Molecular Dynamics Simulations of Elastin

Bin Li, Darwin Alonso and Valerie Daggett 1999

Simulations of elastin were run at different temperatures, and the movie link below shows the simulations at 10 C and 40 C. Collapse occurs at high temperature with decreases in radius of gyration, solvent accessible surface area and end-to-end distance. At the lower temperature, the molecule undergoes extensive conformational changes but remains extended. The lower temperature (10 C) simulation is shown on top in CYAN, and the higher temperature (40 C) one on the bottom in RED. Only the backbone protein atoms are shown.

Initial (0 ns)

Final (6 ns)

Molecular dynamics simulations were performed using the program ENCAD (Levitt et al, 1993) using the force field described by Levitt et al (J. Phys. Comm. 1994). All water and protein atoms were explicitly included, and the systems contained approximately 11400 water atoms (3800 molecules) and 1083 protein atoms. The simulations lasted 6 ns and consisted of 3,000,000 timesteps.

Movies:
Movies: Quicktime movie of two 6 ns simulations at low and high temperature.
MOVIE of 0-4 ns 400 frames at 10 ps/frame. Large!!!! 35 MB
MOVIE Final 4-6 ns of the simulation. 200 frames at 10 ps/frame. 1.8 MB
Other movie formats and representative shorter time samples of the simulation are being constructed.