20 loop that may alter the conformational space explored by DHFR. Such mutational changes are anticipated to adjust the hydride transfer efficacy of DHFR by modifying equilibrium distributions of hydride transfer barriers found in the enzyme.

Pivotal Role of Gly 121 in Dihydrofolate Reductase from Escherichia coli: The Altered Structure of a Mutant Enzyme May Form the Basis of Its Diminished Catalytic Performance

The structure and folding of dihydrofolate reductase (DHFR) from Escherichia coli and the mutant G121V-DHFR, in which glycine 121 in the exterior FG loop was replaced with valine, were studied by molecular dynamics simulations and CD and fluorescence spectroscopy. The importance of residue 121 for the chemical step during DHFR catalysis had been demonstrated previously. High-temperature MD simulations indicated that while DHFR and G121V-DHFR followed similar unfolding pathways, the strong contacts between the M20 loop and the FG loop in DHFR were less stable in the mutant. These contacts have been proposed to be involved in a coupled network of interactions that influence the protein dynamics and promote catalysis [Benkovic, S. J., and Hammes-Schiffer, S. (2003) Science 301, 1196-1202]. CD spectroscopy of DHFR and G121V-DHFR indicated that the two proteins existed in different conformations at room temperature. While the thermally induced unfolding of DHFR was highly cooperative with a midpoint at 51.6 +/- 0.7 degrees C, G121V-DHFR exhibited a gradual decrease in its level of secondary structure without a clear melting temperature. Temperature-induced unfolding and renaturation from the urea-denatured state revealed that both proteins folded via highly fluorescent intermediates. The formation of these intermediates occurred with relaxation times of 149 +/- 4.5 and 256 +/- 13 ms for DHFR and G121V-DHFR, respectively. The fluorescence intensity for the intermediates formed during refolding of G121V-DHFR was approximately twice that of the wild-type. While the fluorescence intensity then slowly decayed for DHFR toward a state representing the native protein, G121V-DHFR appeared to be trapped in a highly fluorescent state. These results suggest that the reduced catalytic activity of G121V-DHFR is the consequence of nonlocal structural effects that may result in a perturbation of the network of promoting motions.

How dihydrofolate reductase facilitates protonation of dihydrofolate

Dihydrofolate Reductase (DHFR) catalyzes the reduction of dihydrofolate (H2F) to tetrahydrofolate. On the basis of 10-12.5 ns molecular dynamics simulations of two conformations (closed and occluded) of the ternary DHFR/NADPH/H2F complex from Escherichia coli and a free energy perturbation approach, we have calculated the pKa value for the N5 atom in H2F. Our results suggest that the N5 atom in H2F is responsible for the pH dependency of the catalyzed reaction, meaning that DHFR facilitates protonation of H2F by approximately 4 pKa units. The mechanism behind this increase is due to favorable electrostatic interactions between the Asp27 residue and a proton at the N5 atom. The electrostatic interactions are enhanced by a hydrophobic active site, which to a large extent is made hydrophobic by the M20 loop in DHFR. Moreover, we find that the conformation imposed on H2F by DHFR to some extent also favors protonation of the N5 atom. Our results add support to previous findings and suggestions by Callender and co-workers [e.g., Deng, J.; Callender, R. J. Am. Chem. Soc. 1998, 120, 7730-7737] and explain why mutation of Asp27 may lead to severely reduced activity at neutral pH.