Thm (Hess et al., 1997) was applied to constrain bond lengths. The timestep was 2 fs, and coordinates have been saved every 0.1 ps. Secondary structure content was calculated using DSSP (Kabsch and Sander, 1983). Other analyses were performed applying GROMACS and/or nearby code. Molecular graphics images have been prepared employing VMD (Humphrey et al., 1996).Domene et al.Final results Simulation systems The structure of KirBac is shown in Fig. 1 A. As might be observed the molecule is composed of distinct TM and intracellular domains. To focus on events at the filter, and to facilitate comparison with simulations of KcsA (for which the structure on the C-terminal domain has not been determined at higher resolution) it was decided to concentrate simulation studies around the TM domain only. Therefore all simulations have been for residues 4053, the N-terminal residues becoming absent in the crystal structure. Note that the slide helix runs from residues 477. Two models of a membrane have been used for the simulations (see Table 1), an explicit lipid bilayer in addition to a bilayer-mimetic octane slab. In simulations PC1 C3 a lipid bilayer produced up of 208 POPC molecules was employed, as in prior simulations of K channels. From prior simulations of, e.g., KcsA (Domene et al., 2003b) we’ve shown that lipid/protein interactions fluctuate on an ;2-ns timescale. Thus, we can expect that ten ns ought to be extended enough for any main modifications in KirBac/POPC interactions to relax. On the other hand, it’s probably that the higher viscosity of POPC could be like to restrict the motions on the protein observable inside a timescale directly addressable by simulations. To overcome this attainable restriction we’ve got also performed a couple of simulations in which the POPC bilayer was replaced by a slab of octane molecules. An octane slab features a considerably decrease viscosity than POPC, and so may be anticipated to be a lot more permissive of possible protein conformational modifications, but is a reasonable approximation to a lipid bilayer, as demonstrated inside a quantity of prior simulation studies (Tieleman et al., 2001a; Capener and Sansom, 2002). The density profiles for simulations Oct1 and PC1 are shown in Fig. two. It may be observed that the octane slab is ;2.8nm thick whereas the POPC bilayer is ;four.0-nm thick. This difference reflects the absence of your lipid headgroups in the former system. Hence, on the list of important differences in between the two sets of simulations will be the atmosphere experienced by the slide helices (discussed in a lot more detail under).Biophysical Journal 87(1) 256FIGURE 1 (A) Structure of KirBac, with the TM domain (residues 40155) in red and the C-terminal intracellular domain (residues 15209) in blue. All 4 subunits are integrated. The green ellipse indicates the place with the selectivity filter along with the horizontal dotted lines indicate the approximate place in the lipid headgroups of a membrane. (B) Structure from the selectivity filter (residues 11014) showing just two subunits for clarity. The four K1 ions observed in the crystal structure (at websites S0, S1, S2, and S3) are shown.The filter is shown in far more detail in Fig. 1 B. 152044-54-7 manufacturer Within the crystal K1 ions are positioned at DBCO-?C6-?acid medchemexpress internet sites S1, S2, S3, and in between the SEXT and S0 websites. Obviously, the crystal structure is definitely an typical (spatial and temporal) and it truly is not envisaged that all 4 internet sites are occupied simultaneously by K1 ions. Note that no ion is observed at internet site S4 inside the crystal structure. To explore the behavior in the selectivity filter as a function of initial ion configuration, two poss.
