| Dissecting enzyme catalysis: assessing the impact of reaction molecularity | To eXplore the consequences of this tradeoff in enzymatic reactions, we uniformly sampled the kinetic space of three ordered mechanisms following different molecularities: Uni-Uni, BiBi and Ter-Ter, under different Gibbs free energy differences and a constant reference flux. |
| E-glc-atp | high substrate concentrations and almost no products, a reference Gibbs free energy difference of - 100 kI/mol was used. |
| Parameterization and sampling of the catalytic mechanism | Where AG, represents the Gibbs free energy difference of reaction, R denotes the universal gas constant, T is the absolute temperature and vref denotes the reaction reference flux. |
| Revealing the impact of thermodynamics on enzyme kinetics | substrate and product elasticities, at different Gibbs free energy differences ranging from -1 (close to equilibrium) to -80 kI/mol (practically irreversible). |
| Analytical Models of Distribution of Affinity, Equilibrium Constants, Specificity and Kinetics | In other words, by knowing the distribution of free energy, one can derive the probability distribution of the equilibrium constant K (logK = %) as well since the logarithm of the equilibrium constant K is directly related to the free energy difference between the native and nonnative states (the nonnative states are Gaussian distributed while the native state is very narrowly distributed). |
| Analytical Models of Distribution of Affinity, Equilibrium Constants, Specificity and Kinetics | Therefore, the time scale of binding from one binding state to a neighboring state is determined by the free energy difference of these two states. |
| Microscopic Atomic Binding Model and Simulation Results | From this data, the statistical distribution of the affinity (defined as the free energy difference between the native state and the average of the free energy) of 720 small molecules with COX-2 was described. |
| Theory and Analytical Models | Since Log K is proportional to the free energy difference between the native and nonnative states termed as the stability or affinity, this infers that the free energy also has a distribution. |
| Path optimisation | The sign and magnitude of this energy difference agrees well with the experimentally observed difference [28] in reactivity for magnesium and manganese, although considering the accuracy limits of the computational methods employed, this could be just a coincidental agreement. |
| Reactant and product structures | To create a clearly understandable visualisation with physically relevant contour lines, these points were removed prior to visuali-sation when their energy differed by more than 2 kcal mol‘jL from the average of four directly adjacent points (for interior points) or two adjacent points along the boundary (for points on surface boundary). |
| leaving phosphate. | 1 kcal mol‘1 deep, and such a subtle energy difference is at the limit of the accuracy provided by applicable theoretical modeling approaches. |