Development of the protein tertiary structure prediction system III
-Simulation of folding process of lysozyme-

Kouji TABUCHI[1]
Tamio YASUKAWA[1]
Masaki FUMOTO[2]

[1]Tokyo University of Agriculture & Technology
[2]TEIJIN Ltd.

Abstract

Protein folding simulation is useful for the prediction of its tertiary structure, as well as for detailed analysis of folding process. In a preceding paper, we have proposed a simplified simulation model where spherical elements representing respective residues are connected by virtual bonds of 3.8Å in length. Each element has specific soft repulsive potential and hydrophobic attractive potential and undergoes random motions under these potentials and elastic force operative between chain ends originating from conformational entropy. In the present work, this model was applied to folding simulation of lysozyme and obtained fairly satisfactory results on the end-to-end distance and radius of gyration, as well as the time variations of the distance of separations of Cys-Cys pairs.

Results obtained by extended models with Lennard-Jones type inter-residue interactions and module structures have also been presented and compared with intermediate conformations estimated by NMR spectroscopy.