Dimitri Antoniou

Barrier crossing in dihydrofolate reductase does not involve a rate-promoting vibration

We have studied atomic motions during the chemical reaction catalysed by the enzyme dihydrofolate reductase of Escherichia coli (EcDHFR), an important enzyme for nucleic acid synthesis. In our earlier work on the enzymes human lactate dehydrogenase and purine nucleoside phosphorylase, we had identified fast sub-ps motions that are part of the reaction coordinate. We employed Transition Path Sampling (TPS) and our recently developed reaction coordinate identification methodology to investigate if such fast motions couple to the reaction in DHFR on the barrier-crossing timescale. While we identified some protein motions near the barrier crossing event, these motions do not constitute a compressive promoting vibration, and do not appear as a clearly identifiable protein component in reaction.

Activated chemistry in the presence of a strongly symmetrically coupled vibration

In the gas phase, tunneling reaction rates can be significantly enhanced if the reaction coordinate is symmetrically coupled to a harmonic oscillation, as has been emphasized by Benderskii and co-workers [Adv. Chem. Phys. 88, 1 (1994)]. This is due to the fact that the symmetric coupling leads to modulation of the barrier height. Similar effects have been observed in reactions in model condensed phase studies, as in the Hamiltonians that have been studied by Borgis and Hynes [J. Chem. Phys. 94, 3619 (1991)] and Suarez and Silbey [J. Chem. Phys. 94, 4809 (1991)]. All of these works assume that tunneling proceeds from the ground state. In this paper, we use the exponential resummation technique that we used in our recent work on the quantum Kramers problem, to study the case when there can be excitations to higher states and activated transmission over a barrier. We present a general methodology to exactly include direct coupling between the reaction coordinate and the symmetrically coupled promoting vibrat...

Quantum proton transfer with spatially dependent friction: Phenol-amine in methyl chloride

In a recent paper [D. Antoniou and S. D. Schwartz, J. Chem. Phys. 110, 465 (1999)] we calculated the reaction rate for a proton transfer reaction in liquid methyl chloride. In that work, we used a spectral density obtained from a molecular dynamics simulation as input to a quantum Zwanzig Hamiltonian which we solved using our exponential resummation method. In the present paper we perform a similar calculation, allowing for a position dependent friction using the method of G. Haynes, G. Voth, and E. Pollak [J. Chem. Phys. 101, 7811 (1994)]. Compared with the results of our previous work, we found that including spatial dependence to the friction led to enhancement of the reaction rate and to reduction of the H/D kinetic isotope effect.

A molecular dynamics quantum Kramers study of proton transfer in solution

We present a quantum study of a proton transfer reaction AH–B⇌A−–H+B in liquid methyl chloride, where the AH–B complex corresponds to phenol-amine. We use the same intramolecular potentials that were used in two earlier studies of this system [H. Azzouzz and D. Borgis, J. Chem. Phys. 98, 7361 (1993); S. Hammes-Schiffer and J. C. Tully, J. Chem. Phys. 101, 4657 (1994).] The former study employed a Landau-Zener approach and a molecular dynamics centroid method, while the latter a surface-hopping method. These studies obtained results that differ by an order of magnitude. In the present work, we first performed a molecular dynamics simulation to obtain the spectral density, which was then used as an input to the method we have developed for the study of the quantum Kramers problem [S. D. Schwartz, J. Chem. Phys. 105, 6871 (1996)]. Thus, in this work both the reaction coordinate and the bath are treated quantum mechanically.

Toward Identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method.

We propose a new method for analyzing an ensemble of transition states to extract components of the reaction coordinate. We use the kernel principal component analysis (kPCA), which is a generalization of the ordinary PCA that does not make a linearization approximation We applied this method to a TPS study of human LDH we had previously published [Quaytman, S.; Schwartz, S. D. Proc. Natl. Acad. Sci. U.S.A.2007, 104, 12253] and extracted a reasonable representation for the reaction coordinate.

Slow Conformational Motions That Favor Sub-picosecond Motions Important for Catalysis

It has been accepted for many years that functionally important motions are crucial to binding properties of ligands in such molecules as hemoglobin and myoglobin. In enzymatic reactions, theory and now experiment are beginning to confirm the importance of motions on a fast (ps) time scale in the chemical step of the catalytic process. What is missing is a clear physical picture of how slow conformational fluctuations are related to the fast motions that have been identified as crucial. This paper presents a theoretical analysis of this issue for human heart lactate dehydrogenase. We will examine how slow conformational motions bring the system to conformations that are distinguished as catalytically competent because they favor specific fast motions.

PROTON TRANSFER IN BENZOIC ACID CRYSTALS : ANOTHER LOOK USING QUANTUM OPERATOR THEORY

We present a calculation of the rate of synchronous double proton transfer in benzoic acid crystals. Experiments on these systems have been performed over a wide range of temperatures (roughly 10–400 °K). Even though the energetic barrier for proton transfer is rather high, the observed activation energy is low, while kinetic isotope experiments seem to indicate classical transfer. The system exhibits significant quantum character even at high temperatures and we show that the observed low activation energies can be reproduced assuming that the reaction is “assisted” by a low-frequency intramolecular mode, as has been suggested in different contexts by Benderskii [V. A. Benderskii, S. Yu. Grebenshchikov, and G. V. Mil’nikov, Chem. Phys. 194, 1 (1995)], Hynes [D. Borgis and J. Hynes, J. Chem. Phys. 94, 3619 (1991)] and Silbey [A. Suarez and R. Silbey, J. Chem. Phys. 94, 4809 (1991)]. We use our previous work on the quantum Kramers problem to perform a fully quantum calculation that incorporates symmetric coupling to the intramolecular mode and coupling to the condensed environment to all orders. We calculate the activation energies for hydrogen and deuterium transfer and we show that our results are in quantitative agreement with the experiment.

Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies

Escherichia coli dihydrofolate reductase (ecDHFR) is used to study fundamental principles of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the hydride transfer catalyzed by ecDHFR. Previous studies with heavy ecDHFR proteins labeled with (13)C, (15)N, and nonexchangeable (2)H reported enzyme mass-dependent hydride transfer kinetics for ecDHFR. Here, we report refined experimental and computational studies to establish that hydride transfer is independent of protein mass. Instead, we found the rate constant for substrate dissociation to be faster for heavy DHFR. Previously reported kinetic differences between light and heavy DHFRs likely arise from kinetic steps other than the chemical step. This study confirms that fast (femtosecond to picosecond) protein motions in ecDHFR are not coupled to hydride transfer and provides an integrative computational and experimental approach to resolve fast dynamics coupled to chemical steps in enzyme catalysis.

Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling

The mechanisms involved in enzymatic hydride transfer have been studied for years, but questions remain due, in part, to the difficulty of probing the effects of protein motion and hydrogen tunneling. In this study, we use transition path sampling (TPS) with normal mode centroid molecular dynamics (CMD) to calculate the barrier to hydride transfer in yeast alcohol dehydrogenase (YADH) and human heart lactate dehydrogenase (LDH). Calculation of the work applied to the hydride allowed for observation of the change in barrier height upon inclusion of quantum dynamics. Similar calculations were performed using deuterium as the transferring particle in order to approximate kinetic isotope effects (KIEs). The change in barrier height in YADH is indicative of a zero-point energy (ZPE) contribution and is evidence that catalysis occurs via a protein compression that mediates a near-barrierless hydride transfer. Calculation of the KIE using the difference in barrier height between the hydride and deuteride agreed well with experimental results.

The stochastic separatrix and the reaction coordinate for complex systems

We present a new approach to the identification of degrees of freedom which comprise a reaction coordinate in a complex system. The method begins with the generation of an ensemble of reactive trajectories. Each trajectory is analyzed for its equicommittor position or transition state; then the transition state ensemble is identified as the stochastic separatrix. Numerical analysis of the points along the separatrix for variability of coordinate location correctly identifies the components of the reaction coordinate in a test system of a double well coupled to a promoting vibration and a bath of linearly coupled oscillators.