Free energy standard binding

Since the net free energy change for the cycle is zero, the difference between the computable free energies for transforming L to if, when bound to protein and when dissolved in water, is equal to the difference between the measurable standard free energies of binding L and if to protein, i.e., the difference in affinity... 

Clearly, a free energy of binding computed with (9), (10) and (13) refers to a highly restricted state of the dissociated ligand. In order to convert such a free energy to a free energy relative to a normal standard state with volume per molecule Vg and no restriction on the molecular orientation, the following term must be added... 

Calculation of the standard free energy of binding itself can be viewed as a special case of the above, in which one of the pair of ligands contains no atoms.10 Some care is required to be sure that such calculations yield answers that actually correspond to the desired standard state.11 12 Unfortunately, many calculations of free energies of binding have not made appropriate contact with a standard state, so that results in the literature must be interpreted with caution. 

Kd is an important property of a receptor-ligand system. A ligand with a small KD is said to have a high affinity for the receptor. Affinity is related to binding energy, and the standard free energy of binding can be determined from the association equilibrium constant, KA, or /KV) (Equation 5.10). 

PROBLEM Determine the standard free energy of binding of compound 10.19 based on its /C50 of 0.015 /xM. 

Therefore, by substitution of Equation 12.2 into Equation 12.4, changes in the standard free energy of binding (AG°) are directly proportional to the logarithm of an activity measure (ED5o) (Equation 12.5). 

Avidity versus affinity. The standard free energy of binding of derived from an antiviral IgGis -7 kcal mok (-29 kJ mok ) at25°C. 

The variation of /l with N largely depends on geometric considerations. Consider first a set of one-dimensional rod-shaped polymers, and let 6i RT represent the molar bond energy for joining two monomers. Then the standard free energy of binding of the linear A -mer relative to an arbitrary reference state is found from (5.4.22b) by multiplication with N and discarding the constant term RT nN. Note that there is one fewer bond than the number N of units. We find that... 

Calculation of the standard free energy of binding itself can be viewed as a special case of the above, in which one of the pair of ligands... 

Avidity versus affinity. "Fhe standard free energy of binding of Fab derived from an antiviral IgG is — 29 kj mol (—7 kcal moP ) at 25°C. 

In biochemical literature, binding affinity is commonly expressed as the dissociation constant KV) (the reciprocal of the association constant KA), which can be expressed in terms of the equilibrium concentration of interacting species and from which the change in standard Gibbs free energy for binding (G ) may be calculated ... 

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