Binding equilibrium thermodynamics

Day, Y.S., Baird, C.L., Rich, R.L, Myszka, D.G. Direct comparison of binding equilibrium, thermodynamic, and rate constants determined by surface- and solution-based biophysical methods. Protein Sci. 

As we described in Chapter 3, the binding of reversible inhibitors to enzymes is an equilibrium process that can be defined in terms of the common thermodynamic parameters of dissociation constant and free energy of binding. As with any binding reaction, the dissociation constant can only be measured accurately after equilibrium has been established fully measurements made prior to the full establishment of equilibrium will not reflect the true affinity of the complex. In Appendix 1 we review the basic principles and equations of biochemical kinetics. For reversible binding equilibrium the amount of complex formed over time is given by the equation... 

Thermodynamics of Proteins Calculating the Entropy of a Helix-Coil Transition in a Small Antibacterial Peptide using Statistical Mechanics (J. Mol. Bio. 1999, 294, 785-794. "Thermodynamics of the a-Helix-Coil Transition of Amphipathic Peptides in a Membrane Environment Implications for the Peptide-Membrane Binding Equilibrium")... 

Pistolis et al,73 have shown that the complexation of thermochromic N-5-chlorosalicylideneaniline and A-salicylidene-2-aminopyridine with cyclodextrins (CD) results in the disappearance of thermochromic properties and the appearance of photochromism. From -NMR, UV-visible, and fluorescence studies in dimethylformamide (DMF) solutions, it has been found that P- and a-cyclo-dextrins bind the thermodynamically more stable enol form of anils. Moreover, NMR data indicated that the binding site of the anil in the CD is the imino bridge, which dictates the position of the enol-keto equilibrium. 

Finally, mention must be made to the so-called unfreezable or bound water which exercises the minds of many people. This is a difficult topic because we leave the realm of equilibrium thermodynamics and enter the fuzzy world of metastability and kinetic barriers. It is found that most complex molecules, especially macromolecules and capillary systems immobilize a fraction of the water molecules so that this water does not freeze, even in the presence of ice. This we relate to hindered diffusion rather than to binding (Packer, 1977). Figure 18 shows schematically the problems with the diffusion of water. The two capillary systems might be phospholipid bilayers, or they might be pores or vascular systems. We have a region of thickness x and another region of thick-... 

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