Characterization of the interdomain motions in hen lysozyme using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations.
Hen lysozyme is an enzyme characterized by the presence of two domains whose relative motions are involved in the mechanism of binding and release of the substrates. By using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations, we characterize the breathing motions describing the interdomain fluctuations of this protein. We found that the ensemble of conformations that we determined spans the entire range of structures of hen lysozyme deposited in the Protein Data Bank, including both the free and bound states, suggesting that the thermal motions in the free state provide access to the structures populated upon binding. The approach that we present illustrates how the use of residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations makes it possible to explore conformational fluctuations of a relatively large amplitude in proteins.
Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, United Kingdom.
Alfonso
A
De Simone
Rinaldo W
RW
Montalvao
Christopher M
CM
Dobson
Michele
M
Vendruscolo
D000818:Animals; D002645:Chickens; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry*; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation
C421864:hen egg lysozyme; D009113:Muramidase