Prediction of Structure of Globular Proteins
II. Tertiary Structure

Nobuhiko Saito[1]
Motonori Ota[2]

[1]Department of Applied Physics, Waseda University
3-4-1, Okubo, Shinjuku, Tokyo 169, Japan
[2]Corporate R&D laboratory, Tonen Corporation
1-3-1, Nishi-Tsurugaoka Ohi-machi, Iruma-gun, Saitama 356, Japan


The packing mechanism of the secondary structures has been revealed. The driving force is the hydrophobic interaction between hydrophobic residues which are located at nearest distance along the chain. They are chosen because they can be bound most quickly. In this way local structures of the protein are determined and thus glow into the whole structure. This process is usually done manually, but is now tried to be carried out automatically. This formulation is applied to crambin.