Figure 5.

The constriction region of the simulated AqpM channel. (a) Channel radius calculated with HOLE [39]. The continuous black line represents the radius average over 10000 snapshots of each monomer (40000 snapshots) separated by 2 ps taken from the 20 ns simulation. The red dashed lines represent the channel fluctuations (standard deviation). The horizontal black dashed lines represent the boundaries of the constriction region (-9 Å < z < 11 Å) (zone surrounded by a dashed circle in b). The horizontal blue line indicates the selectivity filter (SF) located in the extra-cellular side (-6 Å < z < -2 Å) that comprises the narrowest part of the channel. The green vertical line indicates the position of the NPA region (2 Å < z < 4 Å) where a minor narrowing of the channel occurs. (b) Snapshot of the AqpM constriction region. The half-helices of the re-entrant loops HE and HB are shown as purple ribbons. The non-helical parts of the loops are shown as white ribbons and the main-chain carbonyl groups that form the hydrogen-bond ladder of the AqpM channel are colored by element (cyan = carbon, red = oxygen, blue = nitrogen). Potential hydrogen bonds between carbonyl groups and water molecules and between the water molecules are shown as black dashed lines. Numbers below the lines represent the average distance between the atoms involved in the hydrogen bond (in Å). The residues comprising the selectivity filter (Phe 62, Ile 187, Arg 202) are colored by element (cyan = carbon, red = oxygen, blue = nitrogen) and non-polar hydrogen atoms were removed for clarity. The two NPA motifs are shown as green ribbons and the sidechains of Asn 82, and Asn 199 are colored by element as described above and non-polar hydrogen atoms were removed for clarity. The region surrounded by a black dashed circle corresponds to the constriction region of the AqpM channel.

Araya-Secchi et al. BMC Genomics 2011 12(Suppl 4):S8   doi:10.1186/1471-2164-12-S4-S8