Structure and dynamics of the pore-lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles

Abstract

Multiple nanosecond duration molecular dynamics simulations on the pore-lining M2 helix of the nicotinic acetylcholine receptor reveal how its structure and dynamics change as a function of environment. In water, the M2 helix partially unfolds to form a molecular hinge in the vicinity of a central Leu residue that has been implicated in the mechanism of ion channel gating. In a phospholipid bilayer, either as a single transmembrane helix, or as part of a pentameric helix bundle, the M2 helix shows less flexibility, but still exhibits a kink in the vicinity of the central Leu. The single M2 helix tilts relative to the bilayer normal by 12 degrees, in agreement with recent solid state NMR data (Opella et al., Nat Struct Biol 6:374-379, 1999). The pentameric helix bundle, a model for the pore domain of the nicotinic receptor and for channels formed by M2 peptides in a bilayer, is remarkably stable over a 2-ns MD simulation in a bilayer, provided one adjusts the pK(A)s of ionizable residues to their calculated values (when taking their environment into account) before starting the simulation. The resultant transbilayer pore shows fluctuations at either mouth which transiently close the channel. Proteins 2000;39:47-55.

The structural basis of function in Cys-loop receptors

“…The structural integrity of the ECD is important as weakening backbone hydrogen bonds in the b7, b9 and b10 sheets abolish receptor function, while photochemically cleaving the backbone between loops A and E has similar effects on GABA activation, but not on activation by pentobarbital (Gleitsman et al 2009 ;Hanek et al 2010). The movement of the ECD, mediated by the M2-M3 linker at the extracellular side of the TMD, destabilizes the hydrophobic ' girdle ' in the channel, which moves away from the centre of the pore into space that resides between the inner and outer rings, opening the channel (Law et al 2000 ;Miyazawa et al 2003). It is often claimed that Miyazawa et al (2003) found a ' rotation ' in the M2 regions, but only rotations in the ECD were identified, along with two alternative structures of the M2 helices : straight in the closed state and kinked in the open state.…”

Conformational Variability of the Glycine Receptor M2 Domain in Response to Activation by Different Agonists

“…The kink may therefore act as a swivel enabling the outer half of M2 to move asynchronously with the inner half, where the gate is most likely positioned. Indeed, several lines of evidence suggest gating is mediated by a backbone rearrangement at this midpoint (7)(8)(9)(10). In addition, a rate equilibrium free energy state analysis shows that the M2-M3 domain is positioned midway along the agonist-induced "conformational wave" that extends from the ligand binding domain to the gate (11).…”

Probing the properties of the second coordination sphere of biologically relevant metal complexes using amide function.

“…These are assemblies of water that are organized in one-dimensional chains. Many fundamental biological processes appear to depend on the unique properties of water chains (Cukierman, S., 2000;Jude, K. M. et al, 2002;Kandori, H., 2000;Lanyi, J. K., 2000;Law, R. J. et al, 2000;Zaslavsky, D. & Gennis, R. B., 2000;Zhong, Q. F. et al, 1998). For example, water chains may assist in proton translocation through membranes by functioning as "proton wires" (Decoursey, T. E., 2003).…”

“…Water chains are also found in membrane aquapores, and are important to the function of the nicotinic receptor M2δ (Law, R. J. et al, 2000) as well as the influenza A M2 virus (Wang, J. F. et al, 2001).…”

“…Water chains are also found in membrane aquapores, which are important to the function of the nicotinic receptor M2δ 5 (Law, R. J. et al, 2000) as well as the influenza A M2 virus (Zhong, Q. F. et al, 1998). Rapid translocation of H + along water chains is important in controlling proton flux in these and related systems, and the mechanism of proton conduction appears to be different from other ions.…”