COMPUTATIONAL APPROACHES TO UNDERSTANDING ION CHANNEL GATING

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Membrane channels and transporters regulate the entry and exit of material from cells. These processes must be tightly regulated to maintain cellular homeostasis. Therefore, it is not surprising that channels and transporters adopted closed and open conformations much like the faucet of a sink can be on or off. Here we propose to study how the central pore of the Kv1.2 voltage-gated potassium channel opens and closes. It is believed that four identical helices that line the channel pore splay apart to allow unobstructed passage of ions through the channel, and that these four helices come together to block the flow in the closed state. Sequence analysis across many potassium channels shows that there are conserved proline and glycine residues at specific positions along the helix, and it is believed that helix bending occurs at these residues. However, there are no high-resolution structures of the same voltage-gated potassium channel in both the open and closed state, so how this bending occurs is not known. We intend to use molecular simulations to study the intrinsic bending ability of the central helix in Kv1.2. Starting from the crystal structure configuration we will run long equilibrium trajectories of wild-type and mutant helices, and we will use umbrella sampling to bias the helix along certain reaction pathways that we believe to be important for channel opening and closing. We will compare our results with experimental mutation analysis in an attempt to relate the energetics of helix bending to the global channel function.