Isabella Feierberg

Q: a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems.

A new molecular dynamics program for free energy calculations in biomolecular systems is presented. It is principally designed for free energy perturbation simulations, empirical valence bond calculations, and binding affinity estimation by linear interaction energy methods. Evaluation of ligand-binding selectivity and free energy profiles for nucleophile activation in two protein tyrosine phosphatases as well as absolute binding affinity estimation for a lysine-binding protein are given as examples.

Free Energy Calculations and Ligand Binding

Publisher Summary This chapter gives an overview of some different methods for calculating ligand binding free energies that are all based on force fields and conformational sampling. Many of these studies of protein–ligand binding in the mid-1980s showed a remarkable agreement between theory and experiment, which led to an explosion of activity in the field of free energy calculations. More recent investigations, however, have demonstrated that significantly longer simulations than those used in the original reports are often required obtaining reliable results in protein–ligand binding studies. The increasing number of applications of free energy calculations also showed that the use of these methods was not as straightforward as expected; therefore, much effort was spent on improving the methodology. The free energy perturbation (FEP)/thermodynamic integration (TI) type of method has not really fulfilled its promise of being able to open a major new avenue to structure-based drug design due to slow convergence and sampling difficulties. In particular, in this type of extrapolation process in which one may want to look at 20 or so new ligands, arriving at the correct end-points by long perturbation paths sometimes seems hopeless. It appears that a better solution to this problem can often be provided by automated docking of individual compounds, at least when they differ significantly from each other, and then to try to evaluate the binding energetic by a method that does not require the unphysical transformations involved in FEP/TI and related methods. The docking problem resembles the protein-folding one in many respects, and the only way to attack difficult cases seems to be by extensive conformational searching in combination with more reliable scoring methods.

Computer simulation of primary kinetic isotope effects in the proposed rate-limiting step of the glyoxalase I catalyzed reaction.

The proposed rate-limiting step of the glyoxalase I catalyzed reaction is the proton abstraction from the C1 carbon of the substrate by Glu172. Here we examine primary kinetic isotope effects and the influence of quantum dynamics on this process by computer simulations. The calculations utilize the empirical valence bond method in combination with the molecular dynamics free energy perturbation technique and path integral simulations. For the enzyme-catalyzed reaction a H/D kinetic isotope effect of 5.0 ± 1.3 is predicted in reasonable agreement with the experimental result of about 3. Furthermore, the magnitude of quantum mechanical effects is found to be very similar for the enzyme reaction and the corresponding uncatalyzed process in solution, in agreement with other studies. The problems associated with attaining the required accuracy in order for the present approach to be useful as a diagnostic tool for the study of enzyme reactions are also discussed.

Energetics of the proposed rate-determining step of the glyoxalase I reaction

The proposed rate‐limiting step of the reaction catalyzed by glyoxalase I is the proton abstraction from the C1 carbon atom of the substrate by a glutamate residue, resulting in a high‐energy enolate intermediate. This proton transfer reaction was modelled using molecular dynamics and free energy perturbation simulations, with the empirical valence bond method describing the potential energy surface of the system. The calculated rate constant for the reaction is approximately 300–1500 s−1 with Zn2+, Mg2+ or Ca2+ bound to the active site, which agrees well with observed kinetics of the enzyme. Furthermore, the results imply that the origin of the catalytic rate enhancement is mainly associated with enolate stabilization by the metal ion.