Enzymatic Processes

The overall objective of these projects is to illuminate the role of hydrogen bonding, hydrogen tunneling, electrostatics, and conformational motions, as well as the impact of distal mutations, in enzyme reactions. Movies of hydrogen tunneling in LADH and DHFR are available below.

We have written several reviews on enzyme motion and catalysis.55, 58, 79, 81, 101, 131, 149171190

Our simulations suggested the concept of a free energy landscape for enzyme catalysis and the significant role of equilibrium, thermal conformational motions that lead to sampling of configurations conducive to chemistry.

Proton and hydride transfer reactions in enzymes

We have developed a hybrid quantum/classical molecular dynamics approach for simulating proton and hydride transfer reactions in enzymes.41, 46, 48 This hybrid approach includes electronic and nuclear quantum effects, as well as the motion of the entire solvated enzyme. The methodology provides detailed mechanistic information at the molecular level and allows the calculation of rate constants and kinetic isotope effects. It also enables us to investigate the relation between enzyme motion and activity.  We have also developed computational methodology for calculating the vibrational shifts of nitrile probes (i.e., the vibrational Stark effect) upon ligand binding and along catalytic cycles in enzymes to investigate the role of electrostatics in enzyme catalysis.159179190

We have applied this hybrid approach to hydride transfer in liver alcohol dehydrogenase (LADH),34, 37, 4148 dihydrofolate reductase (DHFR),50, 51, 56636771808384113165179185 and ketosteroid isomerase (KSI)121, 127, 143159  These simulations have illuminated the roles of hydrogen bonding, hydrogen tunneling, electrostatics, and conformational motions, as well as the impact of distal mutations.

Movies of H tunneling in LADH and DHFR

Proton-coupled electron transfer in enzymes

We have developed a theoretical formulation for proton-coupled electron transfer (PCET) reactions in enzymes. This theory includes the quantum mechanical effects of the active electrons and the transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. We have derived a series of nonadiabatic rate constant expressions that are valid in well-defined regimes. In this theory, the rate constant and kinetic isotope effect (KIE) are strongly influenced by the equilibrium proton donor-acceptor distance and frequency, the vibronic coupling, the reaction free energy, and the protein/solvent reorganization energy.  We have applied this theory to PCET in soybean lipoxygenase.6493126182213216219226

biomd_slo_1
biomd_slo_2

Ribozymes

We have used quantum mechanical/molecular mechanical (QM/MM) free energy simulation methods, as well as other computational approaches, to study the self-cleavage mechanism of the HDV ribozyme.129, 137, 141150, 162, 170, 173, 191 Our calculations indicate that the self-cleavage reaction of the HDV ribozyme is concerted with a phosphorane-like transition state when a divalent ion, Mg2+ or Ca2+, is bound at the catalytic site but is sequential with a phosphorane intermediate when a monovalent ion, such as Na+, is at this site. These observations are consistent with available experimental data.  We have performed similar types of studies for the glmS ribozyme188, 214, 222 and the twister ribozyme.210

biomd_ribozyme_4

DNA Polymerase Eta

We have conducted molecular dynamics and binding free energy calculations on DNA polymerase η to understand the underlying basis for the specificity and effectiveness of this enzyme.198, 199, 223  Currently we are using QM/MM free energy simulations to elucidate the mechanism of this enzyme and to understand the role of the third Mg2+ ion in the active site.