Divergence entropy to characterize the stability in selected enzymes – The role of disulfide bonds in respect to the structure of hydrophobic core
Banach M, Konieczny L, Kalinowska B, Roterman I
Jagiellonian University - Medical College – Krakow,Poland
It is commonly assumed that tertiary structure of proteins is stabilized by hydrophobic core. In some proteins (particularly extracellular proteins) additional stabilization is provided by covalent disulfide bonds between selected Cys residues.
Our analysis focuses on the mutual interplay between these stabilizing factors. The stabilizing role of disulfide bonds is quantitatively assessed using the fuzzy oil drop model. According to this model the structure of hydrophobic core is expressed by 3D Gauss function. This “idealized” structure can be contrasted with the actual (observed) distribution of hydrophobic density which is the result of the amino acid arrangement in protein body. Mutual comparison of both distributions (theoretical and observed) enables to determine the presence of hydrophobic core and to evaluate its status. Quantitative assessment of the correspondence between the observed and idealized distributions bases on the Kullback-Leibler divergence entropy criterion. It can also be applied to recognize the status of certain polypeptide chain fragments – fragments defined by the positions of Cys residues participating in SS-bonds in particular. It makes possible the estimation of the mutual relation between hydrophobic core structure and the role of disulfide bonds which may appear as the constrain introducing local irregularities.
It is shown, that some enzymes are stabilized by highly ordered hydrophobic core additionally supported by the net of disulfide bonds. Other enzymes appeared to represent the contradictory status of these two factors. Some fragments defined by SS-bonds seem to support the aim-oriented local instability in respect to the hydrophobic core structure.