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UBC Theses and Dissertations

Determination of binding constants by computer simulation of affinity capillary electrophoresis Fang, Ning

Abstract

The aim of this work is to test and improve the mathematical models of affinity capillary electrophoresis (ACE), to implement these models by computer simulation, and to use the simulation programs to determine the medium- and high-affinity binding constants for protein-ligand interactions. The first part of this thesis presents the first mathematical model, the one-cell model, of ACE and the derivations of the equations for both 2:1 (analyte:additive) and 1:1 interactions. The steady state equations were also introduced due to their important roles in analyzing the simulated results. The second part of this thesis presents four simulation programs which were based on the one-cell model and used to simulate the ACE processes, to collect and analyze simulation data, and to estimate the binding constants for the protein-ligand interactions. In this work, we performed several series of experiments and used the simulation programs to determine the binding constants for the 2:1 interaction between flurbiprofen and transthyretin, and the binding constant for the 1:1 interaction between chlorpromazine and quaic riboflavin binding protein (qRfBP). The one-cell model is extremely fast in simulating ACE processes, but it cannot accurately describe the ACE experiments with high concentrations of analyte ([A]) and additive ([P]) or a high ratio of [A] to [P]. Thus, in the final part of this thesis, a new model and its improved implementation algorithm were proposed.

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