Structure And Dynamics Of Constrained Water : Microscopic Study Of Macromolecular Hydration Using Computer Simulations

Abstract

The thesis, which contains nine chapters, reports extensive large scale atomistic molecular dynamics (MD) simulation studies of water structure and dynamics at the surface of an anionic micelle, hydration layer of two proteins, and in the grooves of a 38-base pairs long DNA. Understanding the structure and dynamics of water molecules at the surfaces of self-organized assemblies and complex biological macromolecules has become a subject of intense research in recent times. Chapter 1 contains a brief overview of the biomolecular hydration dynamics. Relevant experimental, computational, and theoretical studies of biomolecular hydration and the time scales associated with the water dynamics are discussed. In Chapters 2 and 3, the structure, environment, energetics, and dynamics of constrained water molecules in the aqueous anionic micelle of cesium perfluorooctanoate (CsPFO) have been studied using large scale atomistic molecular dynamics simulations. Based on the number of hydrogen bond (HB) that interfacial water molecule makes with the polar head group (PHG) oxygen of the micelle, we find the existence of three kinds of water at the interface. We introduce a nomenclature to identify the species as IBW2 (form two HBs with two different PHG), IBW1 (form one HB with PHG), and IFW (no HB with PHG). Despite of possessing two strong w-PHG bonds, the concentration of the IBW2 species is rather low due to entropic effect. The ion solvation dynamics study at the interface shows the presence of a slow component, with a relaxation time 1-2 order of magnitude slower than that in the corresponding bulk solvent in agreement with the experimental results. Both the translational and orientational dynamics of the water molecules near the micellar surface is found to be much slower than those in the bulk. The HB between the PHG of the micelle and the water molecule has almost 13 times longer life time than that in the bulk between two tagged water molecules. In Chapter 4, we present results of extensive atomistic MD simulation studies of the structure and dynamics of aqueous protein solution of the toxic domain of Enterotoxin (1ETN) and the chicken villin headpiece sub-domain containing 36 amino acid residues (HP-36). Reduced water structure and the faster water dynamics around the active site of these proteins have been observed which may have biological significance. Chapter 5 presents an extensive atomistic molecular dynamics simulations study of water dynamics in the hydration layer of a 38 base long hydrated DNA duplex. The computed rotational time correlation function (TCF) of the minor groove water dipoles is found to be markedly non-exponential with a slow component at long time. The constrained water molecule is also found to exhibit anisotropic diffusion in both the major and minor grooves. At short-to-intermediate times, translational motion of water molecules in minor groove is sub-diffusive. Chapter 6 presents the study of water entropy in both the grooves DNA. The average values of the entropy of water at 300K in both the grooves of DNA are found to be significantly lower than that in bulk water. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or micro viscosity) of water molecules in a given domain. In Chapter 7, we study the specific DNA base-water hydrogen bond lifetime (HBLT) dynamics at the major and the minor grooves of a hydrated duplex. The base-water HBLT correlation functions are in general multi-exponential and the average lifetime depends significantly on the specificity of the DNA sequence. The average HBLT is longer in the minor groove than that in the major groove by almost a factor of 2. Chapter 8 presents the solvation dynamics of constituent bases of aqueous DNA duplex. The solvation TCFs of the four individual bases display highly non-exponential decay with time. An interesting negative cross-correlation between water and counterions is observed which makes an important contribution to relaxation at intermediate to longer times. In the concluding note, Chapter 9 presents a brief summary of the outcome of the thesis and suggests several relevant problems that may prove w orthwhile to be addressed in future