Molecular Dynamics Simulations of PIP 2-Driven Kir Channel Activation

Abstract

Inwardly rectifying K+ (Kir) channels are gated by the signaling phospholipid phosphatidylinositol-bisphosphate (PIP2). The molecular mechanism of how PIP2 interacts with Kir channels and induces its structural transition from the closed to the open state remains unclear. We used computational approaches, molecular docking and molecular dynamics (MD) simulations, to model the PIP2-driven Kir channel activation based on crystal structures of a Kir3.1 chimera (BacKir3.1, PDB entry: 2QKS). The BacKir3.1 serves as a valid structural and functional model of Kir3 channel behavior (Nishida et al., 2007; Leal-Pinto et al., 2010). BacKir3.1 was crystallized in two conformers, dilated and constricted forms, which differ mainly in the conformations of the cytosolic G-loop gate. We built four channel systems including dilated and constricted BacKir3.1 channels with and without PIP2 present in the explicit POPC membrane environment, and performed 100ns MD simulations, respectively. We monitored the interactions between PIP2 and the channel during the simulations that showed C-alpha RMSD stability after 50ns. Several key residues in the Slide helix and the B-loop were identified to form hydrogen bonds and/or salt bridges with PIP2. Average radii of the ion permeation pathway along the channel were calculated during the 95-100ns simulation interval. Both systems in which PIP2 was present became wider in the G-loop regions along the ion permeation pathway compared to their counterpart systems in the absence of PIP2. In the “dilated + PIP2” system, the MD simulations identified in one subunit of the channel an outward rotation on the residue Phe181, that is located in the helix bundle-crossing (HBC) gate of TM2. The relationship of the channel-PIP2 interacting residues and their effects on the conformations of the G-loop and HBC gates are actively pursued through a systematic examination of hydrogen bond network patterns and principal component analysis.