Secondary structure interpretation of genetic sequence variation in Plasmodium falciparum cell surface antigens

Stanley Adoro1, Roseangela Nwuba, Chiaka Anumudu, Mark Nwagwu, University of Ibadan

Sequencing of the Plasmodium falciparum genome has opened new vistas for the identification of novel antigens and investigation of gene structure, sequence diversity and epitope analysis of candidate antigens being evaluated as vaccines against malaria. In an effort to determine the effect of gene polymorphism on potential epitopes and their structural details we carried out in silico studies on the gene and protein sequences of the following malaria cell surface antigens: circumsporozoite protein (CSP), merozoite surface protein (MSP)-1(19), merozoite surface protein 2 (MSP2), rifin and STEVOR. Of these antigens, MSP1(19) and STEVOR showed the highest degree of sequence conservation between isolates and gene copies respectively. Secondary structure computation was performed with JPRED (, a neural network algorithm, which yielded about 60% of the secondary structure features of MSP119 (PDB: 1CEJ) on which it was initially tested. In MSP1(19), majority of the variable residues were located within loop structures. Helix-loop-helix motifs were found at the N terminal of CSP, STEVOR and rifin proteins suggesting a functional domain location at this region. Indeed the N-terminal of CSP has been implicated in sporozoite invasion of hepatocytes in malaria infections. Unique N and C terminal -strands were identified in MSP2, with an internal helix. Interestingly, all five antigens showed extensive solvent inaccessibility at their C terminals (about 25% exposure) indicating that residues at this region may be buried in the tertiary structure of the proteins and thus, are poor targets for antibodies. Taken together, these data should facilitate structural determination studies and the design and selection of epitopes based on these antigens.