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Robert A. Alberty
Organization: Massachusetts Institute of Technology
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This package shows how to calculate various thermodynamic properties of a protein-ligand binding reaction like hemoglobin plus oxygen. Different sets of independent intensive properties can be specified. At specified temperature and pH, the transformed Gibbs energy G' provides the criterion for spontaneous change and equilibrium, and all the other thermodynamic properties can be obtained by taking partial derivatives of G'. At specified temperature, pH, and concentration of molecular oxygen, the criterion for spontaneous change and equilibrium is provided by the further transformed Gibbs energy G''. The functions for these properties properties are derived using calcappeqconst and calcstdfrtrGe. Very complicated expressions are obtained in taking the partial derivatives, and so Mathematica is needed. It is shown that the most efficient way to store the basic data is the Gibbs energy G and the enthalpy H of a species at a single temperature.

*Science > Physics > Thermodynamics and Statistical Mechanics

proteins, ligands, thermodynamics, chemistry, lifescience, biochemistry
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*Basic Data for Biochemistry   [in MathSource: Packages and Programs]
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ProteinLigandProg.m (6 KB) - Mathematica Package
ProteinLigandProg.nb (1001.3 KB) - Mathematica Notebook