Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer
Figure 5
(A–D) Five most conserved PfEMP1 homology blocks form DBL-core structure. (A) Schematic showing relative positions in DBL domains of HB one to five (S1–3 indicate subdomains) and sequence conservation logos for each homology block alignment. The height of each position in the logos indicate the amino acid conservation level, and the height of the individual amino acids reflect their relative frequencies on the position and thus their contribution to the conservation. A small sample bias correction has been subtracted in the logos, on alignment positions containing few (<40) amino acids, and error bar height is 2× the correction. Polar amino acids are green, neutrally charged are purple, basic are blue, acidic are red, and hydrophobic amino acids are black. HB numbering is based on level of conservation in PfEMP1 and related sequences. (B) HBs shown on PfEBA-175 DBL1 structure, and (C) on VAR2CSA DBLpam3 structure. Side chains are shown for conserved positions with conservation level higher than 50% of maximum, corresponding to 2.16 bits. DBL areas which are not part of HB1–5 are shown as lightgray in rightmost column, while left side shows only HB1–5, color coding as in panel A. Coloring intensity in the structure is proportional to conservation level in the HBs. (D) Polar interactions between conserved positions in EBA-175 and DBLpam3. The conserved pink residues are underlined in Figure 5A. (E–F) Conserved sequence blocks in CIDR domains. Relative homology block positions, and sequence logos (E). HB12, 7, 9 and 6 are all strongly correlated with CIDR domains. (F) HBs shown on the structure of the M2 part of MC179 CIDRα domain. Disulfide bridges are shown in orange.