The aim of this dissertation is to study the structure and dynamics of proteins immersed in trehalose – water and glycerol-water binary mixtures which are known to have bio-protective properties. Fully atomistic molecular dynamics simulations were employed for the study. Hen Egg-White Lysozyme was used as the model protein.
In the first part of the study the behavior of the protein in 0, 10, 20, 30 and 100% by weight trehalose-water binary mixtures was studied. The global structure of the protein in the mixtures was found to be insensitive to the concentration of trehalose while the local structure showed a strong dependence on it. The dynamic behavior of the protein, as quantified by the Incoherent Intermediate Scattering Function, showed a non-monotonic dependence on trehalose content. Indeed, in the case of 30% trehalose – 70% water mixture the protein relaxes faster than in the case of 20% trehalose – 80% water mixture. This counterintuitive behavior is rationalized in terms of the behavior of the solvent - protein hydrogen bonds and indicates the onset of preferential hydration. The dynamic behavior of the hydration layer was also explored. The short-length-scale dynamics of this layer were found to be insenstive to trehalose concentration. However, the long-length-scale behavior showed a significant dependence on trehalose content. Insights into the dynamics of bound and mobile hydration water are also presented.
In the second part of the study the behavior of the protein in 0, 10, 20, 30 and 100% by weight glycerol-water binary mixtures was studied. Similar to the case of trehalose-water binary mixtres, the global structure of the protein was found to be insensitive to the concentration of glycerol while the local structure showed a strong dependence on it. The dynamic behavior of the protein showed a monotonic dependence on glycerol content. The fluctuations of the protein residues with respect to each other were found to be similar in all water-containing solvents but different from those in pure glycerol. The increase in the number of protein-glycerol hydrogen bonds with increasing glycerol content explains the slowing down of protein dynamics as the glycerol content increases. The dynamics of the hydration water were found to be similar to those in trehalose-water mixtures.