2 39.9 220933130 255331744
10.5 256396305 229822375 10.4 Figure 10 TMSs 1–3 compared with TMSs 4–6 of an ABC type 2 ancestral sequence. The comparison score was 39.9 SD with 58.5% similarity and 50.4% identity. The numbers at the beginning of each line refer to the residue buy GDC-0941 numbers in each of the proteins. TMSs are indicated in red lettering. Vertical lines indicate identities; colons indicate close similarities, and periods indicate more distant similarities. Structural superposition of MalF and MalG In Chimera 1.7, we used a function called “MatchMaker” for structural comparisons, always using MalF fragments as reference for all ensuing superimpositions. We iterated by pruning long atom pairs, until no pair exceeded 2 Ångström. For the last Mizoribine price 3 TMS superimposition, the result was excellent. We saved the superimposed structures in a single file. In the “Reply Log”, we could see that the RMSD between 54 atom pairs was 1.156 Ångström. There is a slight shift, based on the start point of the superimposition,
giving slightly higher RMSD values for the last 2 TMSs. The motif “DxW+LAL” is located at the beginning of the long insert in MalF and also in a short insert between TMS1 and TMS2 in MalG. The presence of the short insert between TMS1 and TMS2 in MalG, and the presence and location of this motif, would suggest that it is the first two TMSs in MalF that should be “chopped” or considered as the “extra” TMS pair. The superimposition between TMS 3, 4 and 5 in MalF that corresponds to TMS 1, 2 and 3 in MalG resulted in an RMSD between 37 atom pairs of 0.880 Ångström, confirming our assumptions. To facilitate sequence comparison between the first domain duplicated
3 TMS unit in MalF and MalG, we removed parts of the long insert in MalF (RYV … LSA), and based on the presence of 17 residues after the DxW+LAL motif in MalG, we removed 124 amino acyl residues (GEQ … IQK). We also Decitabine took out the sequence (MAM … GEY). After this editing, the respective sequences had the lengths 166 and 151. Using Protocols 1 and 2, we found that this comparison resulted in a GSAT Z-score of 21 S.D. The importance of the DxW+LAL motif was that it was the only motif conserved between the two sequences that we discovered when we compared MalF and MalG. It was important because it helped to establish correspondance between the long insert in MalF and a shorter, but still extended, loop in MalG. In Chimera, we attempted a superposition of the first and last 3 TMSs of MalG, using the last 3 TMSs as the reference for superimposition (Figure 11). For MalF, we took the last 3 TMSs, and then 270–350 only (this is domain unit 1, only 2 TMSs after the insert). We Fosbretabulin cell line repeated this, but without removing the insert, using residues 65–350 as the reference.