Date of Award

Winter 2012

Project Type


Program or Major


Degree Name

Doctor of Philosophy

First Advisor

Thomas Laue


Our current understanding of molecular interactions, the kinetics, equilibria, and thermodynamics of biochemical reactions, is based mostly on research conducted in dilute solutions. Recent interest in the implications of true physiological concentrations has led to the development of new tools and techniques. In vivo biological systems differ so significantly from dilute solutions that a model is required to conceptualize them. The excluded volume theory is one such model. In this framework macromolecules are regarded as hard spherical volumes, holding only the property of size, and not those of shape or charge. Alternatively, the proximity energy framework considers molecules as having a complex web of various properties, including charge, that extend into the solution.

The experimental hypothesis tested in this dissertation was whether the proximity energy framework was sufficient to explain analytical ultracentrifugation data gathered in complex biological solutions. Additional hypotheses tested were as follows: The Fluorescence Detection System for the Analytical Ultracentrifuge will enable the tracking of a single component is a complex mixture; The nonideality of a molecule present in a trace amount in a crowded solution will differ from the nonideality of the background solution; Sedimentation velocity can be used in place of sedimentation equilibrium and provide similar insights into interactions in complex solutions.

The proximity energy framework was found to account for analytical ultracentrifugation data gathered in both model solutions and biologically relevant solutions such as serum. Tracking a single component in a complex solution with the fluorescence detection system proved challenging and did not work in all cases. The nonideality of a molecule present in a trace amount in a crowded solution was found to differ significantly from the nonideality of the background solution. Finally, it was found that sedimentation velocity is best used in conjunction with sedimentation equilibrium, as, while there is some overlap, both methods provide unique information about complex solutions and molecular interactions therein.