Free energy, conformational

Unger, R. and Moult, J. (1993) Finding the lowest free energy conformation of a protein is a NP-hard problem proof and implications, Bull. Math. Biol., 55, 1183-1198. 

Activation free energies, conformational behaviour and dynamics... 

Table 5 Relative free energy, conformer population, and free energy of activation for 2-carbonyl furan...

An analysis of the distribution of distinct minima, as given by Table XVI, reveals that the results are qualitatively consistent with those produced by the EDA. It should be noted that in aU cases the lowest free energy bin is as densely populated as the corresponding EDA bins, which indicates that each run using the FEDA was able to find a better distribution of low free energy conformers near the FEGM. This is not unexpected, considering that the FEDA mns were... 

If we average the absolute values of the various sub components in column 4 across inhibitors we obtain, = 1.92 kcal/mol, < A[A(AG, )]> = 2.11 kcal/mol, < -TA(AS , J> = 0.27 kcal/mol, and = 0.13 kcal/mol. This analysis reveals that the molecular mechanics energy terms and the electrostatic solvation terms are by far the most important contributors to the relative binding free energy. Conformational entropy and solute-solvent van der Waals interaction play little role in the relative binding thermodynamics for these systems. 

Some rules have been suggested to determine the packing of secondary structures. Most approaches assume two main principles (1) residues that become buried in the interior of a protein close pack and they occupy a volume similar to that which they occupy in crystals of their amino acids (2) associated secondary structures retain a conformation close to the minimum free energy conformation of the isolated secondary structures. 

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