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Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

Aragam NR, Thayer KM, Nge N, Hoffman I, Martinson F, Kamwendo D, Lin FC, Sutherland C, Bailey JA, Juliano JJ - PLoS ONE (2013)

Bottom Line: Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches.In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids.In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

View Article: PubMed Central - PubMed

Affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.

ABSTRACT
Circumsporozoite protein (CS) is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates) and Malawi (235 isolates), we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

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Related in: MedlinePlus

TH2 and TH3 Pairings from Malawi and the Gambia.(a) This figure shows all TH2-x/TH3-y haplotype pairings comparing observed and expected. Those that are that are statistically over and under represented based upon our contingency table analysis (p≤0.00009 for Malawi and p≤0.003 for the Gambia) are colored blue. (b) The data shown are for those pairings in Malawi (blue) and the Gambia (green) that are either observed >5 times in our data, or those predicted to occur >5 times based upon our contingency analysis. Each pairing is represented a unique symbol. Of note, three pairings (TH2-1/TH3-1, TH2-6/TH3-1, and TH2-3/TH3-2) were over represented in both populations. In both figures, the diagonal line represents if there were non-random association of pairings based on predicted and observed values. Points above the line represent pairing over represented in the population, while those represented below the line are those under represented in the population. A complete list of these significant pairings is provided in Table S2 and S3.
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pone-0062427-g003: TH2 and TH3 Pairings from Malawi and the Gambia.(a) This figure shows all TH2-x/TH3-y haplotype pairings comparing observed and expected. Those that are that are statistically over and under represented based upon our contingency table analysis (p≤0.00009 for Malawi and p≤0.003 for the Gambia) are colored blue. (b) The data shown are for those pairings in Malawi (blue) and the Gambia (green) that are either observed >5 times in our data, or those predicted to occur >5 times based upon our contingency analysis. Each pairing is represented a unique symbol. Of note, three pairings (TH2-1/TH3-1, TH2-6/TH3-1, and TH2-3/TH3-2) were over represented in both populations. In both figures, the diagonal line represents if there were non-random association of pairings based on predicted and observed values. Points above the line represent pairing over represented in the population, while those represented below the line are those under represented in the population. A complete list of these significant pairings is provided in Table S2 and S3.

Mentions: Previous reports have suggested that the association between TH2 and TH3 epitopes is not random [1]. We assessed the distribution of the specific epitopes of TH2 and TH3 among the 235 Malawian and 55 Gambian variants identified. We used simulations to test whether the TH2 and TH3 epitopes were randomly associated within the sequence haplotypes. Based on these simulations, a model of random associations was rejected in Malawi [p<0.001, Degrees of freedom (df) = 490, G2 statistic = 824]. Among the Gambian isolates, we did not see a statistically significant overall departure from the model of random assortment for the entire population [p = 0.298, df = 171, G2 statistic = 180.3]; perhaps secondary to the lower statistical power due to limited number of isolates. However, there was significant over-representation of certain combinations. If the assortment of T cell epitopes were non-random, we would expect the observed frequencies to be equal to the predicted frequencies from the contingency table analysis. Instead, we see many pairings in which the observed frequency is significantly higher or lower than the predicted frequency of a pairing (Figure 3). The complete contingency table is shown in Table S1 and the list of all statistically significant pairing is shown in Table S2 and Table S3. This suggests that similar to what was seen in Kenya, the associations between TH2 and TH3 are not random and the possible combinations that occur within natural populations are constrained by biology and/or by limited time for recombination to randomly reassort the mutations.


Diversity of T cell epitopes in Plasmodium falciparum circumsporozoite protein likely due to protein-protein interactions.

Aragam NR, Thayer KM, Nge N, Hoffman I, Martinson F, Kamwendo D, Lin FC, Sutherland C, Bailey JA, Juliano JJ - PLoS ONE (2013)

TH2 and TH3 Pairings from Malawi and the Gambia.(a) This figure shows all TH2-x/TH3-y haplotype pairings comparing observed and expected. Those that are that are statistically over and under represented based upon our contingency table analysis (p≤0.00009 for Malawi and p≤0.003 for the Gambia) are colored blue. (b) The data shown are for those pairings in Malawi (blue) and the Gambia (green) that are either observed >5 times in our data, or those predicted to occur >5 times based upon our contingency analysis. Each pairing is represented a unique symbol. Of note, three pairings (TH2-1/TH3-1, TH2-6/TH3-1, and TH2-3/TH3-2) were over represented in both populations. In both figures, the diagonal line represents if there were non-random association of pairings based on predicted and observed values. Points above the line represent pairing over represented in the population, while those represented below the line are those under represented in the population. A complete list of these significant pairings is provided in Table S2 and S3.
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Related In: Results  -  Collection

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pone-0062427-g003: TH2 and TH3 Pairings from Malawi and the Gambia.(a) This figure shows all TH2-x/TH3-y haplotype pairings comparing observed and expected. Those that are that are statistically over and under represented based upon our contingency table analysis (p≤0.00009 for Malawi and p≤0.003 for the Gambia) are colored blue. (b) The data shown are for those pairings in Malawi (blue) and the Gambia (green) that are either observed >5 times in our data, or those predicted to occur >5 times based upon our contingency analysis. Each pairing is represented a unique symbol. Of note, three pairings (TH2-1/TH3-1, TH2-6/TH3-1, and TH2-3/TH3-2) were over represented in both populations. In both figures, the diagonal line represents if there were non-random association of pairings based on predicted and observed values. Points above the line represent pairing over represented in the population, while those represented below the line are those under represented in the population. A complete list of these significant pairings is provided in Table S2 and S3.
Mentions: Previous reports have suggested that the association between TH2 and TH3 epitopes is not random [1]. We assessed the distribution of the specific epitopes of TH2 and TH3 among the 235 Malawian and 55 Gambian variants identified. We used simulations to test whether the TH2 and TH3 epitopes were randomly associated within the sequence haplotypes. Based on these simulations, a model of random associations was rejected in Malawi [p<0.001, Degrees of freedom (df) = 490, G2 statistic = 824]. Among the Gambian isolates, we did not see a statistically significant overall departure from the model of random assortment for the entire population [p = 0.298, df = 171, G2 statistic = 180.3]; perhaps secondary to the lower statistical power due to limited number of isolates. However, there was significant over-representation of certain combinations. If the assortment of T cell epitopes were non-random, we would expect the observed frequencies to be equal to the predicted frequencies from the contingency table analysis. Instead, we see many pairings in which the observed frequency is significantly higher or lower than the predicted frequency of a pairing (Figure 3). The complete contingency table is shown in Table S1 and the list of all statistically significant pairing is shown in Table S2 and Table S3. This suggests that similar to what was seen in Kenya, the associations between TH2 and TH3 are not random and the possible combinations that occur within natural populations are constrained by biology and/or by limited time for recombination to randomly reassort the mutations.

Bottom Line: Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches.In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids.In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

View Article: PubMed Central - PubMed

Affiliation: Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America.

ABSTRACT
Circumsporozoite protein (CS) is a leading vaccine antigen for falciparum malaria, but is highly polymorphic in natural parasite populations. The factors driving this diversity are unclear, but non-random assortment of the T cell epitopes TH2 and TH3 has been observed in a Kenyan parasite population. The recent publication of the crystal structure of the variable C terminal region of the protein allows the assessment of the impact of diversity on protein structure and T cell epitope assortment. Using data from the Gambia (55 isolates) and Malawi (235 isolates), we evaluated the patterns of diversity within and between epitopes in these two distantly-separated populations. Only non-synonymous mutations were observed with the vast majority in both populations at similar frequencies suggesting strong selection on this region. A non-random pattern of T cell epitope assortment was seen in Malawi and in the Gambia, but structural analysis indicates no intramolecular spatial interactions. Using the information from these parasite populations, structural analysis reveals that polymorphic amino acids within TH2 and TH3 colocalize to one side of the protein, surround, but do not involve, the hydrophobic pocket in CS, and predominately involve charge switches. In addition, free energy analysis suggests residues forming and behind the novel pocket within CS are tightly constrained and well conserved in all alleles. In addition, free energy analysis shows polymorphic residues tend to be populated by energetically unfavorable amino acids. In combination, these findings suggest the diversity of T cell epitopes in CS may be primarily an evolutionary response to intermolecular interactions at the surface of the protein potentially counteracting antibody-mediated immune recognition or evolving host receptor diversity.

Show MeSH
Related in: MedlinePlus