Essential theoretical concepts related to specificity

Specificity of protein-protein, protein-ligand, anti-body-antigen, etc. interaction comes from a large difference between binding constants characterizing binding of specific and nonspecific ligands. Thermo-dynamically, the higher binding constants for specific ligands arise from stronger overall 'forces' (Gibbs free energy differences) between the antibody and the antigen.

Quantitatively, the notion of binding specificity derives from comparison of association constants, Kas, characterizing the reaction

Antigen + antibody = complex

Molar concentrations of the three molecular species are measured at equilibrium, and the strength (specificity) of the complex is estimated from it relative concentration, i.e. the ratio K xs |complcx|/|antibody||antigenj. Related expressions involve the dissociation constant, K,,s = affin ity (Kns expressed in molar units) and pK,\ = logKAS. The experimentally measured Kns relates to the Gibbs free energy of complex formation, AG, as AG = RTlogK ixs (R, the gas constant, is the product of the Boltzmann constant, k, and the Avogadro constant, L: R = 8.314 kj mol 1 K '; T is temperature in degrees kelvin). Changes in Gibbs free energy, a thermodynamic quantity, can in principle be obtained from atomic structures of all the molecules involved in the reaction, provided all the physical forces responsible for complex formation are accurately known. Traditionally, the Gibbs free energy is partitioned into two components, the enthalpy, H (the internal potential energy of the system), and the entropy, S (indicative of distribution of energy among all the different states available to the system): AG = AH - TA.S.

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