Intrinsic binding free energy

In other words, the intrinsic binding energies of the two steps are additive but not the entropy losses [130], which means that the intrinsic binding free energy of the first step AG1 (carb) contributes to NCA stabilization. On the other hand, free energies corresponding to the overall entropy losses as-... 

Intrinsic Binding Free Energy and Enzyme Conformational Energy. 126... 

The intrinsic binding free energy of the substrate corresponds to the free energy of transfer from water into the enzyme active site, which is related to the free energies of solvation of the substrate in these two environments. Here, we use the generic term solvation to describe the free energy of transfer from the gas phase into a specific environment. Computationally, the free energy perturbation (FEP) method has been estabUshed as an ideal approach for these calculations [54] ... 

Fig. 7 Schematic illustration of the origin of catalysis by the enrjrme ODCase. Arrows indicate the free energy decomposition of Eqs. 2 and 3 that separate the binding free energy into a protein distortion term and an intrinsic substrate-protein interaction component. The figure shows that the protein has a smaller distortion energy than that in the reactant state, so the change in protein conformational energy provides the predominant contribution to the lowering of the activation free energy of the catalyzed reaction...

Each of the intrinsic binding constants may be interpreted either as a probability ratio or as a free-energy change for a specific binding process. Both meanings are derived directly from definitions (2.2.6). For instance,... 

In summary, the intrinsic binding constant to be used throughout this book always refers to a specific set of sites. They are defined in terms of the molecular properties of the system through the corresponding canonical PFs. They are also interpreted as probability ratios or as free energies of binding processes. In subsequent chapters we shall see how to extract from these quantities various correlation functions or, equivalently, cooperativities. 

Intrinsic Binding Constants, Correlation Functions, and Corresponding Free Energies (in kcal/mol) for Various Carboxylic Acids ... 

Individual operator sites are denoted O if vacant, or R2 if occupied by a repressor dimer. Pairwise interactions between adjacent occupied sites are denoted ( ) AG 2 and AG23 the free energies of cooperative interaction between adjacent occupied sites, defined as the difference between AG, for any species and the sum of the intrinsic free enei es of binding to occupied sites. 

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