Ion channels formed by HIV-1 Vpu: a modelling and simulation study

AbstractVpu is an oligomeric integral membrane protein encoded by HIV-1 which forms ion channels, each subunit of which contains a single transmembrane helix. Models of Vpu channels formed by bundles of N=4, 5 or 6 transmembrane helices have been developed by restrained molecular dynamics and refined by 100 ps simulations with water molecules within the pore. Pore radius profiles and conductance predictions suggest that the N=5 model corresponds to the predominant channel conductance level of the channel. Potential energy profiles for translation of Na+ or Cl− ions along the Vpu N=5 pore are consistent with the weak cation selectivity of Vpu channels

Alamethicin channels – modelling via restrained molecular dynamics simulations

AbstractAlamethicin channels have been modelled as approximately parallel bundles of transbilayer helices containing between N=4 and 8 helices per bundle. Initial models were generated by in vacuo restrained molecular dynamics (MD) simulations, and were refined by 60 ps MD simulations with water molecules present within and at the mouths of the central pore. The helix bundles were stabilized by networks of H-bonds between intra-pore water molecules and Gln-7 side-chains. Channel conductances were predicted on the basis of pore radius profiles, and suggested that the N=4 bundle formed an occluded pore, whereas pores with N≥5 helices per bundle were open. Continuum electrostatics calculations suggested that the N=6 pore is cation-selective, whereas pores with N≥7 helices per bundle were predicted to be somewhat less ion-selective

Insights into the structural nature of the transition state in the Kir channel gating pathway

YesIn a previous study we identified an extensive gating network within the inwardly rectifying Kir1.1 (ROMK) channel by combining systematic scanning mutagenesis and functional analysis with structural models of the channel in the closed, pre-open and open states. This extensive network appeared to stabilize the open and pre-open states, but the network fragmented upon channel closure. In this study we have analyzed the gating kinetics of different mutations within key parts of this gating network. These results suggest that the structure of the transition state (TS), which connects the pre-open and closed states of the channel, more closely resembles the structure of the pre-open state. Furthermore, the G-loop, which occurs at the center of this extensive gating network, appears to become unstructured in the TS because mutations within this region have a 'catalytic' effect upon the channel gating kinetics.Deutsche Forschungsgemeinschaft, the Wellcome Trust (083547/ Z/07/Z and 092970/Z/10/Z) and the British Heart Foundation (PG/09/016/ 26992)

Modelling packing interactions in parallel helix bundles: pentameric bundles of nicotinic receptor M2 helices

The transbilayer pore of the nicotinic acetylcholine receptor (nAChR) is formed by a pentameric bundle of M2 helices. Models of pentameric bundles of M2 helices have been generated using simulated annealing via restrained molecular dynamics. The influence of: (a) the initial C α template; and (b) screening of sidechain electrostatic interactions on the geometry of the resultant M2 helix bundles is explored. Parallel M2 helices, in the absence of sidechain electrostatic interactions, pack in accordance with simple ridges-in-grooves considerations. This results in a helix crossing angle of ca. + 12°, corresponding to a left-handed coiled coil structure for the bundle as a whole. Tilting of M2 helices away from the central pore axis at their C-termini and/or inclusion of sidechain electrostatic interactions may perturb such ridges-in-grooves packing. In the most extreme cases right-handed coiled coils are formed. An interplay between inter-helix H-bonding and helix bundle geometry is revealed. The effects of changes in electrostatic screening on the dimensions of the pore mouth are described and the significance of these changes in the context of models for the nAChR pore domain is discussed.</p

Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study

The ion channel of the nicotinic acetylcholine receptor is a water-filled pore formed by five M2 helix segments, one from each subunit. Molecular dynamics simulations on bundles of five M2α7 helices surrounding a central column of water and with caps of water molecules at either end of the pore have been used to explore the effects of intrapore water on helix packing. Interactions of water molecules with the N-terminal polar sidechains lead to a conformational transition from right- to left-handed supercoils during these simulations. These studies reveal that the pore formed by the bundle of M2 helices is flexible. A structural role is proposed for water molecules in determining the geometry of bundles of isolated pore-forming helices.</p