Team:NYMU-Taipei/modelling-protein-structure-champ-design

Fig. 1a: Close-up of the predicted tightly packed interface between designed peptides and target protein. The target protein is represented by a red surface with a blue “hot spot”. Fig. 1b: The CHAMP backbone is depicted in ribbon representation with key positions designated for computational design shown in green (Hang Yin, et al., 2007)

Fig. 2: The figure in the left is our initial design by using BRET phenomenon to generate the light. As for the right one, we make a little change using BiFC-based BRET with CHAMP, our designed peptides to make the light wobbling and induce the on-and-off neural control system.

Fig. 6: The critical G-X3-G motifs on helix1 of the Mms13

Selection of a nativelike helical-pair backbone within the chosen structural motif

After the selection of a helical-pair structural motif, we have to select a nativelike helical-pair backbone as the templates for our CHAMP design. First, we follow the instructions to determine the template cluster. (R. F. S. Walters, et al., 2006) A library of 445 helical pairs from 31 proteins in the paper was clustered into groups based on their three-dimensional similarity. Different clusters have specific features and also show varying degrees of homogeneity. We finally choose cluster 2 as our candidates because of the antiparallel helices on Mms13 and the traits which belong to right-handed crossing angle on helix1. (For examples, the helix1 have small residues at the helix–helix interface, and they are also spaced at four-residue intervals.) The pie chart (See Figure 7) shows the fraction of the total number of pairs that fall within a given cluster and Table 1 (See Figure 8) shows some characteristics of the top 14 clusters.

Fig. 11a: The whole 1iwg protein. Figure 11b: The selected template pairs of 1iwg. Figures are graphed using YASARA View (Krieger E., et al., 2011)

Fig. 19: Parts of cross-ranking results.

How to Design the CHAMP Peptides?

We followed the design protocols in the paper- ''Supporting Online Material for Computational Design of Peptides That Target Transmembrane Helices'' (Hang Yin, et al., 2007) and "Understanding Membrane Proteins. How to Design Inhibitors of Transmembrane Protein–Protein Interactions" (J.S. Slusky, et al., 2009). However, because of the limited resources, we made little adjustments by using different programs, such as TMhit (Lo A., et al., 2009), ProtMod (Godzik A., et al., 2011), YASARA (Krieger E., et al., 2011), VMD (Klaus Schulten., et al., 2011), ΔG prediction server v1.0 (Hessa, T., et al., 2007) to finalize our CHAMP design. The study by "Interaction and conformational dynamics of membrane-spanning protein helices'" (D Langosch, et al., 2009) and "Helix-helix interaction patterns in membrane proteins" (D Langosch, et al., 2010) gave us more knowledge about protein-protein interactions in transmembrane domains, and helped us during the CHAMP designing process.