Haplotype analysis of Pfs25 in Thailand
Pfs25 sequences of P. falciparum from Thailand were retrieved from GenBank and PubMed databases. Six full-length Pfs25 sequences (654 bp in size) of P. falciparum isolates from the Tak province, Northern-Western Thailand, were obtained [12]. The sequences were classified into two haplotypes: haplotype 1 (n = 4, same as that of P. falciparum 3D7) and H2 (n = 2).
To expand the database, genomic DNA of P. falciparum isolates from six other endemic regions in Thailand were obtained (n = 83) and used as templates for PCR amplification of full-length coding sequences of Pfs25. All PCR products were single amplicons and subsequently sequenced. Combining these with the two sequences from GenBank and PubMed, a database of 89 full-length sequences of Pfs25 of P. falciparum isolates in Thailand were generated (Additional file 4: Table S1).
Sequence analysis of Pfs25 identified five additional haplotypes: H3 to H7. In total, there were seven Pfs25 haplotypes in the P. falciparum population in Thailand (Table 1 and Fig. 1). Most of the sequences were H2, representing 69% of the parasite population in Thailand. H2 was also the most widely distributed haplotype as it was detected in all regions. H1 was the second major haplotype, representing 15% of the parasite population, which was highly prevalent in the north-western regions of Thailand. The others were minor haplotypes and locality-specific. These included three haplotypes (H4, H5, and H7) were specific to the P. falciparum populations in Yala; H6 was detected in P. falciparum in Mae Hong Son and Kanchaburi. Table 1 shows that more than one haplotypes co-existed in each parasite population, with an average haplotype diversity of 0.507 ± 0.059. Interestingly, the highest diversity appeared in P. falciparum in Yala in southern Thailand, wherein four haplotypes were identified with Hd of 0.654 ± 0.106. The lowest diversity was detected in Trat in eastern Thailand, where two haplotypes were detected, with Hd of 0.327 ± 0.153. This result indicates that the haplotype diversity of Pfs25 could vary geographically in different parasite localities in Thailand.
Table 1
Allelic distribution of Pfs25 gene in Plasmodium falciparum from Thailand
Population | n | H | Hd | H1 | H2 | H3 | H4 | H5 | H6 | H7 |
Mae Hong Son | 15 | 4 | 0.467 ± 0.148 | 1 | 11 | 2 | 0 | 0 | 1 | 0 |
| | | | 7% | 73% | 13% | 0 | 0 | 7% | 0 |
Tak* | 6 | 2 | 0.533 ± 0.172 | 4 | 2 | 0 | 0 | 0 | 0 | 0 |
| | | | 67% | 33% | 0 | 0 | 0 | 0 | 0 |
Kanchanaburi | 16 | 3 | 0.508 ± 0.126 | 3 | 11 | 0 | 0 | 0 | 2 | 0 |
| | | | 18% | 69% | 0 | 0 | 0 | 13% | 0 |
Ranong | 15 | 3 | 0.514 ± 0.116 | 4 | 10 | 1 | 0 | 0 | 0 | 0 |
| | | | 27% | 66% | 7% | 0 | 0 | 0 | 0 |
Trat | 11 | 2 | 0.327 ± 0.153 | 0 | 9 | 2 | 0 | 0 | 0 | 0 |
| | | | 0 | 82% | 18% | 0 | 0 | 0 | 0 |
Ubon Ratchathani | 13 | 3 | 0.295 ± 0.156 | 1 | 11 | 1 | 0 | 0 | 0 | 0 |
| | | | 8% | 84% | 8% | 0 | 0 | 0 | 0 |
Yala | 13 | 4 | 0.654 ± 0.106 | 0 | 7 | 0 | 1 | 1 | 0 | 4 |
| | | | 0 | 54% | 0 | 8% | 8% | 0 | 31% |
All samples | 89 | 7 | 0.507 ± 0.059 | 13 | 61 | 6 | 1 | 1 | 3 | 4 |
| | | | 15% | 69% | 7% | 1% | 1% | 3% | 4% |
H, the number of haplotypes; Hd, haplotype diversity index. *Data were obtained from Da et al. (2013). |
Next, distribution patterns of Pfs25 haplotypes among the malaria parasite populations in Thailand were compared using Wright’s (Fst) statistics. Table 2 shows that Fst values were low and non-significant when Pfs25 haplotypes of P. falciparum from four provinces in north-western regions, Mae Hong Son, Tak, Kanchanaburi, and Ranong, were compared. Low and non-significant Fst values were also detected between P. falciparum populations in eastern and southern Thailand, including Ubol Ratchatani, Trat, and Yala. In contrast, significant Fst values were detected when the Pfs25 alleles from the north-western region were compared with those from the eastern and southern regions. This result indicates genetic differentiation in the P. falciparum populations in Thailand, wherein one comprised P. falciparum in north-western Thailand and the other in eastern and southern Thailand.
Table 2
Fst analysis of Pfs25 alleles in different populations of Plasmodium falciparum in Thailand
| MH | K | TK | RN | TD | UB |
K | 0.01575 (P = 0.28) | 0 | | | | |
TK | 0.40276 (P = 0.018) | 0.21298 (P = 0.14) | 0 | | | |
RN | -0.21980 (P = 0.77) | -0.02995 (P = 0.71) | 0.29766 (P = 0.10) | 0 | | |
TD | -0.03086 (P = 0.61) | 0.16062 (P = 0.02) | 0.64136 (P = 0.00) | 0.09518 (P = 0.09) | 0 | |
UB | -0.05186 (P = 0.99) | 0.07249 (P = 0.07) | 0.59351 (P = 0.00) | 0.01027 (P = 0. 30) | -0.03143 (P = 0.58) | 0 |
YA | 0.12240 (P = 0.00) | 0.18895 (P = 0.01) | 0.49092 (P = 0.00) | 0.17167 (P = 0.00) | 0.13916 (P = 0.05) | 0.12500 (P = 0.06) |
MH, Mae Hong Son; K, Kanchanaburi, TK, Tak, RN, Ranong, UB, Ubol; Ratchatani; YA, Yala. |
Global haplotype diversity of Pfs25
To compare the Pfs25 haplotype diversity of P. falciparum in Thailand with other populations of P. falciparum worldwide, Pfs25 sequences were retrieved from public databases. Our search identified 30 Pfs25 sequences (10 full-length sequences and 20 partial sequences) in the “nucleotide collections” and 37 full-length Pfs25 sequences in the “whole-genome shotgun” database in GenBank (https://www.ncbi.nlm.nih.gov/genbank/). Additionally, there were 218 sequences (202 full-length sequences and 16 partial sequences) in PlasmoDB (https://plasmodb.org/plasmo/app). Excluding the partial sequences as well as sequences of the same parasites or parasite with the same origins (i.e., 3D7 and NF54), there were a total of 218 full-length Pfs25 sequences in the public databases. On combining these with the Pfs25 sequences generated in this study, a global Pfs25 database from 307 geographically different isolates of P. falciparum was established. The origins of the P. falciparum parasites in the global database were from 22 countries, including 10 countries in Africa (n = 173, including 3D7), 4 countries in Central and South America (n = 29), and 8 countries in Asia (n = 105; Table S1).
The haplotype analysis of the Pfs25 global database revealed 11 unique haplotypes. Of these, H1 and H2 were the dominant haplotypes, representing 70% and 22%, respectively, of the parasite populations (Fig. 2a). The other nine haplotypes were minor haplotypes, constituting 8% of the parasite population. The levels of Pfs25 haplotype diversity were different in P. falciparum from different continents. For instance, P. falciparum from Central and South America had only three Pfs25 haplotypes (Hd = 0.197). Of these, H1 was detected in all countries, with a frequency of 90%. H2 and H9 were detected in two and one P. falciparum isolates, respectively, in Brazil (Fig. 2b). Plasmodium falciparum from Africa also carried three haplotypes, H1, H8, and H10 (Hd = 0.034). H1 was detected in all countries in Africa with a 98% frequency; meanwhile, H8 and H10 were rare haplotypes that were identified in two and one P. falciparum isolates in Gambia and Senegal, respectively (Fig. 2c). Interestingly, eight haplotypes were identified in P. falciparum in Asia (Hd = 0.564). H1 and H2 were the two major haplotypes, representing 19% and 63% of the parasite population in Asia. In addition to Thailand, H2 was detected in Laos, People’s Republic of China, and Vietnam, whereas H1 was detected in Cambodia, Malaysia, the Philippines, and India (Fig. 2d). This result indicates that the highest Pfs25 diversity in P. falciparum was detected in Asia. Additionally, the distribution patterns of Pfs25 haplotypes in different parasite populations varied geographically, with H1 being the major haplotype in P. falciparum in Africa and South America, and H2 in Asia.
To compare the Pfs25 haplotype patterns among P. falciparum populations in three continents, Wright’s statistics were calculated between pairs of parasite populations. Significant Fst values were detected between all parasite pairs. Fst values were 0.67745 (P = 0), 0.44847 (P = 0), and 0.7858 (P = 0.00901) between P. falciparum in Asia and Africa, Asia and South America, and Africa and South America, respectively. This finding inferred that population differentiation exists among P. falciparum populations in Asia, Africa, and South America. This was because of the fact that unique haplotypes existed among different populations. As shown in Fig. 2, H8 and H10 were only detected in P. falciparum in Gambia and Senegal, H9 only in Brazil, and four other haplotypes (H4, H5, H6, H7, and H11) in Thailand and Vietnam.
Haplotype network of Pfs25
To postulate the origins of Pfs25 haplotypes, a Pfs25 haplotype network was constructed. As shown in Fig. 3, the majority of rare Pfs25 haplotypes were associated with one of the two major haplotypes, H1 and H2. Four minor haplotypes, including H6, H8, H9, and H10, were closely associated with H1. Other four haplotypes, H3, H4, H5, and H7, were closely related to H2. Interestingly, H11, which was present in a single parasite isolate in Vietnam, was associated with H3. This result suggested that Pfs25 minor haplotypes in P. falciparum from Africa, South America, and Central America could arise from H1, whereas Pfs25 minor haplotypes from Asia could arise from H2.
Table 3
Single nucleotide polymorphism (SNP) sites in the Pfs25 gene of Plasmodium falciparum
Haplotype | Nucleotide position |
| 117 | 226 | 333 | 392 | 412 | 428 | 433 | 519 | 561 | 651 |
H1 | AGT | GAT | AAG | GGA | GGC | GTA | GAT | GGA | AAT | ATG |
| Ser | Asp | Lys | Gly | Gly | Val | Asp | Gly | Asn | Met |
H2 | - | - | - | GCA | - | - | - | - | - | - |
| - | - | - | Ala | - | - | - | - | - | - |
H3 | - | - | - | GCA | - | GCA | - | - | - | - |
| - | - | - | Ala | - | Ala | - | - | - | - |
H4 | - | - | - | GCA | - | - | AAT | - | - | - |
| - | - | - | Ala | - | - | Asn | - | - | - |
H5 | - | - | AAA | GCA | - | - | - | - | - | - |
| - | - | Lys | Ala | - | - | - | - | - | - |
H6 | AGC | - | - | - | - | - | - | - | - | - |
| Ser | - | - | - | - | - | - | - | - | - |
H7 | - | AAT | - | GCA | - | - | - | - | - | - |
| - | Asn | - | Ala | - | - | - | - | - | - |
H8 | - | - | - | - | - | - | - | - | - | ATA |
| - | - | - | - | - | - | - | - | - | Ile |
H9 | - | - | - | - | - | GCA | - | - | - | - |
| - | - | - | - | - | Ala | - | - | - | - |
H10 | - | - | - | - | - | - | - | GGG | - | - |
| - | - | - | - | - | - | - | Gly | - | - |
H11 | - | - | - | GCA | AGC | GCA | - | - | AAA | - |
| - | - | - | Ala | Ser | Ala | - | - | Lys | - |
Frequency | 0.990 | 0.987 | 0.997 | 0.726 | 0.997 | 0.964 | 0.997 | 0.997 | 0.997 | 0.994 |
of H1 SNP | | | | | | | | | | |
Underlined letters indicate the SNP sites. Gray boxes indicate synonymous SNPs. |
To further study the genetic relationship of Pfs25 haplotypes, a Bayesian phylogenetic tree was constructed. Consistent with the haplotype network, Pfs25 haplotypes were clustered into three major clades (Fig. 4). H1 clade comprised five haplotypes: H1, H6, H8, H9, and H10. In the H2 clade, two sub-clades were detected. H2 clade comprised H4, H5, and H7. H3 and H11 were separated into a distinct clade, although the H3 clade was more closely related to the H2 clade, rather than the H1 clade. Additionally, a phylogenetic tree was constructed using the NJ approach. Unfortunately, the tree was multifurcated and thus excluded from analysis (Additional file 2: Fig. S2). Taken together, the results from the haplotype network and the phylogenetic tree consistently support that H1 and H2 could contribute mainly to the genetic diversity of Pfs25 in P. falciparum populations.
Molecular basis of Pfs25 variations
To investigate the sequence polymorphisms in Pfs25, nucleotide sequences of 11 unique haplotypes of Pfs25 were aligned. The analysis identified 10 single nucleotide polymorphisms (SNPs) (Table 3), with an average pairwise nucleotide difference between sequences (k) of 0.559 and an average nucleotide diversity at each locus (π) of 0.00085. Of these, three SNPs at nucleotide positions 117 (AGT/AGC), 333 (AAG/AAA), and 519 (GGA/GGG) resulted in synonymous amino acid substitutions at amino acid residues 39 Ser, 111 Lys, and 173 Gly, respectively. The SNP frequencies at positions 117, 333, and 519 were T/C (0.992/0.001), A/G (0.997/0.003), and A/G (0.997/0.003), respectively. The other SNPs detected at the nucleotide positions 226 (GAT/AAT), 392 (GGA/GCA), 412 (GGC/AGC), 428 (GTA/GCA), 433 (GAT/AAT), 561 (AAT/AAA), and 651 (ATG/ATA) resulted in non-synonymous amino acid substitutions at amino acid residues 76 Asp/Asn, 131 Gly/Ala, 141 Gly/Ser, 143 Val/Ala, 145 Asp/Asn, 187 Asn/Lys, and 217 Met/Ile, respectively. The SNP frequencies at positions 226, 392, 412, 418, 433, 561, and 651 were G/A (0.987/0.013), G/C (0.726/0.274), G/A (0.997/0.003), T/C (0.964/0.036), G/A (0.997/0.003), T/A (0.997/0.003), and G/A (0.994/0.006), respectively. The SNP frequency analysis showed that the frequencies of the H1 allele were higher than 0.95 at all SNP sites, except at position 392, where the frequency was 0.726. This indicated that most SNPs detected in Pfs25 were rare. Notably, eight SNPs at positions 116, 226, 333, 412, 433, 519, 516, and 651 were haplotype-specific (Table 3). Interestingly, the SNP at nucleotide position 392 differentiated the two major haplotypes, H1 and H2. In the phylogenetic tree (Fig. 4), all Pfs25 haplotypes (H6, H8, and H8) in the H1 clade carried 392 G, whereas all haplotypes in the H2 clade carried 392 C.
The SNP distribution analysis of Pfs25 revealed that nine SNPs were located in the EGF domains and one SNP was mapped to the transmembrane (anchor) domain (Fig. 5). Of these, five SNPs were mapped to the EGF domain 3. No SNPs were observed in the signal peptide sequences. To further compare the levels of nucleotide diversity in different domains of Pfs25, a sliding window plot of the nucleotide diversity index (π) was analyzed (Fig. 5). Results showed that the average π for EGF domains 1, 2, 3 and 4, and the transmembrane domain were 0.00017, 0.0018, 0.00361, 0.00011, and 0.00018, respectively. This result indicated that sequence diversity was highest in the EGF domain 3 of Pfs25.
Additionally, the nucleotide sequence diversity indices of Pfs25 were calculated to compare the level of diversity among different malaria parasite populations. In agreement with the analysis of the haplotype diversity, the highest π and k values were detected in the P. falciparum population in Asia (Table 4). Notably, π and k values of the Pfs25 sequence from P. falciparum population in Asia were higher than the average values. Interestingly, although P. falciparum in Africa and South America comprised three haplotypes of Pfs25, the π value of Pfs25 in P. falciparum in Africa was lower than that of South and Central America. When the levels of nucleotide diversity were analyzed for P. falciparum in individual countries (excluding countries with one sample), Pfs25 in Asia (Thailand, Cambodia, India, and Vietnam) and Brazil had a nucleotide diversity higher than the average (Table 4). In contrast, Pfs25 from the parasite population from all African countries and in French Guiana exhibited extremely low sequence diversity. No sequence variation was observed in P. falciparum in Mali (n = 24), Uganda (n = 11), and French Guiana (n = 23). This reveals that haplotype and nucleotide sequence diversity in Pfs25 of P. falciparum in Asia is higher than that of other parasite populations.
Table 4
Nucleotide diversity and signature of natural selection in Pfs25 in the global population of Plasmodium falciparum
Origin | n | H | Hd | SNP | nsSNP | sSNP | k | π | Tajima’s D | Fu and Li’s D* | Fu and Li’s F* | dN˗dS |
Asia* | 105 | 8 | 0.564 ± 0.049 | 8 | 6 | 2 | 0.726 | 0.00111 ± 0.00014 | -1.26649 | -1.99461 | -2.06811 | 0.8 |
| | | | | | | | | P > 0.10 | P > 0.05 | P > 0.05 | P > 0.10 |
Thailand | 89 | 7 | 0.400 ± 0.237 | 6 | 4 | 2 | 0.623 | 0.00095 ± 0.00014 | -1.08677 | -0.75414 | -1.01903 | 0.45 |
| | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P > 0.10 |
Cambodia | 5 | 2 | 0.400 ± 0.237 | 2 | 2 | 0 | 0.8 | 0.00122 ± 0.00073 | -0.97256 | -0.97256 | -0.9544 | 1.44 |
| | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P > 0.10 |
People’s Republic of China | 2 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | nd | nd | nd | 0 |
| | | | | | | | | | | | P > 0.10 |
India | 2 | 2 | 1.000 ± 0.500 | 2 | 2 | 0 | 2 | 0.00306 ± 0.00153 | nd | nd | nd | 1.41 |
| | | | | | | | | | | | P > 0.10 |
Vietnam | 4 | 3 | 0.833 ± 0.222 | 3 | 3 | 0 | 1.667 | 0.00255 ± 0.00092 | 0.16766 | 0.16766 | 0.14992 | 1.85 |
| | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P < 0.10 |
Africa** | 173 | 3 | 0.034 ± 0.019 | 2 | 1 | 1 | 0.035 | 0.00005 ± 0.00003 | -1.25871 | -1.19341 | -1.42933 | -0.45 |
| | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P > 0.10 |
Gambia | 65 | 2 | 0.061 ± 0.040 | 1 | 1 | 0 | 0.061 | 0.00009 ± 0.00006 | -0.89732 | 0.52193 | 0.12296 | 1 |
| | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P > 0.10 |
Mali | 24 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | nd | nd | nd | 0 |
| | | | | | | | | | | | P > 0.10 |
Senegal | 66 | 2 | 0.030 ± 0.029 | 1 | 0 | 1 | 0.03 | 0.00005 ± 0.00004 | -1.07373 | -1.9202 | -1.93912 | -1.04 |
| | | | | | | | | P > 0.10 | P > 0.05 | P > 0.05 | P > 0.10 |
Uganda | 11 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | nd | nd | nd | 0 |
| | | | | | | | | | | | P > 0.10 |
South and Central | 29 | 3 | 0.197 ± 0.095 | 2 | 2 | 0 | 0.202 | 0.00031 ± 0.00015 | -1.24882 | -0.72622 | -1.00802 | 1.42 |
America *** | | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P > 0.10 |
Brazil | 4 | 3 | 0.833 ± 0.222 | 2 | 2 | 0 | 1.167 | 0.00178 ± 0.00056 | 0.59158 | 0.59158 | 0.50356 | 1.5 |
| | | | | | | | | P > 0.10 | P > 0.10 | P > 0.10 | P > 0.10 |
French Guiana | 23 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | nd | nd | nd | 0 |
| | | | | | | | | | | | P > 0.10 |
Total | 307 | 11 | 0.456 ± 0.028 | 10 | 7 | 3 | 0.559 | 0.00085 ± 0.00007 | -1.43957 | -2.78081* | -2.74867* | 1.01 |
| | | | | | | | | P > 0.10 | P < 0.05 | P < 0.05 | P > 0.10 |
n, number of samples, SNP, total number of single nucleotide polymorphism sites; nsSNP, non-synonymous SNP; ssSNP, synonymous SNP; k, average pairwise nucleotide difference between sequences; π, average nucleotide diversity at each locus; nd, not determined because of insufficient sequence data. |
* three Pfs25 sequences of P. falciparum isolates from Laos (n = 1), Malaysia (n = 1), and Philippines (n = 1) were included. |
** seven Pfs25 sequences of P. falciparum isolates from Congo (n = 1), Ghana (n = 1), Guinea (n = 1), Kenya (n-1), Sudan (n = 1), Togo (n = 1), and that of the P. falciparum reference strain 3D7 were included. |
*** two Pfs25 sequences of P. falciparum isolates from El Salvador (n = 1) and Honduras (n = 1) were included. |
Signature of natural selection against Pfs25
To determine the evidence of natural selection on Pfs25, three neutrality tests were performed. Fu and Li’s D* and Fu and Li’s F* statistic tests were negative and significant (D* = -2.78081, P < 0.05; F* = -2.74867, P < 0.05), whereas Tajima’s D test was negative, but not significant (D = -1.43957, P > 0.10; Table 4). When the neutrality tests were analysed using the sequence data from the parasite populations of each continent, non-significant values were detected in all tests. Furthermore, the sliding window plots of Tajima’s D, Fu and Li’s D*, and Fu and Li’s F* values were constructed (Fig. 6). The evidence of negative selection was detected in the EGF domain 3 of Pfs25 in the sliding window plots of Fu and Li’s D* and Fu and Li F* tests. Additionally, the dN˗dS value of Pfs25 was also analysed using all parasite populations. The test showed a positive, but non-significant value (z test = 1.01, P > 0.10; Table 4 and Fig. 6). When the dN˗dS values were calculated using the sequence datasets, the results were positive and non-significant for the parasite populations in Asia and South America. Negative and non-significant dN˗dS value was detected in the parasite populations in Africa. This result showed the tendency of negative selection operating in Pfs25.
Contribution of the G131A mutation on the structural conformation of Pfs25
MD was performed on the crystal structure of Pfs25 (PDB ID: 6PHB [65]), and the homology models of Pfs25 haplotypes H1 and H2 to gain insight into the effects of G131A mutation of H2 on structural conformations. The crystal structure of Pfs25 comprises unique amino acid residues of Q91, Q144, and Q166, whereas they are N112, N165, and N187 in case of H1 and H2. MD results showed that RMSF value trends of the crystal structure of Pfs25 and homology model of H1 and H2 were relatively similar (Fig. 7a), indicating that the flexibilities of these three proteins are quite similar. The structure closest to the average structure of the 80–100 ns trajectory of each system was selected as the representative structure for the crystal structure of Pfs25 and homology models of H1 and H2. The superimposition of the three representative structures showed that they were relatively similar (Fig. 7b). Specifically, the backbone RMSD values of the differences between the crystal structure and H1, crystal structure and H2, and H1 and H2 were 1.19 Å, 1.04 Å, and 1.17 Å, respectively. Furthermore, the percentages of secondary structures (helix, β-sheet, and random coil) of all three proteins (Table 5 and additional file 3: Fig. S3) were predicted to be relatively similar, suggesting that the structural conformations of H1, H2, and the crystal structure of Pfs25 were relatively similar despite the fact that the crystal structure of Pfs25 had three unique residues that were different from H1 and H2, and that H2 was different from H1 because of the G131A mutation. Furthermore, these findings suggest that the polymorphisms in the major Pfs25 haplotypes (G131A mutation) do not cause significant structural changes in terms of secondary structures and stability. As Pfs25 was essential to the malaria parasite, it should thus be a potential target for malaria transmission-blocking vaccine.
Table 5
The percentages of β-sheet, helix, and random coil of the crystal structure of Pfs25, and the homology models of Pfs25 haplotypes H1 and H2 as calculated by define secondary structure of protein (DSSP)
System | β-sheet (%) | Helix (%) | Random coil (%) |
Parallel | Anti-parallel | Total | α- helix | 310-helix | π-helix | Total | Coil | Turn | Bend | Total |
Pfs25 (crystal structure) | 1.2 | 38.1 | 39.3 | 0.0 | 2.5 | 0.0 | 2.5 | 26.5 | 21.6 | 10.1 | 58.2 |
Pfs25 haplotype H1 | 1.2 | 38.9 | 40.1 | 0.0 | 2.2 | 0.0 | 2.2 | 26.9 | 19.1 | 11.7 | 57.7 |
Pfs25 haplotype H2 | 1.3 | 38.3 | 39.6 | 0.0 | 2.5 | 0.0 | 2.5 | 26.9 | 19.3 | 11.7 | 57.9 |