Native protein structures energy components

Two additional decoy data sets of misfolded proteins [17] and of predicted protein structures from the Critical Assessment of Techniques for Protein Stmcture Prediction (CASP) [67] are also used to illustrate the method and its utility. Individual components of the energy perform worse than the total energy for example, for the bulk of the well-packed decoys, the van der Waals energy provides very little information about structural similarity between a well-packed non-native structure and the native state. It is also shown that some aspects of the SGB model results can be mimicked by a screened electrostatic energy, although the SGB approximation provides a better discriminatory measure between non-native and native states. 

It is currently believed that the three dimensional structure of a native protein in a given environment (solvent, pH, ionic strength, presence of other components, temperature, etc.) is the one in which the Gibbs free energy of the whole system is a minimum with respect to all degrees of freedom, i.e., that the native conformation is determined by the various interatomic interactions and hence by the amino acid sequence, in a given environment. ... 

This approximate law holds for both native structure [22] and folding dynamics [2], In this regard, this wrapping motif may be regarded as a structural element that captures the basic component of energy transduction from hydrophobic association to structure formation. Furthermore, it implies that a fundamental constraint in protein architecture applicable to native structures applies also throughout the folding trajectory. 

The partial molar heat capacity can be considered to be composed of intrinsic and hydration contributions. The intrinsic component contains contributions from covalent and non-covalent interactions. It has been shown that about 85% of the total heat capacity of the native state of a protein in solution is due to the covalent structure [72]. Changes in the heat capacity upon unfolding are therefore primarily interpreted as due to changes in the hydration. A physical picture of energy fluctuations means changing the conformation between ordered and less ordered structures. This can be achieved by hindered internal rotations, low frequency... 

---