Macromolecular dynamics and structure in crowded and confined environments

Palit, Swomitra (2018) Macromolecular dynamics and structure in crowded and confined environments. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Macromolecular crowding and confinement, the effects caused by high concentrations of macromolecules in solution and/or in small compartments, are believed to influence diffusion processes, intermolecular interactions, protein folding, and intracellular transport in living cells. Understanding mechanisms of transport in biological systems (such as living cells) is complex and challenging. We construct cell mimetic environments in which the artificial macromolecules (e.g. polyethylene glycol, Ficoll70) are compartmentalized not in cells but in concentrated environments and agarose gel networks. In this work we have established a system to generate stable and monodisperse droplets of hierarchical confinement. The goal of this study is to measure translational diffusion in crowded and confined geometries of varying concentrations of different macromolecules on diffusion. We have combined the use of pulsed-fieldgradient nuclear magnetic resonance (PFG NMR) with small-angle neutron scattering (SANS) in order to obtain new insights in simple model systems of macromolecular crowding. The NMR and SANS techniques complement each other. Using PFG NMR technique, we have monitored the dynamics of synthetic macromolecules with multiple chemical components in complex environments. SANS, on the other hand, yields structure (size) of macromolecules. Our experimental findings in cell mimetic environments provide an important step towards gaining further insights into the effects of macromolecular crowding on diffusion and conformation.

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