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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

Calculated ΔΔG of observed polymorphic amino mutations from the ancestral amino acid residue compared relative to median of all possible mutations at each position.Free energy changes of polymorphisms in TH2 and TH3 are shown relative to the median change from all 19 substitutions from the predicted ancestral allele determined from Plasmodium sp. phylogeny. Mutations that have higher energy than the median are shown in red, while those with lower energy are shown in blue. Positive values represent increases in free energy and thermodynamic instability while negative values represent decline in free energy and greater stability. Neutral sequence where energetics have no effect would be expected to occur 50/50 above and below the median, while conservation of intramolecular function would be expected to minimize entropy and lead to lower energy states. Intermolecular interactions can lead to selection for less favorable states which are significantly enriched in the observed polymorphisms (17 increased vs 5 decreased, p = 0.00845).
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pone-0062427-g008: Calculated ΔΔG of observed polymorphic amino mutations from the ancestral amino acid residue compared relative to median of all possible mutations at each position.Free energy changes of polymorphisms in TH2 and TH3 are shown relative to the median change from all 19 substitutions from the predicted ancestral allele determined from Plasmodium sp. phylogeny. Mutations that have higher energy than the median are shown in red, while those with lower energy are shown in blue. Positive values represent increases in free energy and thermodynamic instability while negative values represent decline in free energy and greater stability. Neutral sequence where energetics have no effect would be expected to occur 50/50 above and below the median, while conservation of intramolecular function would be expected to minimize entropy and lead to lower energy states. Intermolecular interactions can lead to selection for less favorable states which are significantly enriched in the observed polymorphisms (17 increased vs 5 decreased, p = 0.00845).

Mentions: To determine if intermolecular forces play a role in shaping the diversifying polymorphisms in TH2 and TH3, we devised a simple and conservative test for intermolecular forces. If there are no intermolecular selective forces acting on a site then we expect that observed mutations will be energetically more favorable and increase protein stability. In the worse case, a protein may be under no constraints and essentially adrift with random residue changes occurring regardless of energetics. In this case we would expect that observed residue changes would be equally likely to be greater than or less than the median ΔΔG at a given position. Thus, we would expect a 50/50 neutral model if we aggregated across TH2 and TH3. However, we observe 17 polymorphisms with ΔΔG greater than the median and only 5 less than the median (p = 0.00845, exact binomial distribution) from the predicted ancestral state (Figure 8). For example position 317 contains Lys and Glu whereas favorable energetic mutations to Leu, Ile, Val, Tyr, Trp, and Phe do not substantively populate position 317. Similarly, the dominant mutations 318 Glu/Gln/Lys, 321 Gln/Lys, 322 Lys/Thr, 324 Gln/Lys, and 361 Gly/Glu all have more energetically favorable options which do not appreciably manifest themselves. Given this relative unfavorability within the context of the protein compared to our conservative neutral model (presuming this protein has no energetic constraints), this suggests that outside intermolecular selective pressures, either immunological or functional (e.g. receptor binding), have shaped the pattern and nature of the TH2 and TH3 polymorphisms.


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)

Calculated ΔΔG of observed polymorphic amino mutations from the ancestral amino acid residue compared relative to median of all possible mutations at each position.Free energy changes of polymorphisms in TH2 and TH3 are shown relative to the median change from all 19 substitutions from the predicted ancestral allele determined from Plasmodium sp. phylogeny. Mutations that have higher energy than the median are shown in red, while those with lower energy are shown in blue. Positive values represent increases in free energy and thermodynamic instability while negative values represent decline in free energy and greater stability. Neutral sequence where energetics have no effect would be expected to occur 50/50 above and below the median, while conservation of intramolecular function would be expected to minimize entropy and lead to lower energy states. Intermolecular interactions can lead to selection for less favorable states which are significantly enriched in the observed polymorphisms (17 increased vs 5 decreased, p = 0.00845).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3646838&req=5

pone-0062427-g008: Calculated ΔΔG of observed polymorphic amino mutations from the ancestral amino acid residue compared relative to median of all possible mutations at each position.Free energy changes of polymorphisms in TH2 and TH3 are shown relative to the median change from all 19 substitutions from the predicted ancestral allele determined from Plasmodium sp. phylogeny. Mutations that have higher energy than the median are shown in red, while those with lower energy are shown in blue. Positive values represent increases in free energy and thermodynamic instability while negative values represent decline in free energy and greater stability. Neutral sequence where energetics have no effect would be expected to occur 50/50 above and below the median, while conservation of intramolecular function would be expected to minimize entropy and lead to lower energy states. Intermolecular interactions can lead to selection for less favorable states which are significantly enriched in the observed polymorphisms (17 increased vs 5 decreased, p = 0.00845).
Mentions: To determine if intermolecular forces play a role in shaping the diversifying polymorphisms in TH2 and TH3, we devised a simple and conservative test for intermolecular forces. If there are no intermolecular selective forces acting on a site then we expect that observed mutations will be energetically more favorable and increase protein stability. In the worse case, a protein may be under no constraints and essentially adrift with random residue changes occurring regardless of energetics. In this case we would expect that observed residue changes would be equally likely to be greater than or less than the median ΔΔG at a given position. Thus, we would expect a 50/50 neutral model if we aggregated across TH2 and TH3. However, we observe 17 polymorphisms with ΔΔG greater than the median and only 5 less than the median (p = 0.00845, exact binomial distribution) from the predicted ancestral state (Figure 8). For example position 317 contains Lys and Glu whereas favorable energetic mutations to Leu, Ile, Val, Tyr, Trp, and Phe do not substantively populate position 317. Similarly, the dominant mutations 318 Glu/Gln/Lys, 321 Gln/Lys, 322 Lys/Thr, 324 Gln/Lys, and 361 Gly/Glu all have more energetically favorable options which do not appreciably manifest themselves. Given this relative unfavorability within the context of the protein compared to our conservative neutral model (presuming this protein has no energetic constraints), this suggests that outside intermolecular selective pressures, either immunological or functional (e.g. receptor binding), have shaped the pattern and nature of the TH2 and TH3 polymorphisms.

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