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. 2010 Sep 11;68(7):1227–1239. doi: 10.1007/s00018-010-0519-z

Fig. 2.

Fig. 2

Representative paths in the wild-type (top), D564(6.30)G (middle) and D578(6.44)H (bottom). The receptor structures are seen in a direction parallel to the putative membrane surface, the cytosolic side being on top. The longest paths with the highest relative frequency amongst the total number of paths (i.e., paths with frequency ≥ 10% and length ≥ 3) are shown on the bundle. In contrast, paths selected among those characterized by frequency ≥ 30% and length ≥ 5, i.e., most frequent paths, are shown outside the bundle. The amino acid composition of the longest path is reported below, whereas those of the most frequent paths are listed in Tables S1–S3. In general, nodes are represented by spheres centered on the Cα-atoms and connections between nodes are represented by green sticks. In those cases in which multiple paths are shown, green sticks indicate the shared portion of the paths. Here, the identification number of the selected paths together with their respective frequency are reported. In this respect, those paths graphically shown for the wild-type are: a L502–F444–F448–L452–W491–T456–L401–M398–Y623–R395–K390–D633 the longest path with the relative highest frequency (13.79%); b paths 1, (44.55%; red stick) and 5 (33.88%; purple stick); and c paths 2 (41.37%; red stick) and 3 (39.05%; purple stick). Those paths graphically shown for D564(6.30)G are: d F335–K605–F588–L608–F515–Y612–M408–S616–D405–N619–L457–Y623–Y546–M571 the longest path with the relative highest frequency (11.07%); e paths 8 (47.2%; red sticks), 9 (43.72%; purple sticks) and 10 (43.28%; cyan stick); f path 23 (35.60%); and g path 46 (30.33%). Those paths graphically shown for D578(6.44)H are: h S440–Y508–P501–Y527–I531–E451–N535–H578–N615–N619–D405–N377–P620–V380 the longest path with the relative highest frequency (11.58%); i paths 1 (56.46%; red sticks) and 4 (46.85%; cyan stick); j paths 6 (46.09%; blue stick) and 9 (43.16%; red stick); and k paths 24 (35.77%; purple stick), 29 (33.78%; cyan sticks), and 38 (31.26%; blue sticks)