PREDICTING EQUILIBRIUM PROTEIN FOLDING PATHWAY OF STAPHYLOCOCCAL NUCLEASE

点击翻译按钮获取中文摘要

The equilibrium folding pathway of Staphylococcal Nuclease (SNase) has been approximated using a statistical thermodynamic formalism that utilizes the high resolution structure of the native state as a template to generate a large ensemble of partially folded states. A total of 163,822 different states ranging from the native to the completely unfolded state were included in the analysis. The probability of each state was estimated using an empirical parametrization of the energetics. In this paper the predicted apparent folding constants per residue are compared to the native state hydrogen exchange protection factors obtained by NMR at 37 C. This formalism predicts accurately the protection factors of 114 out of 137 residues (83 %) in the protein. The difference between predicted and experimental free energies averages 0.14 kcal/mol. In particular, it is shown that the least stable regions of the protein involve the loop region following the third b strand up through the first half of helix 1 (residues 41-58), and the loop region between the fourth and fifth b strands (residues 77-88). The most stable regions of the protein involve those residues which contribute to the b barrel and the remaining helical structure. Examination of the residue folding probabilities as a function of the microscopic degree of folding shows that the regions of the protein which are most stable in molecules with a high degree of structure do not necessarily correspond to the most stable regions in molecules with little structure (< 10 %). For the latter case local propensities dominate folding probabilities while in the former case cooperative interactions between local regions serve to increased the combined stabilities.