computer modeling in molecular biology.pdf

6 Theory of Transport in Zon Channels 145finement of the pore [28, 311; ion and water cannot pass each other as they movethrough the channel and permeation proceeds by a single-file mechanism [29, 33,361. It may be expected that the hydrogen bonds involving internal waters and thechannel backbone must be modified as a result of the displacement of the ion withits single-file hydration complex. To gain more insight on the properties of the watermolecules inside the channel, a molecular dynamics simulation of the fully solvatedchannel in a simplified membrane-like environment was performed. The simulatedsystem, shown in Figure 6-2, includes one gramicidin dimer channel, 188 TIP3Pwater molecules and 85 electrically neutral spheres introduced to mimic thehydrocarbon region of the membrane. The construction of the initial water configurationin biomolecular simulations is a critical step. Because this is particularlytrue for a narrow membrane channel, the technique employed to generate the startingcoordinates is described in the next section.6.3.2.1 Building the Initial SystemThere remains some uncertainty on the membrane-bound ion-conducting structureof the gramicidin A channel in lipid bilayers. Proton-proton NOE distances determinedby two-dimensional NMR experiments have demonstrated that the structureof gramicidin A is a right-handed P-helix head-to-head dimer when incorporated inSDS micelles [45], in contrast to the left-handed P-helix that was originally proposedby D. W. Urry [41] and supported by 13C Na" induced chemical shifts measurementsin lecithin vesicles [43]. Recent results from solid state 15N and 13C NMR ofgramicidin in oriented dimyristoylphosphatidylcholine (DMPC) membranes havebeen used to support both the left-handed [47, 771 and right-handed [48, 501 structures.In view of the extreme sensitivity of gramicidin to the environment [46], it maywell be that both the left- and right-handed helices, which are plausible on energeticand structural grounds, are found in membranes. For the present study thegramicidin channel was constructed as a left-handed head-to-head dimer, althoughthe conclusions are not expected to depend essentially on this choice because the propertiesof the right- and left-handed dimer are very similar.The initial conformation was constructed from the backbone dihedral angles ofVenkatachalam and Urry [30], and was further optimized by energy minimizationusing the ABNR algorithm [65]. The resulting structure is shown in Figure 6-1. Theprimary solvation of the channel structure was introduced by building 25 watermolecules in the vicinity of the structure, i. e., 10 water molecules along the axis ofthe channel inside the pore, the rest at the extremities of the channel. The 10 watersinside the pore were constructed along the channel axis in single-file fashion,separated by 0.27 nm. The bulk-like water regions at either end of the channel wereconstructed by overlaying water molecules taken from the coordinates of a pure