Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations.
We explore possible molecular mechanisms behind the coupling of protein and solvent dynamics using atomistic molecular-dynamics simulations. For this purpose, we analyze the model protein lysozyme in glycerol, a well-known protein-preserving agent. We find that the dynamics of the hydrogen bond network between the solvent molecules in the first shell and the surface residues of the protein controls the structural relaxation (dynamics) of the whole protein. Specifically, we find a power-law relationship between the relaxation time of the aforementioned hydrogen bond network and the structural relaxation time of the protein obtained from the incoherent intermediate scattering function. We demonstrate that the relationship between the dynamics of the hydrogen bonds and the dynamics of the protein appears also in the dynamic transition temperature of the protein. A study of the dynamics of glycerol as a function of the distance from the surface of the protein indicates that the viscosity seen by the protein is not the one of the bulk solvent. The presence of the protein suppresses the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity higher than the one of the bulk solvent. We also found significant differences in the dynamics of surface and core residues of the protein. The former is found to follow the dynamics of the solvent more closely than the latter. These results allowed us to propose a molecular mechanism for the coupling of the solvent-protein dynamics.
Dirama
Taner E
TE
Department of Polymer Science, The University of Akron, Ohio 44325, USA.
Carri
Gustavo A
GA
Sokolov
Alexei P
AP
D000465:Algorithms; D003198:Computer Simulation; D005990:Glycerol / Q000737:chemistry*; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D009113:Muramidase / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics; D014783:Viscosity
D012997:Solvents; D009113:Muramidase; D005990:Glycerol