Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force
Helmut Grubmüller, Berthold Heymann, Paul Tavan
MPEG Movies:
Below you will find two movies showing part of a 1 nanosecond molecular dynamics simulation of the rupture process. Three numbers are shown at the bottom of each of the movies, indicating the elapsed time in picoseconds (left side), the distance in angstrom the pulling "spring" has traversed (middle), and the actual force in piconewton measured with the "spring" using Hooke's law (right side).
The frames were drawn with MolScript v1.4 [P. J. Kraulis, J. Appl. Cryst. 24, 946 (1991)] and Raster3D [Bacon and Anderson, J. Molec. Graphics 6, 219 (1988), and Merritt and Murphy, Acta Cryst. D50, 869 (1994)].
1. A global view of the rupture process. (0.9 Mbytes) The protein streptavidin is sketched with red ribbons; the ligand biotin is drawn as a yellow ball-and-stick model. The biotin is pulled towards the right using a harmonic potential (symbolized by a spring). (European readers can visit the Grubmüller et al. Home Page)
2. A detailed view of the binding pocket. (1.5 Mbytes) Only the ligand and the residues involved in ligand binding are shown. As above, biotin is pulled towards the right. (European readers can visit the Grubmüller et al. Home Page)
