Thermodynamic Activation Parameters for Chemical Reactions in Enzymes and Solution from Computer Simulations at a...

There is considerable interest in being able to address the temperature dependence of enzyme reactions by computer simulations. One reason for this is that enzymes that are adapted to different temperature regimes generally show distinct signatures in terms of their activation enthalpies and entropies, to the extent that it is basically possible to predict whether an enzyme is psychrophilic or mesophilic just by examining these activation parameters. The standard approach to this problem is to calculate reaction free energy profiles at a series of different temperatures. Computational Arrhenius plots can then be constructed from the data, analogous to the experimental procedure. This method has been shown to work well in a number of cases that have examined orthologous pairs of psychrophilic and mesophilic enzymes. The drawback is that the simulations have to be repeated at several temperatures. However, while multitemperature simulations may be computationally demanding they can be informative in revealing deviations from linear Arrhenius behavior. Another issue is that the calculated activation enthalpies obtained in this way cannot be readily decomposed into different energy terms. An alternative approach to the problem would be to just carry out free energy simulations at a single temperature and instead obtain the enthalpy profile by plain averaging of the total energy. The entropy term would then simply be calculated as the difference between free energy and enthalpy. This averaging approach was earlier considered unreliable due to convergence problems for the total energy, even for moderately sized systems. Here, we re-examine the performance of the averaging method for two solution reactions and one enzyme reaction and conclude that it works surprisingly well with sufficient data. This opens up new ways of analyzing nonlinearity of Arrhenius plots in terms of energetics, since the enthalpy is decomposable.