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These steps were carried out within VMD 47, using the membrane, solvate and autoionize plug-ins. The net charge of the system was neutralized with 54 Na + and 89 Cl -counter-ions, achieving a salt concentration of 100 mM. The model was inserted in a fully hydrated palmitoyl-2-oleoyl-sn-glycerol-phosphatidylcholine (POPC) lipid bilayer (307 lipids, 43992 water molecules) leading to an initial system size of 130 Å # 130 Å # 150 Å dimension. Based on these calculations, we assigned the non- standard protonation states shown in table S3.
VUE ESPRIT SOFTWARE
pKa calculations were carried out with the Yasara software 46 in order to determine the most likely protonation state of all ionizable residues at pH 4.6. A minus sign indicates that initial positioning of the chosen probe ion at the given binding pocket was not possible via our approach. For instance, Ca " Cl means that Ca 2+ cannot be displaced by Cl. The table indicates whether exchange from X to Y is possible (!) or impossible ("). On the other hand, magnesium cannot be displaced by any of the other two cations, corroborating the magnesium selectivity of this site. Those ions are however easily displaced by magnesium. Site 3 can accommodate sodium and calcium in agreement with the 1ATN crystal structure. Site 4 is deeply buried and does not permit binding of the two bigger positive ions (r Ca2+ =1.71 Å r Na+ =1.87 Å). Sites 3 and 4 are selective towards the small divalent Mg 2+ cation (r Mg2+ =0.79 Å). Generally, Mg 2+ can displace Ca 2+ but the opposite remains impossible, except for the exposed calcium selective site 2. The favourable substitution of Na + with Ca 2+ requires little user forces, whereas Na + can only displace Ca 2+ using excessive force. In the latter case, haptic feedback helps the user to distinguish between favourable and unfavourable substitutions. Generally speaking, buried and narrow sites are unreachable for large ions, whereas sites localized at the enzyme surface are readily subject to ion exchange. This may be related to the simplicity of our model in which selectivity depends on the shape of the pocket itself and the pathway for accessing it. It is however surprising that magnesium is able to substitute for calcium at site 1. Sites 1 and 2 are calcium selective, which is generally verified. As might be expected, chloride as an anion cannot be stabilized within any of the four cation binding pockets, nor can it displace a bound cation. Figure 5 and Table 1 illustrate and summarize the results for these ion substitution "molecular-billiard" simulations. We considered magnesium, calcium, sodium and chloride ions as probes. We then tried to interactively substitute the probe by another ion.
VUE ESPRIT SERIES
For this purpose, we have carried out a series of additional experiments, each starting with a different ionic probe at a given site. We did however not assess their selectivity.
VUE ESPRIT HOW TO
the previous section, we successfully described how to locate the four DNase I cation binding sites.