Author's School

School of Engineering & Applied Science

Author's Department/Program

Biomedical Engineering


English (en)

Date of Award

January 2010

Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

David Sept


The long term goal of this research is to study the structure and function of the BKCa channels, by focusing on the effect of a single residue mutation, the epilepsy mutation. BKCa channels are potassium channels, activated by voltage, Ca2+ and Mg2+ ions. These factors control the opening and closing of the channel pore and thus regulate the large K+ current passing through them. Recently, a mutation D434G in humans, was found to make the channel hyperactive and more sensitive to the Ca2+ ions. The single residue mutation, resulting from a substitution of an Asp to Gly, was found to be linked with epilepsy and paroxysmal dyskinesia. The central focus of this thesis is to identify the molecular mechanism behind the structural and functional changes caused by this mutation. Using comparative modeling and molecular dynamics simulations, it is revealed that the epilepsy mutation reduces the flexibility of the channel protein and drives it to a rigid conformation. The loss in dynamics is seen around the Ca2+ binding site which reflects its direct impact on the Ca2+ activation of the channel. Comparison with experimental results show that the change in dynamics is targeted to regions which possibly connects the Ca2+ –binding site to the pore and thus transfer this effect to the pore. The thesis also presents a new method of representation of cations in computational techniques, the multisite cation model. The model presents improvement in the reproduction of accurate structural and thermodynamical properties of ion–mediated mechanisms. The successful implementation of the model in protein and water systems show that the model will prove very useful in increasing the accuracy and precision of metal mediated simulations and energy calculations.


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