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Degree

Doctor of Philosophy, University of Akron, Polymer Science, 2005.

Abstract

The main objective of the work presented in this thesis is to understand the dynamic behavior of proteins immersed in bio-preserving liquids and glasses. For this purpose, the model protein lysozyme was chosen. The two solvents selected were glycerol, a triol, and trehalose, a carbohydrate, which are known to be very effective bio-preserving agents. In the first part of this research project the dynamics of glycerol, trehalose and their mixtures were investigated using atomistic molecular dynamics simulations. It was found that a mixture of 5% glycerol and 95% trehalose had the most suppressed dynamics in a one-nanosecond time window. This result agreed with the experimental analysis of the mean-square displacement of the hydrogen atoms, as measured by neutron scattering. Moreover, this result correlates with the experimentally observed enhancement of the stability of some enzymes immersed in a trehalose-glycerol mixture with this particular concentration. The microscopic analysis suggested that the formation of a robust intermolecular hydrogen bonding network was most effective at this concentration and was the main mechanism for the suppression of the fast dynamics. Afterward, the study of the dynamics of the protein embedded in the same unary solvents and binary mixtures was done. The results showed that the protein had the most suppressed dynamics in a 10% glycerol and 90% trehalose mixture, a result that correlated with the internal dynamics of the glass surrounding the protein. It was also found that the hydrogen bonding network formed between the protein and the solvent was more robust for this particular mixture. Possible molecular mechanisms behind the coupling of protein and solvent dynamics were also explored for lysozyme in pure glycerol and trehalose systems. The dynamics of the hydrogen bonding network between the solvent molecules in the first shell and the surface residues of the protein were found to control the structural relaxation of the whole protein. Additionally, a study of the dynamics of the solvent as a function of the distance from the surface of the protein indicated that the viscosity seen by the protein was not the one of the bulk solvent. The presence of the protein changed the dynamics of the surrounding solvent. This implies that the protein sees an effective viscosity that can be higher or lower than the one of the bulk solvent. Moreover, the dynamics of the surface and core residues of the protein were found to differ significantly. The former followed the dynamics of the solvent more closely than the latter. Based on these results a molecular mechanism for the coupling of the solvent-protein dynamics was proposed.

Keywords

protein dynamics; molecular dynamics simulation; glassy solvents; bio-preservation

Advisor

Gustavo A Carri

Pages

142p.

Document number: akron1133800339
Permalink: http://rave.ohiolink.edu/etdc/view?acc_num=akron1133800339

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