A combined molecular dynamic simulation and urea 14N NMR relaxation study of the urea-lysozyme system

Urea in the lysozyme solvation shell has been studied by utilizing a combination of urea 14N, water 17O NMR relaxation experiments and a molecular dynamics simulation of the urea-lysozyme system. Samples with lysozyme in the native fold in water as well as in 3M urea have been studied, as well as denatured lysozyme in a 8.5M urea solvent. The spin relaxation rates of the samples with folded protein show a clear field dependence, which is consistent with a few urea molecules having long residence times on the protein surface and preferentially located in pockets and grooves on the protein. By combining the 3M urea NMR relaxation data and data from the MD simulation, a full parameter set of the relaxation model is found which can successfully predict the experimental relaxation rates of the 3M urea sample. However, in the parameter fitting it is evident that the rotational dynamics of urea in the MD simulation is slightly too fast to be consistent with the NMR relaxation rates, perhaps a result of the fast dynamics of the TIP3P water model. The relaxation rates of urea in the proximity of the unfolded lysozyme lack field dependence, which can be interpreted as a loss of pockets and grooves on the denatured protein. The extracted model parameters from the 3M sample are adjusted and tested on a simple model of the unfolded protein sample and are seen to be in agreement with the relaxation rates. It is shown that the combination of NMR relaxation and MD simulations can be used to create a microscopic picture of the solvent at the protein interface, which can be used for example in the study of chemical denaturation.