Mechanism of protein folding. II. Lysozyme and phospholipase

Refolding of hen egg-white lysozyme assuming the formation of secondary structures (alpha-helices and beta-sheets) is carried out by the method presented in the previous paper (N. Saitô et al., Proteins; Struct. Funct. Genet. 3 (1988) 199-208). To do this, the hydrophobic interactions between the hydrophobic residues which are located at the key positions for folding and can be identified without the knowledge of the native structure, and the nonbonded interactions between every pair of atoms (except hydrogen) or groups are introduced successively from short- to medium-distance pairs. The search for the energy minimum by these interactions can afford a conformation of especially the mutual arrangements between neighboring secondary structures. When these local structures are accomplished, some of the long-distance amino-acid pairs come close together and then the possible interactions (hydrophobic, nonbonded) are introduced. The three-dimensional structure of lysozyme thus obtained is shown to have locally correct arrangements of the secondary structures, but mutual relations between long-distance parts of the chain are not similar to the native structure. The introduction of disulfide bonds between appropriate cysteine residues is necessary to reach the native structure. The choice of cysteine pairs for disulfide bonding is made by the criterion given in the paper to follow (K. Watanabe, A. Nakamura, Y. Fukuda and N. Saitô. Biophys. Chem. 40 (1991) 293). The same treatment is applied to bovine pancreatic phospholipase with 7 disulfide bonds. The formation of the antiparallel beta-structures from neighboring beta-strands and the problem of the folding order are also discussed.