Structure Topology Prediction of Discriminative Sequence Motifs in Membrane Proteins with Domains of Unknown Functions

Figure 3

LOP heat maps of the LG5 and LY6 motif. LOP heat maps reflect the propensities of each amino acid relative to natural amino-acid-specific frequencies. Increasing amino acid propensities are illustrated by an increased red colour content. The below listed colour scale represents the colour assigning to each amino acid propensities. This visualisation allows a sensitive approach to analyse amino acid propensities of each variable position of a motif according to topology states. Here, the LOP heat map is separated by topology states, so that amino acid propensities become obvious. For example, cysteine can be observed more frequently at the second variable position of transmembrane-located LY6 motif. This results in two spatially adjacent cysteine residues which form a bulky surface in transmembrane helices. Such a bulky helix surface might be important in mediating helix-helix interactions, as knob-to-hole helix packing has been reported as a key folding process in many studies (e.g., [1, 35]).