Origin of diverse time scales in the protein hydration layer solvation dynamics: A simulation study

• Published in: The Journal of chemical physics 2017-10, Vol.147 (15), p.154901-154901
• Main Authors: Mondal, Sayantan, Mukherjee, Saumyak, Bagchi, Biman
• Format: Article
• Language: English
• Subjects: Chains; Chemical bonds; Computer simulation; Decay rate; Density functional theory; Hydration; Hydrogen storage; Kinetics; Lysozyme; Models, Chemical; Molecular dynamics; Molecular Dynamics Simulation; Muramidase - chemistry; Myoglobin - chemistry; Myoglobins; Proteins; Proteins - chemistry; Solvation; Time dependence; Tryptophan; Tryptophan - chemistry; Variation; Water - chemistry
• ISSN: 0021-9606; 1089-7690
• DOI: 10.1063/1.4995420

In order to inquire the microscopic origin of observed multiple time scales in solvation dynamics, we carry out several computer experiments. We perform atomistic molecular dynamics simulations on three protein-water systems, namely, lysozyme, myoglobin, and sweet protein monellin. In these experiments, we mutate the charges of the neighbouring amino acid side chains of certain natural probes (tryptophan) and also freeze the side chain motions. In order to distinguish between different contributions, we decompose the total solvation energy response in terms of various components present in the system. This allows us to capture the interplay among different self- and cross-energy correlation terms. Freezing the protein motions removes the slowest component that results from side chain fluctuations, but a part of slowness remains. This leads to the conclusion that the slow component approximately in the 20–80 ps range arises from slow water molecules present in the hydration layer. While the more than 100 ps component has multiple origins, namely, adjacent charges in amino acid side chains, hydrogen bonded water molecules and a dynamically coupled motion between side chain and water. In addition, the charges enforce a structural ordering of nearby water molecules and helps to form a local long-lived hydrogen bonded network. Further separation of the spatial and temporal responses in solvation dynamics reveals different roles of hydration and bulk water. We find that the hydration layer water molecules are largely responsible for the slow component, whereas the initial ultrafast decay arises predominantly (approximately 80%) due to the bulk. This agrees with earlier theoretical observations. We also attempt to rationalise our results with the help of a molecular hydrodynamic theory that was developed using classical time dependent density functional theory in a semi-quantitative manner.