Stability of two natural homologous proteins with different folds

The applicability of the model for protein folding process simulation is presented using as the test two homologous proteins of different fold: helical in 3BD1 and β-structural form in 2PIJ [L. van Dorn, T. Newlove, S. Chang, W. Ingram, M. Cordes. Biochemistry 45, 10542 (2006)]. The folding process is assumed to be directed by hydrophobic core directing the hydrophobic residues toward the center of the molecule and exposing the hydrophilic residues on the surface. The “fuzzy oil drop” model is expressed by the 3-dimensional Gauss function which mimics the external force field. The value of Gauss function is interpreted as the hydrophobicity density calculated in any point of the space of the protein body. The accordance of idealized and observed hydrophobicity distributions (calculated according to Levitt function) measured using the Kullback-Leibler divergence entropy reveals good accordance in two homological proteins of different folds. The structural differences appeared to be easily explainable on the basis of “fuzzy oil drop” model.