Uncovering the Functional Effects of Multifaceted Cholesterol-Kir2 Interactions via Molecular Modeling

Cholesterol is a major component of mammalian cell membranes and an important regulator of membrane biophysical phenomena, including membrane thickness, membrane fluidity, and lipid domain compartmentalization. Moreover, cholesterol has been shown to be a key player in the regulation of membrane protein function, particularly with respect to ion channels. This thesis specifically focuses on understanding the regulation of inwardly rectifying potassium (Kir) channels, a major class of ion channels, by cholesterol. In particular, two questions were asked: i) how does cholesterol interact with its putative binding sites on the Kir channel, and ii) once bound, how does cholesterol alter the dynamic structure of the channel and regulate its function? Three complementary approaches were used to investigate this question: molecular docking, coarse-grained molecular dynamics simulations, and a novel, network-theory based analysis. Overall, it was found that cholesterol-Kir interactions are multifaceted and complex, with multiple cholesterol molecules interacting with the channel simultaneously and at different, conformation state-dependent sites. These sites were likewise found to be promiscuous: cholesterol and its chiral isomers ent-cholesterol and epicholesterol interact with sites on the channel with similar favorability, and cholesterol was found to be highly flexible within its binding site. Finally, it was found that cholesterol binding events regulate channel function by mediating the interactions between important functional domains of the channel, with an increase in membrane cholesterol leading to a “de-coupling” effect between these domains. Significantly, these de-coupling events were found to be governed by specific residue-residue interactions, which could be correlated to cholesterol binding.