• Loading metrics

Structural Analysis of the Synthetic Duffy Binding Protein (DBP) Antigen DEKnull Relevant for Plasmodium vivax Malaria Vaccine Design

  • Edwin Chen,

    Affiliation Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, Saint Louis, Missouri, United States of America

  • Nichole D. Salinas,

    Affiliation Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, Saint Louis, Missouri, United States of America

  • Francis B. Ntumngia,

    Affiliation Global Health Infectious Disease Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America

  • John H. Adams,

    Affiliation Global Health Infectious Disease Research, Department of Global Health, College of Public Health, University of South Florida, Tampa, Florida, United States of America

  • Niraj H. Tolia

    Affiliations Department of Molecular Microbiology and Microbial Pathogenesis, Washington University School of Medicine, Saint Louis, Missouri, United States of America, Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri, United States of America

Structural Analysis of the Synthetic Duffy Binding Protein (DBP) Antigen DEKnull Relevant for Plasmodium vivax Malaria Vaccine Design

  • Edwin Chen, 
  • Nichole D. Salinas, 
  • Francis B. Ntumngia, 
  • John H. Adams, 
  • Niraj H. Tolia


The Plasmodium vivax vaccine candidate Duffy Binding Protein (DBP) is a protein necessary for P. vivax invasion of reticulocytes. The polymorphic nature of DBP induces strain-specific immune responses that pose unique challenges for vaccine development. DEKnull is a synthetic DBP based antigen that has been engineered through mutation to enhance induction of blocking inhibitory antibodies. We determined the x-ray crystal structure of DEKnull to identify if any conformational changes had occurred upon mutation. Computational and experimental analyses assessed immunogenicity differences between DBP and DEKnull epitopes. Functional binding assays with monoclonal antibodies were used to interrogate the available epitopes in DEKnull. We demonstrate that DEKnull is structurally similar to the parental Sal1 DBP. The DEKnull mutations do not cause peptide backbone shifts within the polymorphic loop, or at either the DBP dimerization interface or DARC receptor binding pockets, two important structurally conserved protective epitope motifs. All B-cell epitopes, except for the mutated DEK motif, are conserved between DEKnull and DBP. The DEKnull protein retains binding to conformationally dependent inhibitory antibodies. DEKnull is an iterative improvement of DBP as a vaccine candidate. DEKnull has reduced immunogenicity to polymorphic regions responsible for strain-specific immunity while retaining conserved protein folds necessary for induction of strain-transcending blocking inhibitory antibodies.

Author Summary

Plasmodium vivax is an oft neglected causative agent of human malaria. It inflicts tremendous burdens on public health infrastructures and causes significant detrimental effects on socio-economic growth throughout the world. P. vivax Duffy Binding Protein (DBP) is a surface protein that the parasite uses to invade host red blood cells and is a leading vaccine candidate. The variable nature of DBP poses unique challenges in creating an all-encompassing generalized vaccine. One method to circumvent this problem is to synthetically engineer a single artificial protein antigen that has reduced variability while maintaining conserved protective motifs to elicit strain-transcending protection. This synthetic antigen is termed DEKnull. Here, we provide structural and biochemical evidence that DEKnull was successfully engineered to eliminate polymorphic epitopes while retaining the overall fold of the protein, including conserved conformational protective epitopes. Our work presents validation for an improved iteration of the DBP P. vivax vaccine candidate, and provides evidence that protein engineering is successful in countering DBP polymorphisms. In doing so, we also lay down the foundation that engineering synthetic antigens is a viable approach and should be considered in future vaccine designs for pathogens.


Plasmodium vivax is a causative agent of malaria, inflicting significant morbidity and impeding economic growth in highly endemic areas [1,2]. Increasing evidence indicates the severity of disease, economic impact, and burden of P. vivax has been severely underestimated [1,2]. Among the proposed methods for disease control, vaccines are appealing for a multitude of reasons. Vaccines are cost-effective, efficient, and have been historically successful in combating infectious diseases especially in resource poor environments [3]. Individuals living in regions with P. vivax develop naturally acquired protective immunity and antibodies isolated from those naturally immune have anti-DBP inhibitory effects that correlate with results from in vitro functional assays [46].

Establishment of a successful host infection necessitates specific receptor-ligand interactions between host red blood cells and Plasmodium parasites [7]. For P. vivax, the critical interaction is that between the merozoite Duffy binding protein (DBP) and the Duffy antigen receptor for chemokines (DARC) on reticulocytes. DARC-negative individuals are resistant to clinical P. vivax infection, and naturally immune individuals can possess anti-DBP antibodies that inhibit the DBP-DARC interaction and prevent parasite growth [6,812]. Additionally, polyclonal antibodies elicited by recombinant DBP exhibit similar protective and inhibitive effects to naturally acquired antibodies [6,11,13,14]. Certain isolates of P. vivax have been reported to invade Duffy-negative cells [15]. However, sequencing of these isolates identified a gene encoding a DBP paralog suggesting the increased copy number and/or expression of DBP may enable invasion into Duffy-negative cells [16]. Together, this highlights the central importance of the DBP-DARC interaction in P. vivax infection and presents DBP as a crucial parasite protein that can be developed as a vaccine target.

DBP is a member of the Duffy binding-like erythrocyte binding protein (DBL-EBP) family, and binds DARC through a conserved cysteine-rich DBL domain known as region II (DBP-II) [1722]. DBP-II engages DARC through a multimeric assembly mechanism where two DBP-II domains initially bind one DARC to form a heterotrimer that rapidly recruits a second DARC to form a heterotetramer [2326]. DBP-II amino acids F261-T266, L270-K289, and Q356-K367 form critical contacts with the DARC ectodomain during this process [23]. This receptor-induced ligand-dimerization model is conserved amongst other members of the DBL-EBP family and provides spatial orientation for DBL domains at the parasite-RBC membrane interface [2430]. Residues that mediate multimeric assembly are important targets of protective immunity as the epitopes of naturally acquired anti-DBP-II antibodies that disrupt the DBP-DARC interaction localize to residues at the dimerization interface, DARC binding pockets, and the RBC proximal face of DBP-II [10]. However, clusters of highly polymorphic residues flank these protective epitopes, which is a pattern seen in pathogens undergoing selective pressure that results in an immune evasion where allelic variants can escape immunity elicited by a previous infection [10,21,26,3137]. Therefore, polymorphic residues of DBP appear to have a high potential to be the basis of strain specific immune responses that misdirects immune responses away from conserved targets of broadly neutralizing protection. Although strain specific immunity can be protective these seemingly more immunogenic epitopes offer limited value because of the strain-limited nature of the immunity. Genetic analysis of DBP-II alleles reveal a high dN/dS ratio often seen when selection pressure drives allelic diversity as a mechanism for immune evasion [3842]. In order to proceed with DBP as a P. vivax vaccine target, it is therefore critical to address the challenges presented by polymorphism and immune misdirection inherent in this allelic diversity.

Immunization with DBP-II elicits weakly reactive and allele specific immune responses, a far cry from the end objective of inducing strain-transcending protection [38]. The poor protectivity appears to be due in part to polymorphic non-functional residues diverting the immune response away from the more conserved, less immunogenic, critical receptor binding residues [10,38,4345]. Consistent with this view, the most polymorphic region, identified as the DEK epitope, is positioned immediately adjacent to the conserved DARC-binding groove (Fig. 1) [10,23]. Antibodies to the DEK epitope can disrupt DBP function, but inhibition is strain limited. Therefore, we refer to DEK as a decoy epitope that distracts the immune response away for more conserved functional epitopes that could serve as basis of a broadly neutralizing protective immunity. To overcome this inherent deficiency of DBP as an immunogen, a novel synthetic DBP-II antigen termed DEKnull was engineered where the polymorphic residues that comprise the DEK epitope were mutated to amino acids not usually present (Fig. 1, S1 Fig) [38]. These proof of principle studies demonstrated the feasibility of redirecting the immune response to conserved, critical residues by eliminating polymorphic epitopes with the goal to create a vaccine that induces a greater percentage of protective antibodies to more conserved, less immunogenic epitopes. Indeed, anti-DEKnull sera lost reactivity towards the polymorphic patch as predicted, but still retained the ability to generate inhibitory antibodies, including epitopes reactive to naturally-occurring immune antibodies of persons infected with P. vivax [38,46]. DEKnull also induced strong anamnestic responses that were protective and cross-reactive against a panel of different DBP-II alleles [5]. Furthermore, DEKnull produced a more consistent inhibitory profile across variants [46].

Fig 1. Location of DEK polymorphisms on Sal1 DBP-II.

DEK polymorphisms (DEKAQQRRKQ) mapped onto the Sal1 DBP-II and DARC heterotetramer. DEK residues are shown in brown and side chains are displayed as sticks. The two DBP-II molecules are in green and yellow. The two DARC peptides are in purple and blue.

However, mutation can alter the three-dimensional structure of a protein that in turn would alter the available epitopes presented in a synthetic antigen. This study presents the structure of a synthetic Plasmodium antigen and its implications for the future of vaccine design in targeting malaria. We determined the structure of DEKnull to identify if any shifts in fold and secondary structure or sub-domain rearrangements had occurred, and whether these changes affect DEKnull’s potential as a vaccine surrogate for native alleles [26]. The effects of mutating the DEK polymorphic patch on conserved protective epitopes was identified by comparison with the pre-existing Sal1 structure [26]. We examined and compared the epitope profile of DEKnull to DBP-II using computational approaches as well as through interrogation with a panel of DBP monoclonal antibodies [47]. Together these studies inform future efforts to guide the rational design of the next iteration of a synthetic DBP-II antigen to improve its immunogenicity and ability to mount a thoroughly protective response.

Materials and Methods

Protein expression and purification

DEKnull was obtained by oxidative refolding. Inclusion bodies expressed in E. coli were solublized in 6 M guanidinium hydrochloride and refolded via rapid dilution in 400 mM L-arginine, 50 mM Tris pH 8.0, 10 mM EDTA, 0.1 mM PMSF, 2 mM reduced glutathione, and 0.2 mM oxidized glutathione. Refolded protein was captured on SP Sepharose Fast Flow resin (GE Healthcare), eluted with 50 mM MES pH 6.0, 700 mM NaCl, and dialyzed overnight in 50 mM MES pH 6.0, 100 mM NaCl. The protein was subsequently purified by sequential size exclusion chromatography (GF200) and ion exchange chromatography (HiTrapS). Protein was finally buffer exchanged into 10 mM HEPES pH 7.4, 100 mM NaCl with size exclusion chromatography. Sal1 DBP-II was purified similarly as DEKnull, but without overnight dialysis.

Protein crystallization and data collection

DEKnull crystals were grown by hanging-drop vapor diffusion. First, 1 μL of protein solution at 3–9 mg/mL was mixed with 1 μL of reservoir containing 0.2 M di-sodium tartrate, 20% PEG 3350 to create needle clusters. Crystals were shattered and microseeded into a mix of 1 μL of protein solution at 4 mg/mL and 1 μL of reservoir containing 0.2 M lithium chloride, 20% PEG 3350. Large needle rods of DEKnull grew within a week and were flash frozen in liquid nitrogen. Data was collected to a resolution of 2.1 Å at beamline 4.2.2 of the Advanced light Source, Lawrence Berkeley National Laboratory and processed with XDS [48].

Structure solution and analysis

The DEKnull structure was solved by molecular replacement in PHASER [49] using a single Sal1 DBP-II domain from 3RRC as a starting model. Manual rebuilding in COOT [50] and refinement in PHENIX led to a final refined model with final R-factor/R-free of 21.77%/25.88% with good geometry as reported by MOLPROBITY [5052]. The MOLPROBITY score of 0.81 places this structure in the top 100th percentile of structures 1.85–2.35 Å. 98.22% of residues lie in favored, 1.78% of residues lie in additionally allowed, and 0% lie in disallowed regions of the Ramachandran plot. Atomic coordinates and structure factors have been deposited into the Protein Data Bank with accession code 4YFS.

ELISA assays with anti-DBP antibodies

The ELISAs were performed as previously described [28]. Briefly, BSA, Sal1 DBP-II, and DEKnull were coated on the plate overnight at 4°. The plates were washed with PBS/Tween-20 and then blocked with 2% BSA in PBS/Tween-20 for one hour at room temperature. The plates were washed with PBS/Tween-20 and then incubated with anti-DBP antibodies (2C6, 2D10, 2H2, 3C9, 2F12, 3D10) individually for one hour at room temperature. The plates were again washed with PBS/Tween-20 and then incubated with an anti-mouse secondary antibody conjugated to Alexafluro-488 for 30 minutes at room temperature. After a final wash step, the fluorescence was measured using a POLARstar Omega (BMG Labtech) plate reader.


Structure of the synthetic DEKnull antigen

We obtained the crystal structure of the DEKnull antigen to a resolution of 2.1 Å (Table 1). DEKnull maintains the overall fold and conserved disulfide bonding patterns of a DBL domain similar to that found in P. vivax DBP Sal1, from which DEKnull is derived [23,26]. The DBL fold is a conserved structural feature in other important Plasmodium adhesion proteins, including the P. falciparum EBA-175 and EBA-140, P. knowlesi α-DBP protein, and the NTS-DBL1α1, DBL6ε, and DBL3x domains of PfEMP-1 (Fig. 2A) [26,27,5358]. DEKnull also retains the characteristic three sub-domain architecture of DBL domains with critical intra-domain disulfide bonding patterns (Fig. 2B). Sub-domain 1 (S1) contains residues K215 to L253 with two disulfide bonds, C217-C246 and C230-C237. Sub-domain 2 (S2) contains residues H262 to E386 and has a single disulfide bond C300-C377. Sub-domain 3 (S3) contains residues P387 to S508 and has three disulfide bonds: C415-C432, C427-C507, and C436-C505. All cysteines in DEKnull are involved in disulfide bonding and are structurally conserved with Sal1 DBP-II [26].

Fig 2. DEKnull is structurally similar to Sal1 DBP-II.

(A) DEKnull separated into three sub-domains, sub-domain 1 (S1—red), sub-domain 2 (S2—blue), and sub-domain 3 (S3—green). (B) S1 (red) contains a β-hairpin, S2 (blue) is a helix bundle, and S3 (green) is a helix bundle. Domain boundaries and disulfide bonding cysteines are labeled. (C) Structural alignment of DEKnull (solid colors) with Sal1 DBP-II (light tinted colors) with r.m.s. deviation of 0.435Å. (D) Structural alignment of individual DEKnull sub-domains (solid colors) with Sal1 DBP-II sub-domains (light tinted colors). S1 alignment has a r.m.s. deviation of 0.308 Å. S2 alignment has a r.m.s. deviation of 0.288 Å. S3 alignment has a r.m.s. deviation of 0.310 Å.

Alignment of DEKnull and Sal1 DBP-II structures shows minimal differences with an overall root-mean-square (r.m.s.) deviation of 0.435 Å (Fig. 2C), indicating there is minimal differences overall between the native and engineered domains. S1 alignment has a r.m.s. deviation of 0.308 Å and is not significantly different (Fig. 2D). S2 alignment has a r.m.s. deviation of 0.288 Å, and the only change is the region comprising K366 to I376, which is now structured in DEKnull as compared to Sal1 DBP-II (Fig. 2D). S3 alignment has a r.m.s. deviation of 0.310 Å and show shifts in loops G417 to D423 and K465 to T473, changes that can be attributed to solvent exposed flexible loops (Fig. 2D). Strikingly, the DEKAQQRRKQ polymorphic stretch within S2 overlaps well between DEKnull and Sal1 DBP-II. Alteration of these amino acids to ASTAATSRTS had no affect on the secondary structure nor do they shift peptide backbone Cαs (Fig. 3A, 3B).

Fig 3. DEKnull mutations do not affect protein secondary structure.

(A) and (B) Two views of a structural alignment of Sal1 DBP-II DEKAQQRRKQ polymorphic region (white) and DEKnull ASTAATSRTS mutant region (blue). Mutated residues are labeled and shown as sticks. (C) Structural alignment of DARC binding sites on Sal1 DBP-II (white) and DEKnull (blue). DARC binding residues are labeled and shown as sticks. (D) Structural alignment of DBL dimerization interfaces on Sal1 DBP-II (white) and DEKnull (blue). Dimerization residues are labeled and shown as sticks.

The dimer interface and DARC binding residues play important roles in host-receptor binding [23,26]. These functional regions are recognized by naturally acquired antibodies that block the DBP-DARC interaction [10,23]. Any DBP-II based synthetic antigen must accurately replicate the three-dimensional conformation of these regions for antibody generation and epitope recognition. We therefore examined if the changes in DEKnull altered these important functional regions. The dimerization and DARC binding surfaces overlap well with the parental Sal1 DBP-II; there is no allosteric change to secondary structure or peptide backbone Cαs, retaining the conformational shape of protective targets (Fig. 3C, 3D). Furthermore, Define Secondary Structure of Proteins (DSSP) analysis assigns identical secondary structure elements between that of Sal1 DBP-II and DEKnull [59,60]. Together, these structural data demonstrate that the DEKnull conformation is not significantly different from that of the naturally occurring allele, except for the polymorphic DEK epitope, and supports the development of DEKnull as a DBP vaccine.

Epitope changes in DEKnull

B-cell epitopes fall within two classes: linear and conformational. Linear epitopes are continuous stretches of amino acids in which the primary structure alone is responsible for immunogenicity and antibody recognition. Conformational epitopes can be continuous or discontinuous, but require a fold for immunogenicity and antibody binding. Ablation of the fold through the use of denaturants eliminates antibody recognition of conformational epitopes. While vaccines are able to induce either class, natively folded antigens tend to have a bias towards inducing conformational-dependent antibodies that are protective [61,62]. As a result, it is important to identify and characterize inhibitory and non-inhibitory epitopes on Sal1 DBP-II.

Bioinformatic B-cell epitope prediction methods for conformational epitopes are a powerful tool that can aid in the rational design and analysis of vaccine targets. DiscoTope is a widely used web-based computational algorithm that focuses on identifying potential discontinuous conformational epitopes based on available crystal structures [63]. DiscoTope analysis of Sal1 DBP-II identifies several distinct epitopes with the strongest signal located at the DEKAQQRRKQ polymorphic patch that is altered within DEKnull (Fig. 4A). The predicted residues are all solvent exposed and are spread across the entire surface of the protein, with no discernible predilection for certain sub-domains (Fig. 4B). DEKnull is predicted to have similar patches of epitopes, but lacks the signal at the DEK location induced by the mutational changes (Fig. 4A, 4C). Comparisons between the Sal1 DBP-II and DEKnull prediction results demonstrate only the DEKAQQRRKQ region is significantly different (Fig. 4A). An important concern of removing decoy-epitopes through mutation is the possibility of introducing novel epitopes caused by the amino acid changes. DiscoTope analysis determines that no new epitopes specific to DEKnull are introduced further demonstrating that DEKnull is a suitable surrogate antigen from native alleles of DBP-II.

Fig 4. DiscoTope B-cell epitope prediction of Sal1 DBP-II and DEKnull.

(A) Graphical representation of DiscoTope B-cell epitope scores for Sal1 DBP-II (blue line) and DEKnull (red line). Prediction threshold is shown in green. DEK residues are located at amino acids 339–348 and shown above the corresponding location in the graph. (B) Two views of Sal1 DBP-II predicted epitopes mapped onto crystal structure. (C) Two views of DEKnull predicted epitopes mapped onto crystal structure.

Functional epitopes are conserved in DEKnull

The structural and computation approaches indicate that there are no signification changes to epitopes in DEKnull with the exception of the mutated DEKAQQRRKQ epitope. We sought to independently assess the DEKnull antigen retained recognizable epitopes by interrogation with a panel of conformationally dependent anti-Sal1 DBP-II antibodies [47] in ELISA assays. Two non-inhibitory and four inhibitory antibodies were probed; all six antibodies showed no difference in antigen recognition between that of Sal1 DBP-II and DEKnull (Fig. 5). This provides evidence that the DEKnull mutations have minimal effect on the overall structural fold of the protein, and are consistent with the antigenicity results seen in the DiscoTope B-cell epitope prediction (Fig. 4). It is interesting to note that two non-inhibitory antibodies, 3D10 and 2F12, bound to both DBP-II Sal1 and DEKnull equally well (Fig. 5). This suggests that DEKnull still retains at least one other immunogenic region that may continue to function in immune evasion, necessitating further development of DEKnull as a vaccine candidate.

Fig 5. ELISA with anti-DBP conformational specific antibodies.

ELISA assays for conformational anti-DBP antibodies with BSA as a negative control, Sal1 DBP-II as a positive control, and DEKnull protein. Four inhibitory (3C9, 2H2, 2C6, 2D10) and two non-inhibitory (3D10, 2F12) antibodies were tested.


The central role of P. vivax DBP and the necessity of DARC recognition in parasite invasion during the asexual red blood stage makes it an ideal vaccine target [8]. Anti-DBP antibodies isolated from naturally immune individuals and those generated through immunization are able to prevent DBP-DARC interactions and inhibit parasite growth [6]. However, the inherent polymorphic nature of DBP poses challenges that must be overcome in order to maximize its effectiveness as a vaccine [39,40]. Polymorphic immunodominant epitopes divert the immune system away from weakly immunogenic protective epitopes that are conserved across alleles, resulting in strain-specific responses as opposed to strain-transcending protection [43,45]. This is seen not only with DBP, but is an inherent problem observed with other Plasmodium vaccine candidates wherein single allele vaccinations often provide strain-specific inhibition but are yet susceptible to alternate alleles [4,10,6472].

Currently two parallel strategies exist to enhance DBP as a vaccine candidate and to bypass the issue of polymorphism—a multi-allele vaccine composed of variants found in endemic areas, and a modified vaccine that directs immune responses towards conserved epitopes in order to impart broad protection [46,66,73,74]. The synthetic antigen DEKnull is the brainchild of the latter, an antigen in which a dominant variant B-cell epitope is mutated from the parent Sal1 allele [38]. Vaccination studies with DEKnull demonstrate early proof-of-concept success in manipulating the immune system towards protective responses [5,46]. Further iterations in design are expected to improve immunogenicity, protectivity, and cross-reactivity [5,46].

Here, we present the first structure of DEKnull, a synthetic Plasmodium vaccine candidate. These results demonstrate that the DEKnull antigen has insignificant structural changes relative to the parent Sal1 structure [26]. There are virtually no differences in overall DBL fold, orientations of sub-domains 1–3, disulfide bonding, or within the secondary structure and backbone of the mutated region itself (Fig. 2, Fig. 3). The conservation of DBL fold in DEKnull is confirmed with immunological assays examining reactivity against a panel of conformational dependent α-DBP-II(Sal1) antibodies [47]. Of the six antibodies tested, none had significant binding differences between Sal1 and DEKnull (Fig. 5).

The structure of DEKnull additionally allowed us to perform state-of-the-art bioinformatic B-cell epitope analysis through the use of DiscoTope [63]. The prediction results are significant for several reasons. First, the strong signal of the DEK polymorphic patch on the DBP-II Sal1 allele supports that it is strongly immunogenic and can divert immune responses away from conserved protective epitopes. Second, the loss of DEK antigenicity in DEKnull compared to Sal1 further reflects a success in synthetic antigen design in achieving the desired manipulation of epitopes. Third, the DEK mutation did not confound the design of the synthetic antigen by introducing novel epitopes. And finally, the conservation of the remaining epitopes between Sal1 and DEKnull indicates that the mutation does not change the protein’s overall epitope profile suggesting protective epitopes have been retained.

The results first and foremost reflect a success in the strategy of using a modified antigen to bypass DBP allele polymorphisms and poor-protectivity induced by strain-specific epitopes. This study demonstrate that antigen engineering to focus the immune response to conserved functional regions, such as the DARC binding residues and/or DBP dimer interface, is a viable and practical approach. The predicted dominant variant B-cell epitope was eliminated without affecting immunogenicity of the remaining epitopes. Furthermore, the results presented here build upon previous works to establish that protein engineering is a viable approach towards problematic multi-allelic vaccine targets and should guide future vaccine design in other pathogens [5,38].

It has been shown that preliminary immunogenicity studies with DEKnull elicited an immune response comparable to Sal1 DBP-II [5]. A next key step in evaluating DEKnull as a vaccine construct is to demonstrate that DEKnull is able to generate highly potent antibodies that are broadly protective across multiple strains. As a corollary, and one that is predicted in silico by DiscoTope results presented here (Fig. 4), DEKnull must also not generate DEKnull-specific antibodies that would be useless against natural alleles.

The ELISA data presented show that DEKnull still possess non-inhibitory epitopes (Mab 3D10 and Mab 2F12, Fig. 5). Characterizing these antibodies will give insight towards the design of future versions of DEKnull. A continual process of eliminating non-protective epitopes from this synthetic antigen will better focus immune responses towards protective targets. Future studies will examine further iterations of DEKnull to improve upon its overall immunogenicity, broad-spectrum inhibitory profile across different P. vivax DBP alleles, as well as to address the antigenicity of remaining non-protective epitopes.

Supporting Information

S1 Fig. Sequence alignment of Sal1 DBP-II and DEKnull.

Sequence alignment of Sal1 DBP-II and DEKnull. The highly polymorphic stretch (DEKAQQRRKQ) is underlined and mutated residues (ASTAATSRTS) in DEKnull are denoted with asterisks (*).



We thank J. Nix and ALS Beamline 4.2.2 for assistance with data collection, and A. Odom for use of a plate reader.

Author Contributions

Conceived and designed the experiments: EC NDS NHT. Performed the experiments: EC NDS NHT. Analyzed the data: EC NDS NHT. Contributed reagents/materials/analysis tools: FBN JHA. Wrote the paper: EC FBN JHA NHT.


  1. 1. Price RN, Tjitra E, Guerra CA, Yeung S, White NJ, Anstey NM. Vivax malaria: Neglected and not benign. Am J Trop Med Hyg. 2007 Dec;77(6 Suppl):79–87. pmid:18165478
  2. 2. Mendis K, Sina BJ, Marchesini P, Carter R. The neglected burden of Plasmodium vivax malaria. Am J Trop Med Hyg. 2001;64(1–2 Suppl):97–106.
  3. 3. Chen RT, Orenstein W a. Epidemiologic Methods in Immunization Programs. Epidemiol Rev. 1996 Jan 1;18(2):99–117. pmid:9021306
  4. 4. King CL, Michon P, Shakri AR, Marcotty A, Stanisic D, Zimmerman P a, et al. Naturally acquired Duffy-binding protein-specific binding inhibitory antibodies confer protection from blood-stage Plasmodium vivax infection. Proc Natl Acad Sci U S A. 2008 Jun 17;105(24):8363–8. pmid:18523022
  5. 5. Ntumngia FB, Barnes SJ, McHenry AM, George MT, Schloegel J, Adams JH. Immunogenicity of a synthetic vaccine based on Plasmodium vivax Duffy binding protein region II. Clin Vaccine Immunol. 2014 Sep;21(9):1215–23. pmid:24964808
  6. 6. Grimberg BT, Udomsangpetch R, Xainli J, McHenry A, Panichakul T, Sattabongkot J, et al. Plasmodium vivax invasion of human erythrocytes inhibited by antibodies directed against the Duffy binding protein. PLoS Med. 2007 Dec;4(12):e337. pmid:18092885
  7. 7. Cowman AF, Crabb BS. Invasion of red blood cells by malaria parasites. Cell. 2006 Feb 24;124(4):755–66. pmid:16497586
  8. 8. Miller LH, Mason SJ, Clyde DF, McGinniss MH. The resistance factor to Plasmodium vivax in blacks. The Duffy-blood-group genotype, FyFy. N Engl J Med. 1976;295(6):302–4. pmid:778616
  9. 9. Xainli J, Cole-Tobian JL, Baisor M, Kastens W, Bockarie M, Yazdani SS, et al. Epitope-specific humoral immunity to Plasmodium vivax Duffy binding protein. Infect Immun. 2003 May;71(5):2508–15. pmid:12704122
  10. 10. Chootong P, Ntumngia FB, VanBuskirk KM, Xainli J, Cole-Tobian JL, Campbell CO, et al. Mapping epitopes of the Plasmodium vivax Duffy binding protein with naturally acquired inhibitory antibodies. Infect Immun. 2010 Mar;78(3):1089–95. pmid:20008533
  11. 11. Michon P, Fraser T, Adams JH. Naturally acquired and vaccine-elicited antibodies block erythrocyte cytoadherence of the Plasmodium vivax Duffy binding protein. Infect Immun. 2000 Jun;68(6):3164–71. pmid:10816459
  12. 12. Cerávolo IP, Bruña-Romero O, Braga EM, Fontes CJF, Brito CFA, Souza JM, et al. Anti-Plasmodium vivax duffy binding protein antibodies measure exposure to malaria in the Brazilian Amazon. Am J Trop Med Hyg. 2005 Jun;72(6):675–81. pmid:15964949
  13. 13. Yazdani SS, Shakri AR, Mukherjee P, Baniwal SK, Chitnis CE. Evaluation of immune responses elicited in mice against a recombinant malaria vaccine based on Plasmodium vivax Duffy binding protein. Vaccine. 2004 Sep 9;22(27–28):3727–37. pmid:15474708
  14. 14. Russell B, Suwanarusk R, Borlon C, Costa FTM, Chu CS, Rijken MJ, et al. A reliable ex vivo invasion assay of human reticulocytes by Plasmodium vivax. Blood. 2011;118(13):74–82. pmid:21768300
  15. 15. Ménard D, Barnadas C, Bouchier C, Henry-Halldin C, Gray LR, Ratsimbasoa A, et al. Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people. Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5967–71. pmid:20231434
  16. 16. Menard D, Chan ER, Benedet C, Ratsimbasoa A, Kim S, Chim P, et al. Whole genome sequencing of field isolates reveals a common duplication of the Duffy binding protein gene in Malagasy Plasmodium vivax strains. PLoS Negl Trop Dis. 2013 Nov;7(11):e2489. pmid:24278487
  17. 17. Adams JH, Hudson DE, Torii M, Ward GE, Wellems TE, Aikawa M, et al. The duffy receptor family of plasmodium knowlesi is located within the micronemes of invasive malaria merozoites. Cell. 1990 Oct;63(1):141–53. pmid:2170017
  18. 18. Adams JH, Simt BKIMLEE, Dolan SA, Fang X, Kaslow DC, Miller LH, et al. A family of erythrocyte binding proteins of malaria parasites. Proc Natl Acad Sci U S A. 1992 Aug 1;89(15):7085–9. pmid:1496004
  19. 19. Chitnis CE, Chaudhuri A, Horuk R, Pogo AO, Miller LH. The domain on the Duffy blood group antigen for binding Plasmodium vivax and P. knowlesi malarial parasites to erythrocytes. J Exp Med. 1996 Oct 1;184(4):1531–6. pmid:8879225
  20. 20. Ranjan a., Chitnis CE. Mapping regions containing binding residues within functional domains of Plasmodium vivax and Plasmodium knowlesi erythrocyte-binding proteins. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):14067–72. pmid:10570199
  21. 21. VanBuskirk KM, Sevova E, Adams JH. Conserved residues in the Plasmodium vivax Duffy-binding protein ligand domain are critical for erythrocyte receptor recognition. Proc Natl Acad Sci U S A. 2004 Nov 2;101(44):15754–9. pmid:15498870
  22. 22. Peterson DS, Miller LH, Wellems TE. Isolation of multiple sequences from the Plasmodium falciparum genome that encode conserved domains homologous to those in erythrocyte-binding proteins. Proc Natl Acad Sci U S A. 1995;92(15):7100–4. pmid:7624377
  23. 23. Batchelor JD, Malpede BM, Omattage NS, DeKoster GT, Henzler-Wildman K a, Tolia NH. Red blood cell invasion by Plasmodium vivax: structural basis for DBP engagement of DARC. PLoS Pathog. 2014 Jan;10(1):e1003869. pmid:24415938
  24. 24. Malpede BM, Tolia NH. Malaria adhesins: structure and function. Cell Microbiol. 2014 May;16(5):621–31. pmid:24506585
  25. 25. Paing MM, Tolia NH. Multimeric assembly of host-pathogen adhesion complexes involved in apicomplexan invasion. PLoS Pathog. 2014 Jun;10(6):e1004120. pmid:24945143
  26. 26. Batchelor JD, Zahm J a, Tolia NH. Dimerization of Plasmodium vivax DBP is induced upon receptor binding and drives recognition of DARC. Nat Struct Mol Biol. Nature Publishing Group; 2011 Jul 10;18(8):908–14. pmid:21743458
  27. 27. Tolia NH, Enemark EJ, Sim BKL, Joshua-Tor L. Structural basis for the EBA-175 erythrocyte invasion pathway of the malaria parasite Plasmodium falciparum. Cell. 2005 Jul 29;122(2):183–93. pmid:16051144
  28. 28. Salinas ND, Paing MM, Tolia NH. Critical glycosylated residues in exon three of erythrocyte glycophorin a engage Plasmodium falciparum EBA-175 and define receptor specificity. MBio. 2014 Jan;5(5):e01606–14. pmid:25205096
  29. 29. Wanaguru M, Crosnier C, Johnson S, Rayner JC, Wright GJ. Biochemical analysis of the Plasmodium falciparum erythrocyte-binding antigen-175 (EBA175)-glycophorin-A interaction: implications for vaccine design. J Biol Chem. 2013 Nov 8;288(45):32106–17. pmid:24043627
  30. 30. Salinas ND, Tolia NH. A quantitative assay for binding and inhibition of Plasmodium falciparum Erythrocyte Binding Antigen 175 reveals high affinity binding depends on both DBL domains. Protein Expr Purif. Elsevier Inc.; 2014 Mar;95:188–94.
  31. 31. Tsuboi T, Kappe SH, Al-Yaman F, Prickett MD, Alpers M, Adams JH. Natural variation within the principal adhesion domain of the Plasmodium vivax duffy binding protein. Infect Immun. 1994 Dec;62(12):5581–6. pmid:7960140
  32. 32. Hiatt A, Zeitlin L, Whaley KJ. Multiantibody strategies for HIV. Clin Dev Immunol. 2013 Jan;2013:1–11.
  33. 33. Price DA, Goulder PJ, Klenerman P, Sewell AK, Easterbrook PJ, Troop M, et al. Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection. Proc Natl Acad Sci U S A. 1997 Mar 4;94(5):1890–5. pmid:9050875
  34. 34. Borrow P, Lewicki H, Wei X, Horwitz MS, Peffer N, Meyers H, et al. Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus. Nat Med. 1997 Feb;3(2):205–11. pmid:9018240
  35. 35. Smith DJ, Lapedes AS, de Jong JC, Bestebroer TM, Rimmelzwaan GF, Osterhaus ADME, et al. Mapping the antigenic and genetic evolution of influenza virus. Science. 2004 Jul 16;305(5682):371–6. pmid:15218094
  36. 36. Doom CM, Hill AB. MHC class I immune evasion in MCMV infection. Med Microbiol Immunol. 2008 Jun;197(2):191–204. pmid:18330598
  37. 37. Voigt V, Forbes C a, Tonkin JN, Degli-Esposti M a, Smith HRC, Yokoyama WM, et al. Murine cytomegalovirus m157 mutation and variation leads to immune evasion of natural killer cells. Proc Natl Acad Sci U S A. 2003 Nov 11;100(23):13483–8. pmid:14597723
  38. 38. Ntumngia FB, Adams JH. Design and immunogenicity of a novel synthetic antigen based on the ligand domain of the Plasmodium vivax duffy binding protein. Clin Vaccine Immunol. 2012 Jan;19(1):30–6. pmid:22116684
  39. 39. Ampudia E, Patarroyo MA, Patarroyo ME, Murillo LA. Genetic polymorphism of the Duffy receptor binding domain of Plasmodium vivax in Colombian wild isolates. Mol Biochem Parasitol. 1996 Jun;78(1–2):269–72. pmid:8813699
  40. 40. Ju H- L, Kang J- M, Moon S- U, Kim J- Y, Lee H- W, Lin K, et al. Genetic polymorphism and natural selection of Duffy binding protein of Plasmodium vivax Myanmar isolates. Malar J. BioMed Central Ltd; 2012 Jan;11(1):60.
  41. 41. Cole-Tobian J, King CL. Diversity and natural selection in Plasmodium vivax Duffy binding protein gene. Mol Biochem Parasitol. 2003 Apr;127(2):121–32. pmid:12672521
  42. 42. Baum J, Thomas AW, Conway DJ. Evidence for diversifying selection on erythrocyte-binding antigens of Plasmodium falciparum and P. vivax. Genetics. 2003 Apr;163(4):1327–36. pmid:12702678
  43. 43. Welsh RM, Fujinami RS. Pathogenic epitopes, heterologous immunity and vaccine design. Nat Rev Microbiol. 2007 Jul;5(7):555–63. pmid:17558423
  44. 44. Chen E, Paing MM, Salinas N, Sim BKL, Tolia NH. Structural and functional basis for inhibition of erythrocyte invasion by antibodies that target Plasmodium falciparum EBA-175. PLoS Pathog. 2013 Jan;9(5):e1003390. pmid:23717209
  45. 45. Tobin GJ, Trujillo JD, Bushnell RV, Lin G, Chaudhuri a R, Long J, et al. Deceptive imprinting and immune refocusing in vaccine design. Vaccine. 2008 Nov 18;26(49):6189–99. pmid:18852005
  46. 46. Ntumngia FB, Schloegel J, McHenry AM, Barnes SJ, George MT, Kennedy S, et al. Immunogenicity of single versus mixed allele vaccines of Plasmodium vivax Duffy binding protein region II. Vaccine. Elsevier Ltd; 2013 Sep 13;31(40):4382–8. pmid:23916294
  47. 47. Ntumngia FB, Schloegel J, Barnes SJ, McHenry AM, Singh S, King CL, et al. Conserved and variant epitopes of Plasmodium vivax Duffy binding protein as targets of inhibitory monoclonal antibodies. Infect Immun. 2012 Mar;80(3):1203–8. pmid:22215740
  48. 48. Kabsch W. Xds. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):125–32. pmid:20124692
  49. 49. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ. Phaser crystallographic software. J Appl Crystallogr. International Union of Crystallography; 2007 Aug 1;40(Pt 4):658–74. pmid:19461840
  50. 50. Emsley P, Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. International Union of Crystallography; 2004 Dec;60(Pt 12 Pt 1):2126–32. pmid:15572765
  51. 51. Adams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213–21. pmid:20124702
  52. 52. Chen VB, Arendall WB, Headd JJ, Keedy D a, Immormino RM, Kapral GJ, et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr. International Union of Crystallography; 2010 Jan;66(Pt 1):12–21.
  53. 53. Singh SK, Hora R, Belrhali H, Chitnis CE, Sharma A. Structural basis for Duffy recognition by the malaria parasite Duffy-binding-like domain. Nature. 2006 Feb 9;439(7077):741–4. pmid:16372020
  54. 54. Lin DH, Malpede BM, Batchelor JD, Tolia NH. Crystal and solution structures of Plasmodium falciparum erythrocyte-binding antigen 140 reveal determinants of receptor specificity during erythrocyte invasion. J Biol Chem. 2012 Oct 26;287(44):36830–6. pmid:22989878
  55. 55. Juillerat A, Lewit-Bentley A, Guillotte M, Gangnard S, Hessel A, Baron B, et al. Structure of a Plasmodium falciparum PfEMP1 rosetting domain reveals a role for the N-terminal segment in heparin-mediated rosette inhibition. Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5243–8. pmid:21402930
  56. 56. Singh K, Gittis AG, Nguyen P, Gowda DC, Miller LH, Garboczi DN. Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A. Nat Struct Mol Biol. 2008 Sep;15(9):932–8. pmid:19172746
  57. 57. Khunrae P, Philip JMD, Bull DR, Higgins MK. Structural comparison of two CSPG-binding DBL domains from the VAR2CSA protein important in malaria during pregnancy. J Mol Biol. 2009 Oct 16;393(1):202–13. pmid:19695262
  58. 58. Malpede BM, Lin DH, Tolia NH. Molecular basis for sialic acid-dependent receptor recognition by the Plasmodium falciparum invasion protein erythrocyte-binding antigen-140/BAEBL. J Biol Chem. 2013 Apr 26;288(17):12406–15. pmid:23508963
  59. 59. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 1983 Dec;22(12):2577–637. pmid:6667333
  60. 60. Andersen CAF, Palmer AG, Brunak S, Rost B. Continuum secondary structure captures protein flexibility. Structure. 2002 Feb;10(2):175–84. pmid:11839303
  61. 61. Barlow DJ, Edwards MS, Thornton JM. Continuous and discontinuous protein antigenic determinants. Nature. 1986;322(6081):747–8. pmid:2427953
  62. 62. Conway JF, Watts NR, Belnap DM, Cheng N, Stahl SJ, Wingfield PT, et al. Characterization of a conformational epitope on hepatitis B virus core antigen and quasiequivalent variations in antibody binding. J Virol. 2003 Jun 1;77(11):6466–73. pmid:12743303
  63. 63. Haste Andersen P, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci. 2006 Nov;15(11):2558–67. pmid:17001032
  64. 64. VanBuskirk KM, Cole-Tobian JL, Baisor M, Sevova ES, Bockarie M, King CL, et al. Antigenic drift in the ligand domain of Plasmodium vivax duffy binding protein confers resistance to inhibitory antibodies. J Infect Dis. 2004 Nov 1;190(9):1556–62. pmid:15478059
  65. 65. Rénia L, Ling IT, Marussig M, Miltgen F, Holder AA, Mazier D. Immunization with a recombinant C-terminal fragment of Plasmodium yoelii merozoite surface protein 1 protects mice against homologous but not heterologous P. yoelii sporozoite challenge. Infect Immun. 1997 Nov;65(11):4419–23. pmid:9353014
  66. 66. Kusi K a Faber BW, Riasat V Thomas AW, Kocken CHM Remarque EJ. Generation of humoral immune responses to multi-allele PfAMA1 vaccines; effect of adjuvant and number of component alleles on the breadth of response. PLoS One. 2010 Jan;5(11):e15391. pmid:21082025
  67. 67. Remarque EJ, Roestenberg M, Younis S, Walraven V, van der Werff N, Faber BW, et al. Humoral immune responses to a single allele PfAMA1 vaccine in healthy malaria-naïve adults. PLoS One. 2012 Jan;7(6):e38898. pmid:22768052
  68. 68. Hodder AN, Crewther PE, Anders RF. Specificity of the protective antibody response to apical membrane antigen 1. Infect Immun. 2001 May;69(5):3286–94. pmid:11292751
  69. 69. Remarque EJ, Faber BW, Kocken CHM, Thomas AW. A diversity-covering approach to immunization with Plasmodium falciparum apical membrane antigen 1 induces broader allelic recognition and growth inhibition responses in rabbits. Infect Immun. 2008 Jun;76(6):2660–70. pmid:18378635
  70. 70. Kennedy MC, Wang J, Zhang Y, Miles AP, Chitsaz F, Saul A, et al. In vitro studies with recombinant Plasmodium falciparum apical membrane antigen 1 (AMA1): production and activity of an AMA1 vaccine and generation of a multiallelic response. Infect Immun. 2002 Dec 1;70(12):6948–60. pmid:12438374
  71. 71. Genton B, Betuela I, Felger I, Al-Yaman F, Anders RF, Saul A, et al. A recombinant blood-stage malaria vaccine reduces Plasmodium falciparum density and exerts selective pressure on parasite populations in a phase 1–2b trial in Papua New Guinea. J Infect Dis. 2002 Mar 15;185(6):820–7. pmid:11920300
  72. 72. Thera MA, Doumbo OK, Coulibaly D, Laurens MB, Ouattara A, Kone AK, et al. A field trial to assess a blood-stage malaria vaccine. N Engl J Med. 2011 Sep 15;365(11):1004–13. pmid:21916638
  73. 73. Kusi K a Faber BW, Thomas AW Remarque EJ. Humoral immune response to mixed PfAMA1 alleles; multivalent PfAMA1 vaccines induce broad specificity. PLoS One. 2009 Jan;4(12):e8110. pmid:19956619
  74. 74. Dutta S, Lee SY, Batchelor AH, Lanar DE. Structural basis of antigenic escape of a malaria vaccine candidate. Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12488–93. pmid:17636123