Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data.
A comparison of a series of extended molecular dynamics (MD) simulations of bacteriophage T4 lysozyme in solvent with X-ray data is presented. 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 distribution of crystallographic conformations reveals that the N-terminal helix rotates together with either of these two domains. The main domain fluctuation describes a closure mode of the two domains in which the N-terminal helix rotates 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 distribution of crystallographic conformations, experimental results suggest that it might be functionally important. Interestingly, the twisting mode is sampled more extensively in all MD simulations than it is in the distribution of X-ray conformations.
de Groot
B L
BL
Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, the University of Groningen, The Netherlands.
Hayward
S
S
van Aalten
D M
DM
Amadei
A
A
Berendsen
H J
HJ
D017122:Bacteriophage T4 / Q000201:enzymology*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009038:Motion; D009113:Muramidase / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D014764:Viral Proteins / Q000737:chemistry*
D014764:Viral Proteins; D009113:Muramidase