Combining Laue diffraction and molecular dynamics to study enzyme intermediates.
Two separate techniques, Laue diffraction and computational molecular dynamics (MD) simulations, have been independently developed to allow the visualization and assessment of transient structural states. Recent studies on isocitrate dehydrogenase show that computational MD simulations of an enzymatic Michaelis complex are consistent with difference Fourier electron density maps of the same structure from a Laue experiment. The use of independent MD studies during crystallographic refinement has allowed us to assign with confidence a number of additional contacts and features important for hydride transfer. We find that unrestrained independent MD simulations provides a very useful method of cross-validation for highly mobile atoms in regions of experimental density that are poorly defined. Likewise, information from Laue difference maps provides information about substrate conformation and interactions that greatly facilitate MD simulations.
Stoddard
B L
BL
Fred Hutchinson Cancer Research Center, Seattle, Washington 98104, USA.
Dean
A
A
Bash
P A
PA
D003198:Computer Simulation; D018360:Crystallography, X-Ray / Q000379:methods*; D004798:Enzymes / Q000737:chemistry*; D005583:Fourier Analysis; D007521:Isocitrate Dehydrogenase / Q000737:chemistry; D008958:Models, Molecular; D008968:Molecular Conformation; D013269:Stochastic Processes
D004798:Enzymes; D007521:Isocitrate Dehydrogenase