Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO

Abstract

Apical membrane antigen 1 (AMA1) interacts with RON2 to form a protein complex that plays a key role in the invasion of host cells by malaria parasites. Blocking this protein-protein interaction represents a potential route to controlling malaria and related parasitic diseases, but the polymorphic nature of AMA1 has proven to be a major challenge to vaccine-induced antibodies and peptide inhibitors exerting strain-transcending inhibitory effects. Here we present the X-ray crystal structure of AMA1 domains I and II from Plasmodium falciparum strain FVO. We compare our new structure to those of AMA1 from P. falciparum 3D7 and Plasmodium vivax. A combination of normalized B factor analysis and computational methods has been used to investigate the flexibility of the domain I loops and how this correlates with their roles in determining the strain specificity of human antibody responses and inhibitory peptides. We also investigated the domain II loop, a key region involved in inhibitor binding, by comparison of multiple AMA1 crystal structures. Collectively, these results provide valuable insights that should contribute to the design of strain-transcending agents targeting P. falciparum AMA1.

Applications of 19F-NMR in Fragment-Based Drug Discovery

“…The linewidth of the signal from Trp367 is approximately 250 Hz, more than twice that of the native AMA1 Trp signals. This unusually broad linewidth indicates the presence of conformational exchange centered on the DII loop, consistent with our inability to complete the backbone assignments of this region of AMA1 [53] and with the fact that the DII loop is frequently not resolved in AMA1 crystal structures [49].…”

“…Likewise, several peptides derived from phage-display or from AMA1's binding partner in the RON complex, RON2, are inhibitory [45], establishing the AMA1-RON interaction as a potential therapeutic target [39,46]. X-ray crystallography has identified an extended hydrophobic cleft, flanked by flexible and polymorphic loops, which constitutes the RON2 binding site [47][48][49][50] (Figure 3a). The largest of these loops, the so-called DII loop, must be displaced in order to expose the full RON2 binding site, but this loop is not resolved in crystal structures of AMA1 in complex with RON2 or other ligands, leaving the details of this conformational change somewhat obscure.…”

Identification of the Binding Site of Apical Membrane Antigen 1 (AMA1) Inhibitors Using a Paramagnetic Probe

“…This conformational change exposes the hydrophobic pocket in a partially open gap mediated by the DII hairpin and flexible Ib loop. [42] The positiono ft he Ib loop is not resolved in the apo [40] and complex structures of FVO PfAMA1, [31] buti ss tabilised by polar interactions between Thr171a nd Gln174 and resolved in electron density.T hus, binding of the spin-labelled peptidet oF VO PfAMA1 inducedd isplacemento ft he loops that cover the pocket,e xposing the pocket to solvent for small-molecule binding, and is therefore suitable to test compounds in the presence of the probe for PRE.…”

“…Initial phases were obtained by the molecular replacement method using the program PHASER [51] and chain Ao fP DB ID:4 R1A as a search model. [40] Model building and structural validation were performed using Phenix [52] and Coot. [53] The coordinates and structure factors are available from the Protein Data Bank [54] (PDB IDs:6 N7Q and 6N87).…”

Microarray analyses reveal strain-specific antibody responses to Plasmodium falciparum apical membrane antigen 1 variants following natural infection and vaccination

“…Synthetic peptides that bind to this hydrophobic cleft prevent interaction with the red blood cell invasion complex, obstructing parasite invasion 17,18 . The hydrophobic cleft is in the first of AMA1's three domains, surrounded by six flexible, polymorphic loops thought to prevent host antibodies from disrupting the formation of the invasion complex 16,19 . Moreover, polymorphisms in a region known as the cluster 1 loop of domain 1 have been shown to affect the binding of inhibitory monoclonal antibodies in vitro 7,20 .…”