Understanding protein dynamical transition and protein-water interaction from dielectric relaxation calculations
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Sirer, Irmak (2006) Understanding protein dynamical transition and protein-water interaction from dielectric relaxation calculations. [Thesis]
Official URL: http://risc01.sabanciuniv.edu/record=b1158354 (Table of Contents)
Dielectric properties of an aqueous lysozyme solution were calculated from 2 ns long MD simulations in the temperature range of 150-300 K and an 4 ns long simulation at 300 K. Static and frequency dependent dielectric constants of the system were calculated from auto- and cross-correlations of its three components (protein, water, ions). Cole-Cole plots for protein, water and the total solution were obtained. Emergence of an intense protein-water interaction above the dynamical transition between 190 K and 210 K was evidenced by the presence of protein effects in the water components of the Cole-Cole plots and frequency dependent dielectric constants at and above 210 K. Backbone and side chain torsion angle trajectories for surface loop residues within this range of temperatures were calculated. Also, water molecules around side chains were labeled and monitored individually, and radial distribution functions of water around the side chains and in the bulk water were obtained. These data were used to support a model that accounts for the interaction between surface water and protein components, resulting in high mobility of the side chains at the transition temperature range. The water molecules in the vicinity of the protein surface are then propelled into the bulk for a much different electrostatic effect than is immediately expected of the known properties of water alone. The functional protein. therefore, exists as an integral part of a larger protein-water system that cannot be decoupled. The water molecules may even be thought of as information carriers that make other nearby biological molecules aware of the presence of the protein.
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