NEW DEVELOPMENT ON ENERGETIC APPROACH TO THE PACKING IN PROTEINS

The energy minimization in the computer program PACK established for investigating interactions of secondary structures in proteins was based on the finite deference method. It is well known that a minimizer of finite difference method is less efficient than that of analytical gradient method. In this article the equations of the analytical energy gradients for a multiple chain system have been derived and they can be directly incorporated into the PACK program. The revised version, PACK/2, thus obtained is much more efficient. Energy minimizations carried out on the theoretical models of 4-helix bundle, sheet-sheet packing, and beta-barrel indicated that the CPU times were reduced 15- to 20-fold if the revised PACK/2 algorithm was used. In general, the more complicated the computed structure was, the more significantly the computation time was reduced. Furthermore, for the cases demonstrated here, the final minimized energies were always lower than those obtained by the original version of PACK, indicating that a better packing structure was achieved by means of the revised program PACK/2.