Free energy component analysis

Archontis, G. Simonson, T., Proton binding to proteins a free energy component analysis using a dielectric continuum model, Biophys. J. 2005, 88, 3888-3904... 

Archontis G, Simonson T (2005) Proton binding to proteins a free energy component analysis... 

V. Daggett, F. Brown, and P. A. Kollman,/. Am. Chem. Soc., Ill, 8247 (1989). Free Energy Component Analysis A Study of Glutamic Acid 165 - Aspartic Acid 165 Mutation in Triosephosphate Isomerase. 

The equations of free energy component analysis are derived from the statistical mechanical equations behind TI. From equation (32), substituting in a typical expression for the potential energy (equation 2), we get... 

For the three conformers, the binding sequence is Na > K > Rb > Cs. This is supported by energy component analysis on the trajectories, as well as by Free energy perturbation (FEP) calculations. Intrinsically, Cs+ has the weakest interactions with both hosts. The largest contribution of the cation/host interaction energy comes from the ether ring rather than from the aromatic moieties. Each complex displays a clear conformational preference. Sodium is most stable in the cone conformation, whereas cesium is most stable in the 1,3-altemate conformation. 

To sununarize, although the total free energy of a system is a state function, free energy components are not. Free energy components are essentially a reflection of the path (or the reference ensemble) that has been imposed and any analysis or physical interpretation of free energy components based on such calculations is subjective. 

Boresch, S., Archontis, G., Karplus, M. Free energy simulations The meaning of the individual contributions from component analysis. Proteins Str. Funct. Genet., 20 (1994) 25-33... 

Boresch S, G Archontis and M Karplus 1994. Free Energy Simulations The Meaning of the Indi-. id Contributions from a Component. Analysis. Proteins Structure, Function and Gau tics 20 25-33. 

Boresch S and M Karplus 1995. The Meaning of Component Analysis Decomposition of the Free Energy in Terms of Specific Interactions. Journal of Molecular Biology 254 801-807. 

Boresch, S. Karplus, M., The meaning of component analysis decomposition of the free energy in terms of specific interactions, J. Mol. Biol. 1995, 254, 801-807. 

Chan (Chapter 6) presents a simple graphical method for estimating the free energy of EDL formation at the oxide-water interface with an amphoteric model for the acidity of surface groups. Subject to the assumptions of the EDL model, the graphical method allows a comparison of the magnitudes of the chemical and coulombic components of surface reactions. The analysis also illustrates the relationship between model parameter values and the deviation of surface potential from the Nernst equation. 

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