In the present analysis, a total of 85,770 unique helices were ex

In the present analysis, a total of 85,770 unique helices were examined, and the frequencies of different Panobinostat concentration lengths of glycine repeats are shown in Table 2. Table 2 Glycine repeat frequencies in PDB helices Repeat # found % of all helices None 84,337 98.3% GxxxG 1,373 1.6% GxxxGxxxG 53 0.06% GxxxGxxxGxxxG 7 0.008% Longer GxxxG repeats 0 0.0% A total of 85,770 unique helices from 7,963 PDB proteins were searched for the presence of GxxxG repeats. The number of helices containing a repeat of each length is shown. The most obvious conclusion that can be drawn from the data in Table

2 is that the long primary repeat segments found in some of the FliH proteins are – at least as far as this GW4869 nmr dataset is concerned – absolutely unique, which is quite surprising given how nature has a tendency to reuse the same constructs. Information regarding the seven helices that contained a GxxxGxxxGxxxG repeat is provided in Table 3. The amino acids in the variable positions of these repeats are predominantly hydrophobic, and it is obvious that none of these repeat segments are similar to those found in FliH. Table 3 Proteins in the PDB containing the GxxxGxxxGxxxG motif PDB ID Helix ID Repeat 1T5J 1 GSVFGAVIGDALG 1YCE 1 GIGPGVGQGYAAG 2CWC 1 GAFLGLAVGDALG 2CWC 15 AMN-107 cost GAVYGQLAGAYYG 2D2X 5 GGLTGNVAGVAAG 2FOZ 1 GCLAGALLGDCVG 1NLW 1 GLILGAIVGLILG Of the 85,770 unique helices examined form PDB entries, just 7 contained

the GxxxGxxxGxxxG motif. For each sequence, the corresponding Glycogen branching enzyme PDB ID is given, along with the identifier of the helix in which the motif is found. The structure of glycine repeat-containing helices in other proteins as a model for FliH Although no crystal structure has been solved for any

FliH protein, one can still obtain insight into the structure of the FliH glycine repeats by examining the crystal structures of other proteins that also have glycine repeats. Unfortunately, there are no solved structures of proteins having long glycine repeats. The best alternative would be to use one of the proteins given in Table 3, but unfortunately the amino acid composition of the glycine repeats in these helices is so unlike that of the FliH proteins that none would make a good model for the type of interaction that might be formed between helices in FliH. Thus, the remaining approach is to find a protein that contains a single GxxxG repeat having FliH-like amino acids in the variable positions. In their analysis of helical interaction motifs in proteins, Kleiger et al. [26] provide a table of proteins that contain GxxxG repeats that mediate helix-helix interactions. The glycine repeat in each PDB file given by Kleiger and co-authors was identified, and it was found that some of these contained amino acids in the variable positions that were similar to the amino acids that are commonly found in the glycine repeats in FliH. We chose E. coli site-specific recombinase (PDB ID 1HJR) as a model for helix-helix dimerization in FliH.

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