The modes and mechanisms of how this is actually achieved however, remain to be clarified [8 and 9]. Various factors, such as proximity effects [10], acid–base catalysis, near attack conformation [11], strain [12], dynamics [13], desolvation [14] etc. contribute to lowering

the activation barrier as compared to solution reactions. The individual effect of these factors is moderate and results in a rate acceleration < 104 fold. The only factor with major impact on catalysis is the electrostatic preorganization [15••], which can provide 107 to Selleckchem Buparlisib 1010 fold rate acceleration [16]. On the basis of the Marcus theory electrostatic preorganization can be

quantified by the reorganization energy (λ) [ 17]. This expresses the work of the protein while it responds to changing charge distribution of the reactant along the reaction pathway ( Figure 1). Although reorganization energy is the concerted effect of all enzyme dipoles, group contributions could be approximated (see Epacadostat in vivo Box 1). The reorganization energy (λ) was introduced by Marcus for electron transfer reactions [ 17] and establishes relationship between the reaction free energy (ΔG°) and the activation barrier (Δg‡). It can be approximated as: equation(1) Δgij‡≅(ΔGij0+λij)24λij It refers to intersection of free energy functionals of two states (i,j), corresponding to

reactants and products of an elementary PAK5 reaction step. In enzymes reorganization energy expresses the effect of pre-oriented dipoles, which upon charging the TS costs significantly less to reorganize than corresponding solvent dipoles [ 45]. Reorganization energy decrease by enzymes originates in two factors ( Figure 4): (i) decreasing ΔG°, (ii) shifting the diabatic free energy functions as compared to each other. Reorganization energy is computed as the vertical difference between the free energies of the system at reactant and product equilibrium geometries on the diabatic product free energy curve (Figure 1): equation(2) λ=FPS(ξRS)−FPS(ξPS)λ=FPS(ξRS)−FPS(ξPS)where ξRS and ξPS are the values of the reaction coordinate at the reactant and product states and FPS(ξ) is the diabatic product state free energy function. Computing reorganization energy requires the reactant and product potential energy surfaces, which are available within the framework of the Empirical Valence Bond (EVB) method [46]. According to Eqn (2) reorganization energy can be obtained by moving the system from the reactant to the product states using for example Free Energy Perturbation method and then the diabatic product state can be calculated by the Umbrella Sampling technique.