Thermodynamics linkage

H. M. Farrell, T. F. Kumosinski, P. Pulaski, and M. P. Thompson, Calcium-induced associations of the caeins a thermodynamic linkage approach to precipitation and resolubilization, Arch. Biochem. Bio-phys., 265, 146 (1988). 

Doyle, M.L., G. Louie, P.R. Dal Monte, and T.D. Sokoloski. 1995. Tight binding affinities determined from thermodynamic linkage to protons by titration calorimetry. Methods Enzymol 259 183-194. 

Each stepwise microscopic binding reaction follows the same formula, as thermodynamic linkage holds for all binding steps. 

Figure 2 The dependence of O2 binding on Hb concentration. Binding curves are shown (solid black lines) for Hb concentrations of 0.005, 0.04, 0.10, 0.27,1.0, 5.4, and 38 pM (from left to right). Theoretical binding curves (broken red lines) are shown for a pure tetramer solution and a pure dimer solution. The macroscopic, thermodynamic linkage scheme relates the dimer tetramer assembly constants to the O2 binding constants for free dimer and assembled tetramer. The brackets around figurines indicate that the O2 ligand may be bound at any one of the available deoxy hemesites. Thus, the macroscopic constants are average values for multiple microscopic processes.

Gill, S. J. "Thermodynamics of Ligand Binding to Proteins." Pure Appl. Chem., 61,1009-1020 (1989). Freire, E. "Statistical Thermodynamic Linkage Between Conformational and Binding Equilibria." Adv. Protein Chem., 51, 255-279 (1998). 

Gilson, Protein Sci., 8, in press (1999). Thermodynamic Linkage Between Protonation and Binding of Inhibitors to HIV Protease. 

The linkage of microscopic and macroscopic properties is not without challenges, both theoretical and experimental. Statistical mechanics and thermodynamics provide the connection between molecular properties and the behavior of macroscopic matter. Coupled with statistical mechanics, computer simulation of the structure, properties, and dynamics of mesoscale models is now feasible and can handle the increase in length and time scales. 

Ackers, G. (1998), Deciphering the molecular code of hemoglobin allostery , in Di Cera (Ed ), Advances in Protein Chemistry, Vol. 51, Linkage Thermodynamics of Macromolecular Interactions, Academic Press, San Diego, CA, pp. 185-253... 

A thermodynamically stable (silyl)(stannyl)palladium(n) complex is synthesized by an oxidative addition of the Si-Sn linkage to palladium(O) (Scheme 63).267 The complex has the square-planar geometry with a m-arrangement of the silicon and tin atoms. An alkyne reacts with the complex to afford a silastannated product as a mixture of cisjtrans stereoisomers (10 1). 

Despite the fact that Model C65 does not explicitly invoke complexation of the interstitial cation with the alkene linkage, extensive experimental61,62 and computational66 precedent suggests that complexation is thermodynamically favorable. The interaction between the alkene and the cation serves to anchor the substrate near the supercage wall where the cation is located (Fig. 1). The proximity to the framework wall has experimental consequences as revealed by examination of the... 

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