Thrombin thermodynamics

Tetrhedral intermediate, 172 Thermodynamic cycles, 186 Thermolysin, zinc as cofactor for, 204 Thrombin, 170 Torsional potential, 111 Transition states, 41-42,44, 45,46, 88, 90-92 in amide hydrolysis, 219-221 oxyanion hole and, 181 stabilization of, 181,181 carbonium ion, 154,155,156-161, 167-169 for gas-phase reactions, 43... 

Barratt, J.O., Thrombin and calcium chloride in relation to coagulation, Biochem. J. 9, 511-543, 1915 Van der Meer, C., Effect of calcium chloride on choline esterase. Nature 171, 78-79, 1952 Bhat, R. and Ahluwalia, J.C., Effect of calcium chloride on the conformation of proteins. Thermodynamic studies of some model compounds, Int. J. Pept. Protein Res. 30,145-152,1987 Furihata, C., Sudo, K., and Matsushima, T, Calcium chloride inhibits stimulation of replicative DNA... 

Table I Thermodynamic functions of thrombin and inhibitor interactions(25°C) ...

Ayala Y, Di Cera E (1994). Molecular Recognition by thrombin. Role of the slow —> fast transition, site-specific ion binding energetics and thermodynamic mapping of structural components. J. Mol. Biol. 235 733-746. 

Wang J, Szewczuk Z, Yue S-Y, et al. (1995). Calculation of relative binding energies and configurational entropies A structural and thermodynamic analysis of the nature of non-polar binding of thrombin inhibitors based on hirudin. J. Mol. Biol. 253 473-492. 

J. Wang, Z. Szewczuk, S.-Y. Yue, Y. Tsuda, Y. Konishi, and E. O. Purisima,/. Mo/. Biol, 253, 473 (1995). Calculation of Relative Binding Free Energies, and Configurational Entropies A Structural and Thermodynamic Analysis of the Nature of Non-Polar Binding of Thrombin Inhibitors Based on Hirudin ". ... 

As indicated in Chapter III, step 1 of the fibrinogen-fibrin conversion is an example of a limited proteolytic reaction in which hydrolysis does not go to completion. Side-chain hydrogen bonding may stabilize the peptide bond in the manner indicated in Chapter III. We shall therefore discuss the reversibility of step 1 and the thermodynamic parameters for the equilibrium (Laskowski et al., 1960b). As in the case of the kinetic experiments discussed in Section 5b, the medium used was 1 molar NaBr at pH 5.3 to prevent polymerization of fibrin monomer, and the analysis for f was carried out using TAMe as a thrombin inhibitor, as already mentioned The equilibrium position was approached from both directions. 

Winquist, J., Geschwindner, S., Xue, Y., Gustavsson, L, Musil, D., Deinum, J., and Danielson, U.H. (2013) Identification of structural-kinetic and structural-thermodynamic relationships for thrombin inhibitors. Biochemistry, 52 (4), 613-626. 

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