B.L. de Groot, S. Hayward, D.M.F. van Aalten, A. Amadei, H.J.C. Berendsen; "Domain Motions in Bacteriophage T4 Lysozyme; a Comparison between Molecular Dynamics and Crystallographic Data"; PROTEINS: Struct. Funct. Gen. 31: 116-127(1998).
Abstract
A series of extended Molecular Dynamics simulations of bacteriophage
T4 lysozyme in solvent has been performed. Essential Dynamics analyses were
used to derive collective fluctuations
from both the simulated trajectories and a distribution of crystallographic
conformations. In both cases the main collective fluctuations
describe domain motions.
The protein consists of an N- and C-terminal domain connected by a
long helix. The analysis of the cluster of x-ray structures reveals
that the N-terminal helix belongs to either of these
two domains: the
main domain fluctuation describes a closure mode of the two domains in
which the N-terminal helix moves concertedly with the C-terminal
domain, while the domain fluctuation with second largest amplitude
corresponds to a twisting mode of the two domains, with the N-terminal
helix rotating concertedly with the N-terminal domain. For the
closure mode, the difference in hinge-bending angle between the most
open and most closed x-ray structure along this mode is 49 degrees. In
the MD simulation that shows the largest fluctuation along this mode,
a rotation of 45 degrees was observed. Although the twisting mode has
much less freedom than the closure mode in the cluster of
crystallographic structures, analyses suggest that it might be
functionally important. Interestingly, the twisting mode is sampled
more extensively in all MD simulations than it is in the x-ray
cluster.
Calculations
Simulations were carried out using the GROMACS simulation package. Essential Dynamics analyses were run from the WHAT IF package. Domain analyses were performed using DYNDOM .
Animations
In these animations a smooth trajectory is shown between the two extremes
found for each of the modes, i.e. the path that is shown is arteficial, but
the amplitude of the fluctuations is realistic.
These animations were made using Molscript, Raster3D, and gifmerge.
Data
Click here for a
tar file with a collection of the main results. It contains a README with
a description of the files contained in the archive.