Figure 4

Location of immunologically relevant features mapped onto a PfAMA1 structural model. Each panel shows the front, back and top view of the modelled PfAMA1 structure. (a) Polymorphic residues with an underlying minor allele frequency (MAF) greater than 5% are shown colored according to location within domain I (blue), domain II (magenta) or domain III (orange). Sequence polymorphisms were obtained from 65 Gambian isolates²⁴. (b) Spatial averaging of polymorphic residues highlights polymorphic hotspots. The proportion of polymorphic residues within 15 Å is shown for each central residue, with polymorphic residues defined as those with a MAF ≥ 5%. (c) Bepipred 2.0 predictions are shown over the PfAMA1 structure, with epitopes shown for two Bepipred thresholds—predicted epitopes are shown in yellow for a threshold of 0.5 (specificity = 0.57, sensitivity = 0.59) and in dark orange for a threshold of 0.55 (specificity = 0.81, sensitivity = 0.29). (d,e) The location of predicted MHC class II binding peptides are shown for the HLA-DPA1*02:01-DPB1*01:01 (d) and HLA-DQA1*05:01-DQB1*03:01 (e) alleles. Residues involved in a low binding peptide (50 nM < IC50 < 500 nM) are shown in light blue, while residues involved in a high binding peptide (IC50 < 50 nM) residue are shown in orange. Only the core binding region of each peptide binder is indicated on each structure.