Coupling between lysozyme and glycerol dynamics: microscopic insights from molecular-dynamics simulations

Area of Science:

• Biophysics
• Computational Biology
• Materials Science

Background:

• Protein dynamics are crucial for function.
• Solvent interactions significantly influence protein behavior.
• Understanding protein-solvent coupling is key to protein stabilization and function.

Purpose of the Study:

• To elucidate the molecular mechanisms linking protein and solvent dynamics.
• To investigate the role of the solvent's hydrogen bond network in protein structural relaxation.
• To determine the effective viscosity experienced by a protein in a glycerol solution.

Main Methods:

• Atomistic molecular-dynamics simulations.
• Analysis of the hydrogen bond network dynamics.
• Calculation of protein structural relaxation times using incoherent intermediate scattering functions.
• Investigation of solvent dynamics as a function of distance from the protein surface.

Main Results:

• A power-law relationship exists between solvent hydrogen bond network relaxation and protein structural relaxation.
• The protein's dynamic transition temperature reflects the coupled dynamics.
• The effective viscosity experienced by the protein is higher than the bulk glycerol viscosity due to suppressed solvent dynamics near the surface.
• Surface protein residues exhibit dynamics more closely coupled to the solvent than core residues.

Conclusions:

• The dynamics of the solvent's hydrogen bond network directly control protein structural relaxation.
• Proteins experience a higher effective viscosity than the bulk solvent.
• A molecular mechanism for solvent-protein dynamics coupling has been proposed, highlighting the role of surface interactions.