Low frequency motion in proteins - Comparison of normal mode and molecular dynamics of streptomyces griseus protease A

The motion of a chymotrypsin-like serine protease, SGPA, has been studied by torsion space normal mode analysis and by Cartesian space molecular dynamics, and the results have been compared. The molecular dynamics trajectory was analyzed using digital signal processing techniques to provide a set of characteristic modes that can be compared directly with the normal modes. The results were also compared with the motion implied by the crystallographic temperature factors. We find that in spite of the radically different approximations used in the two methods, agreement between the resulting motions and with the experimental data is surprisingly high. We conclude that this agreement probably reflects an underlying robustness in the motion, dictated primarily by van der Waals packing. In contrast to other proteins, there are no large amplitude inter-domain motions. Rather, the low frequency, high amplitude motions are concentrated in three surface hairpin loops. The movement of one these loops, the specificity loop, appears to facilitate substrate binding. (C) 1999 Academic Press.