Structure and dynamics of K channel pore-lining helices: A comparative simulation study

Isolated pore-lining helices derived from three types of K-channel have bee n analyzed in terms of their structural and dynamic features in nanosecond molecular dynamics (MD) simulations while spanning a lipid bilayer. The hel ices were 1) M1 and M2 from the bacterial channel KcsA (Streptomyces livida ns), 2) S5 and S6 from the voltage-gated (Kv) channel Shaker (Drosophila me lanogaster), and 3) M1 and M2 from the inward rectifier channel Kir6.2 (hum an). In the case of the Kv and Kir channels, for which x-ray structures are not known, both short and long models of each helix were considered. Each helix was incorporated into a lipid bilayer containing 127 palmitoyloleoylp hosphatidylcholine molecules, which was solvated with similar to 4000 water molecules, yielding similar to 20,000 atoms in each system. Nanosecond MD simulations were used to aid the definition of optimal lengths for the heli x models from Ky and Kir. Thus the study corresponds to a total simulation time of 10 ns. The inner pore-lining helices (M2 in KcsA and Kir, S6 in Sha ker) appear to be slightly more flexible than the outer pore-lining helices . In particular, the Pro-Val-Pro motif of S6 results in flexibility about a molecular hinge, as was suggested by previous in vacuo simulations (Kerr e t al,, 1996, Biopolymers. 39:503-515). Such flexibility may be related to g ating in the corresponding intact channel protein molecules. Analysis of H- bonds revealed interactions with both water and lipid molecules in the wate r/bilayer interfacial region. Such H-bonding interactions may lock the heli ces in place in the bilayer during the folding of the channel protein las i s implicit in the two-stage model of membrane protein folding). Aromatic re sidues at the extremities of the helices underwent complex motions on both short (<10 ps) and long (>100 ps) time scales.