# In Silico Characterization and Structural Modeling ofDermacentor andersoni p36 Immunosuppressive Protein

Authors: Martin Omulindi Oyugi; Johnson Kangethe Kinyua; Esther Nkirote Magiri; Milcah Wagio Kigoni; Evenilton Pessoa Costa; Naftaly Wang’ombe Githaka
Journal: Advances in Bioinformatics
 (2018)

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## Abstract

Ticks cause approximately $17–19 billion economic losses to the livestock industry globally. Development of recombinant antitick vaccine is greatly hindered by insufficient knowledge and understanding of proteins expressed by ticks. Ticks secrete immunosuppressant proteins that modulate the host’s immune system during blood feeding; these molecules could be a target for antivector vaccine development. Recombinant p36, a 36 kDa immunosuppressor from the saliva of femaleDermacentor andersoni, suppresses T-lymphocytes proliferationin vitro.To identify potential unique structural and dynamic properties responsible for the immunosuppressive function of p36 proteins, this study utilized bioinformatic tool to characterize and model structure ofD. andersoni p36 protein. Evaluation of p36 protein family as suitable vaccine antigens predicted a p36 homolog inRhipicephalus appendiculatus, the tick vector of East Coast fever, with an antigenicity score of 0.7701 that compares well with that of Bm86 (0.7681), the protein antigen that constitute commercial tick vaccine Tickgard™. Ab initio modeling of theD. andersoni p36 protein yielded a 3D structure that predicted conserved antigenic region, which has potential of binding immunomodulating ligands including glycerol and lactose, found located within exposed loop, suggesting a likely role in immunosuppressive function of tick p36 proteins. Laboratory confirmation of these preliminary results is necessary in future studies.


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## Body

## 1. Introduction

Ticks are considered among the most important vectors of livestock diseases worldwide as well as major vectors of pet diseases [1]. In tropical Africa, ticks and the tick-transmissible diseases constitute a major obstacle to livestock development [2]. Like elsewhere in the world, chemical acaricides have been the mainstay of tick control in this region; however, increasing resistance to this group of insecticides threatens livestock production systems, especially small-holding sectors that rely on rearing of exotic cattle breeds that are more susceptible to tick infestation and tick-borne diseases [TBDs] [3]. Integrated tick control incorporating reduced acaricide use, breeding cattle for tick resistance, rotational grazing, and use of vaccines presents a sustainable and long-term strategy to the control of ticks and TBDs in the tropics [4].Numerous studies have shown the potential of immunological methods to control tick infestation by targeting critical tick physiological processes. Existing antitick vaccines work by eliciting humoral and cellular responses against tick cell membrane antigens [5, 6]. Vaccines capable of quelling both the arthropod vector and disease-causing pathogens are also under development [7]. Despite clear advantages of controlling ticks through vaccination, this strategy is presently hampered by antigenic sequence variations between geographically isolated tick populations and species causing vaccine resistance in some regions [8] and lack of efficacy in others [9]. These limitations necessitate search of alternative antigens for inclusion in the next-generation tick vaccines.Proteins found in tick saliva play critical roles during blood meal acquisition [10]. The pharmacologically active components secreted in their saliva help ticks circumvent host defenses such as haemostatic and immune responses of the host, thereby enabling blood feeding in hematophagous arthropods [11]. One such class of biological compounds is immunosuppressant proteins, which modulate the host’s immune system during tick’s blood feeding [12], making them suitable target in the search of novel vaccines against arthropod-transmitted diseases [13]. Low molecular weight proteins 5–36 kDa from tick saliva proteins have been shown to inhibit T-lymphocytes proliferationin vitro[14]. Active immunization of mice with Salp15, a 15 kDa secreted salivary gland protein fromI. scapularis, showed substantial protection (60%) from tick-borneBorrelia[15]. Tick subolesin (SUB), the ortholog of insect and vertebrate akirins (AKR), was discovered as a tick protective antigen inIxodes scapularis[16]. Vaccines containing conserved SUB/AKR protective epitopes have been shown to protect against tick, mosquito, and sandfly infestations, thus suggesting the possibility of developing universal vaccines for the control of arthropod vector infestations [17].Protein antigens conserved across vector species could be used in developing cross-protective vaccines against multiple arthropod vectors and their associated pathogens [17, 18]. Alarcon-Chaidez et al. [19] cloned and characterized a 36 kDa immunosuppressive protein p36 from the salivary glands of partially engorged, femaleD. andersoni, that suppressed Con-A inducedin vitro proliferation of normal murine T-lymphocytes by more than 90% [20]. Genes related toD. andersoni-derived p36 gene, such as Ra-p36, Av-p36, Hl-p36, and Rhp36, have been reported inA. variegatum[21],R. appendiculatus[22],H. longicornis[23], andR. haemaphysaloides [24]. Most proteins are, however, not sufficiently protective on their own suggesting the need for a multiantigen/chimeric vaccine that incorporates critical tick and pathogen antigenic epitopes [16, 25] to elicit synergistic antipathogen and antitick immune responses. Computational characterization and 3D structure modeling ofD. andersoni p36 protein undertaken by this study is an initial step in understanding molecular basis of immune recognition which is a challenge in vaccine development [26]. The p36 conserved antigenic region predicted by this study has binding residues for ligands like glycerol and lactose which are associated with an immunomodulatory role suggesting this site may have a role in suppression of select T-cell receptor induced signaling events ofD. andersoni p36 and its related proteins.


## 2. Methods

### 2.1. Sequence Characterization of Tick p36 Proteins

All tick proteins deposited in National Centre for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov) protein database were retrieved and deposited in a standalone MySQL based database (https://www.mysql.com).D. andersoni p36 protein was used as reference sequence in conducting homology searches, Blastp [27] and OrthoMCL [28, 29], of tick proteins in the database.The identified tick p36-related proteins were subjected to MEME tool search (http://meme-suite.org/tools/meme) to predict conserved motifs characteristic of p36 proteins. Motif search tool (http://www.genome.jp/tools/motif) then searched for function of identified common motifs in the database of known motifs. Tick p36 protein sequences were then aligned by a multiple sequence alignment tool, Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo). Phylogenetic tree construction was by maximum likelihood method [30] and evolutionary distance computed using Poisson correction method [31]. Bootstrap resampling (1000 replicates) assessed robustness of the groupings.


### 2.2. Identification of Antigenic Determinants in the p36 Proteins

SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP), TMHMM (http://www.cbs.dtu.dk/services/TMHMM), and PredGPI (http://gpcr.biocomp.unibo.it/predgpi) servers were used to determine if tick p36 proteins are preferably secretory, transmembrane, or have a glycosylphosphatidylinositol (GPI) sites, respectively. Antigenic potentials of tick p36 proteins against reference Bm86, a known antitick vaccine antigen, were evaluated by vaxijen tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html); the model selected was parasite whose standard threshold is 0.5000. The antigenic regions ofD. andersoni p36 and other p36 proteins predicted with an antigenic score above 0.7000 were mapped by online tools that predict antigenic peptides (Immunomedicine) (http://imed.med.ucm.es/Tools/antigenic.pl) and SVMTrip [32]. Immunogenic segments/residues of the predicted antigenic region were identified by an online Epitopia tool (http://epitopia.tau.ac.il). Sprint-Pep tool (http://sparks-lab.org/server/SPRINT) was then used to predict protein-peptide binding sites while Coach tool (https://zhanglab.ccmb.med.umich.edu/COACH) predicted ligands likely to bind these sites found within the region predicted as a potential p36 protein conserved site.


### 2.3. Structural Modeling ofD. andersoni p36 Protein

Physicochemical properties ofD. andersonip36 protein were analyzed by ExPASyProtParam (https://www.expasy.org) server while its secondary structure was characterized by online tool Spider2 (http://sparks-lab.org/yueyang/server/SPIDER2). The crystal or NMR structure of tick p36 protein is currently not available in the protein data bank (PDB) (https://www.rcsb.org/pdb/). The 3D structure ofD. andersoni p36 protein was developed by QUARK ab initio modeling [33] that builds 3D structure from “Scratch,” based on physical principles rather than previously solved structures. 10 models, designated as 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10, were generated and validated by analyzing Verify 3D scores [34] of Ramachandran plots for each model. Based on the scores, models 2 and 9 were selected as likely 3D structures ofD. andersonip36 protein because they scored 81.41% and 88.44%, respectively, meeting Verify 3D validation tool limit of 80% of the amino acids residues scoring >=0.2 in the 3D/1D profile.The two selected models had their atomic structures refined by ModRefiner [35] after which their respective generated Ramachandran plots were validated by RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) and ProQ (https://proq.bioinfo.se/ProQ/ProQ.html). The validation scores guided selection of model 2 as the best 3D structure ofD. andersonip36 protein. PDBsum (https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html) was used to check location of predicted conserved antigenic region in the 3D structure ofD. andersoni p36 protein.


## 2.1. Sequence Characterization of Tick p36 Proteins

All tick proteins deposited in National Centre for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov) protein database were retrieved and deposited in a standalone MySQL based database (https://www.mysql.com).D. andersoni p36 protein was used as reference sequence in conducting homology searches, Blastp [27] and OrthoMCL [28, 29], of tick proteins in the database.The identified tick p36-related proteins were subjected to MEME tool search (http://meme-suite.org/tools/meme) to predict conserved motifs characteristic of p36 proteins. Motif search tool (http://www.genome.jp/tools/motif) then searched for function of identified common motifs in the database of known motifs. Tick p36 protein sequences were then aligned by a multiple sequence alignment tool, Clustal Omega (https://www.ebi.ac.uk/Tools/msa/clustalo). Phylogenetic tree construction was by maximum likelihood method [30] and evolutionary distance computed using Poisson correction method [31]. Bootstrap resampling (1000 replicates) assessed robustness of the groupings.


## 2.2. Identification of Antigenic Determinants in the p36 Proteins

SignalP 4.1 (http://www.cbs.dtu.dk/services/SignalP), TMHMM (http://www.cbs.dtu.dk/services/TMHMM), and PredGPI (http://gpcr.biocomp.unibo.it/predgpi) servers were used to determine if tick p36 proteins are preferably secretory, transmembrane, or have a glycosylphosphatidylinositol (GPI) sites, respectively. Antigenic potentials of tick p36 proteins against reference Bm86, a known antitick vaccine antigen, were evaluated by vaxijen tool (http://www.ddg-pharmfac.net/vaxijen/VaxiJen/VaxiJen.html); the model selected was parasite whose standard threshold is 0.5000. The antigenic regions ofD. andersoni p36 and other p36 proteins predicted with an antigenic score above 0.7000 were mapped by online tools that predict antigenic peptides (Immunomedicine) (http://imed.med.ucm.es/Tools/antigenic.pl) and SVMTrip [32]. Immunogenic segments/residues of the predicted antigenic region were identified by an online Epitopia tool (http://epitopia.tau.ac.il). Sprint-Pep tool (http://sparks-lab.org/server/SPRINT) was then used to predict protein-peptide binding sites while Coach tool (https://zhanglab.ccmb.med.umich.edu/COACH) predicted ligands likely to bind these sites found within the region predicted as a potential p36 protein conserved site.


## 2.3. Structural Modeling ofD. andersoni p36 Protein

Physicochemical properties ofD. andersonip36 protein were analyzed by ExPASyProtParam (https://www.expasy.org) server while its secondary structure was characterized by online tool Spider2 (http://sparks-lab.org/yueyang/server/SPIDER2). The crystal or NMR structure of tick p36 protein is currently not available in the protein data bank (PDB) (https://www.rcsb.org/pdb/). The 3D structure ofD. andersoni p36 protein was developed by QUARK ab initio modeling [33] that builds 3D structure from “Scratch,” based on physical principles rather than previously solved structures. 10 models, designated as 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10, were generated and validated by analyzing Verify 3D scores [34] of Ramachandran plots for each model. Based on the scores, models 2 and 9 were selected as likely 3D structures ofD. andersonip36 protein because they scored 81.41% and 88.44%, respectively, meeting Verify 3D validation tool limit of 80% of the amino acids residues scoring >=0.2 in the 3D/1D profile.The two selected models had their atomic structures refined by ModRefiner [35] after which their respective generated Ramachandran plots were validated by RAMPAGE (http://mordred.bioc.cam.ac.uk/~rapper/rampage.php) and ProQ (https://proq.bioinfo.se/ProQ/ProQ.html). The validation scores guided selection of model 2 as the best 3D structure ofD. andersonip36 protein. PDBsum (https://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=index.html) was used to check location of predicted conserved antigenic region in the 3D structure ofD. andersoni p36 protein.


## 3. Results and Discussion

### 3.1. Identification and Phylogenetic Analysis of p36 Proteins from Ixodid Ticks

The study identified 32 homologs ofD. andersoni p36 protein among 6 ixodid (hard) tick species (Table 1). These included p36 genes reported in earlier studies fromR. appendiculatus,A. variegatum,H. longicornis, andRhipicephalus haemaphysaloidestick species as well as those found by this study inAmblyomma sculptum andAmblyomma aureolatum. Among these homologs, 4 co-orthologs which are potential orthologs ofD. andersoni p36 protein were identified inR. appendiculatus species (Table 1). Occurrence of p36 protein across a range of tick species may be related to a biological function for this protein in tick feeding [36]. Several p36 immunosuppressant protein sequences were found in a single tick species suggesting functional and structural redundancy in which a tick expresses multiple similar proteins in minute quantities during feeding [37]. Such redundancy may render saliva proteins less immunogenic, as reported with cystatins [38].Table 1
Tick proteins related toD. andersoni p36 protein.
Tick species NCBI accessionnumber Sequence similarity searches Reference Blastp homology search OrthoMCL Search Protein description% identityAlignmentE ValueBit scorelengthaa D. andersoni AAF03683.1 p 36 ∗ 100 220 1.00 E - 165 459 Reference Bergman et al., 2000 R. appendiculatus JAP82151.1 Da-p36 family member 37.72 228 2.00 E - 034 124 Co-ortholog De castro et al., 2016 R. appendiculatus JAP81510.1 Da-p36 family member 37.8 209 3.00 E - 034 123 Co-ortholog De castro et al., 2016 R. appendiculatus JAP87204.1 Da-p36 family member 37.81 201 3.00 E - 033 120 Co-ortholog De castro et al., 2016 R. appendiculatus JAP86350.1 Da-p36 family member 35.82 201 6.00 E - 032 116 Co-ortholog De castro et al., 2016 A. variegatum BAD11807.1 Da-p36 35.04 234 1.00 E - 029 111 In-paralog Roller et al., 2004 R. h. haemaphysaloides ABB90890.1 Rhh-ISP partial 36.71 158 2.00 E - 027 103 In-paralog Xiang et al., 2005 A. sculptum JAU03129.1 Hypothetical protein partial 35.06 231 1.00 E - 026 103 In-paralog Eliane et al., 2016 R. appendiculatus JAP81944.1 Da-p36 family member 32.3 226 2.00 E - 024 97.4 In-paralog De castro et al., 2016 R. appendiculatus JAP88013.1 Da-p36 family member partial 31.58 228 2.00 E - 024 97.4 In-paralog De castro et al., 2016 A. sculptum JAU02613.1 Hypothetical protein partial 27.65 217 2.00 E - 016 74.3 In-paralog Eliane et al., 2016 R. appendiculatus JAP85022.1 Hypothetical protein 25.11 231 7.00 E - 016 72.8 In-paralog De castro et al., 2016 A. sculptum JAU02539.1 partial Da-p36 family member 32 175 2.00 E - 015 70.9 In-paralog Eliane et al., 2016 A. variegatum DAA34595.1 Da-p36 like 27.95 229 3.00 E - 015 70.9 In-paralog Ribeiro et al., 2011 A. aureolatum JAT98922.1 Hypothetical protein partial 31.65 218 4.00 E - 015 70.5 In-paralog Martins et al., 2016 A. aureolatum JAT98921.1 Hypothetical protein 30.19 212 3.00 E - 013 65.5 In-paralog Martins et al., 2016 R. appendiculatus JAP85729.1 Da-p36 family member 26.24 221 4.00 E - 013 65.1 In-paralog De castro et al., 2016 R. appendiculatus JAP85564.1 Da-p36 family member 25.47 212 2.00 E - 012 63.5 In-paralog De castro et al., 2016 R. appendiculatus JAP82143.1 Da-p36 family member 23.31 236 2.00 E - 011 60.1 In-paralog De castro et al., 2016 R. appendiculatus JAP86306.1 Da-p36 family member 25.74 237 3.00 E - 011 60.1 In-paralog De castro et al., 2016 R. appendiculatus JAP81863.1 Da-p36 family member 27.14 210 6.00 E - 011 59.3 In-paralog De castro et al., 2016 A. variegatum DAA34748.1 Da-p36 like 29.24 171 1.00 E - 010 57.8 In-paralog Ribeiro et al., 2011 R. appendiculatus JAP78061.1 Da-p36 family member 26.23 244 3.00 E - 009 54.3 In-paralog De castro et al., 2016 R. appendiculatus JAP86680.1 Da-p36 family member 27.72 202 7.00 E - 009 53.5 In-paralog De castro et al., 2016 R. appendiculatus JAP88255.1 Da-p36 family member 26.73 202 2.00 E - 008 52 In-paralog De castro et al., 2016 R. appendiculatus JAP85730.1 Da-p36 family member 24.82 141 2.00 E - 008 51.2 In-paralog De castro et al., 2016 H. longicornis BAG11660.1 Isp-p36 31.78 107 1.00 E - 007 50.1 In-paralog Nakajima et al., 2008 R. appendiculatus JAP81735.1 Da-p36 family member 24.58 240 6.00 E - 004 38.9 In-paralog De castro et al., 2016 R. appendiculatus JAP86324.1 Da-p36 family member 24.24 198 0.001 38.1 In-paralog De castro et al., 2016 A. sculptum JAU02519.1 Hypothetical protein partial 33.7 92 0.001 36.6 In-paralog Eliane et al., 2016 A. variegatum DAA34145.1 ISP-p36 partial 28.95 76 0.002 36.6 In-paralog Ribeiro et al., 2011 R. appendiculatus JAP81446.1 Da-p36 family member 25.74 237 0.011 35 In-paralog De castro et al., 2016 R. appendiculatus JAP86032.1 Da-p36 family member 25.18 139 0.019 34.3 In-paralog De castro et al., 2016 a aAmino acid; ∗reference p36 protein in D. andersoni.The tick p36 proteins have 3 potential common motifs designated as 1, 2, and 3 with motif 2 being the only one conserved among p36 proteins (Figure1). Motif 2 is located between amino acid positions “107–127” in the referenceD. andersoni p36 protein. This motif 2 may be associated with a functional domain, possibly a role in immunomodulatory activity of tick p36 proteins [39]. The 3 common motifs were not found in the motif database and could be representing an orphan protein family [40].Figure 1
(a)Occurrence of tandem motifs among p36 proteins. Motif 2 is conserved across all homologs; (b)motifs sequence logo analysis.
(a) (b)Alignment of tick p36 proteins revealed a conserved region occurring between amino acid positions “107–115” (“IDKGMLSPF”) in the referenceD. andersoni p36 protein (Figure 2). This region that coincides with location of conserved motif 2 has polar amino acid residue serine (S) and charged residues lysine (K) and aspartate (D), which are associated with potential active sites [41]. Phylogenetic tree (Figure 3) showed that, among homologs with higher amino acid percentage similarity andE-scores,D. andersoni was closely related to homologs fromR. haemophysaloides andR. appendiculatus as compared to homolog fromA. variegatum indicating more recent ancestry betweenDermacentor andRhipicephalusthan withAmblyomma genera as inferred by phylogeny [42].Figure 2
Multiple alignment of p36 homologous amino acid sequences showing likely conservation region. In the case of referenceD. andersoni p36 protein, the conserved region “IDKGMLSPF” is located at positions “107–115.” (:) and (.): marks conservation between groups of strongly or weakly similar properties, respectively.Note. Amino acids colour according to physicochemical properties: red is for small hydrophobic, blue for acidic, magenta for basic, and green for hydroxyl/sulfhydryl/amine amino acid residues. Highlighted region shows conservation in tick p36 proteins.Figure 3
Phylogenetic relatedness between p36 proteins. Bootstrap resampling (1000 replicates) was employed to validate the robustness of the groupings yielded.


### 3.2. Identification and Characterization of Antigenic Regions in the p36 Proteins

Most tick p36 proteins were predicted as secretory with signal peptide cleavage site at position 21-22 (Supplementary TableS1 and Figure S1). Secretory proteins are favoured candidates for vaccine development as they are easily accessible microbial antigens to the immune system [43].D. andersoni p36 protein and most p36 variants were predicted as antigenic with several homologs having antigenicity score above 0.7000 (Table 2, Supplementary Table S1), surpassing the vaxijen tool threshold of 0.5000. JAP81944.1, a homolog inR. appendiculatus had antigenicity score of 0.7701, comparably higher than that of Bm86 (0.7681), the constituent antigen of Tickgard and Gavac™ commercial tick vaccines. Whether this theoretically predicted immunogenicity can confer protection against tick infestation there is need to be evaluated empirically through an immunization/tick challenge set up.Table 2
Conserved motif 2 of tick p36 proteins mapped as a potential antigenic/binding site region.
Tick species NCBI accession number Antigenic score Conserved Motif 2 location Antigenic region antigenic peptide tool/SVM Trip tool Mapped immunogenic segments of Motif 2 Epitopia tool Mapped Binding sites of Motif 2 Sprint pep tool Predicted ligands for Motif 2 Coach tool D. andersoni AAF03683.1 0.5880 107–127 95–128 IDKGMLSPFNLSATVKFPLIP IDKGMLSPFNLSATVKFPLIP Lactose, Glycerol, NAG-(4-1)GAL, Sucrose  R. appendiculatus JAP81944.1 0.7701 117–137 108–137 IDNGIKTPFHLKAVFSFPITG IDNGIKTPFHLKAVFSFPITG -  R. appendiculatus JAP88013.1 0.7379 113–133 104–133 IDNGIKTPFHLKAVFSFPITG IDNGIKTPFHLKAVFSFPITG -  R. appendiculatus JAP81510.1 0.7258 102–122 94–133 IDDSMYSPFNIMTTVAFPLIG IDDSMYSPFNIMTTVAFPLIG B-Octylglucoside  R. appendiculatus JAP86350.1 0.7072 78–98 74–110 IDYGIYSPFNLVTPVQFPLMG IDYGIYSPFNLVTPVQFPLMG Alpha-D-Mannose, Alpha-D-Lactose, B-Octylglucoside Bold sections: tick p36 conserved region residues mapped as potentially antigenic/binding sites.The potentially conserved motif 2 in p36 protein was predicted as a likely epitope-rich antigenic region with binding residues for glycerol and lactose ligands which are associated with an immunomodulatory role [44, 45]. To facilitate tick feeding a single tick saliva protein ligand may bind receptors on several immune cell types in the vertebrate host; alternatively, multiple tick saliva proteins may bind to a common receptor [37].


### 3.3. 3D Structure ofD. andersoni p36 Protein

D. andersoni p36 protein has an instability index of 35.53 and GRAVY score of −0.324 classifying it as a stable, globular protein [46]. The protein’s high aliphatic index of 86.41 is associated with increase in thermostability of globular protein [47]. The stable secondary structures alpha-helix (α) and beta-sheets (β) comprised approximately 55% ofD. andersoni p36 protein amino acid sequence (Supplementary Figure S2). The predicted conserved immunogenic region “74–107” in processed secretoryD. andersoni p36 protein had several segments within loop regions where epitopes are generally found [48]. The combination of α-helixes and β-structures through loops with specific geometric arrangements with respect to each is responsible in forming conserved structural motifs [49, 50].Based on Verify 3D [34] scores of the 10 models designated as 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 generated forD. andersoni p36 protein; models 2 and 9 were selected for further validation as they passed tool limit of 80% of the amino acids residues scoring >=0.2 in the 3D/1D profile (Supplementary Table S2). Comparison of validation scores of the selected models 2 and 9 (Table 3, Supplementary Figures S3 and S4) identified model 2 as the best 3D structure ofD. andersoni p36 protein.Table 3
Validation of 3D structures for models 2 and 9 ofD. andersoni p36 protein.
Number Validation tool Parameter monitored Limit Results Model 2 Model 9 (1) ProQPsiPred LGscore LG score > 1.5 fairly good modelLG score > 2.5 very good modelLG score > 4 extremely good model LGscore 2.797 LGscore 2.366 MaxSub MaxSub > 0.1 fairly good modelMaxSub > 0.5 very good modelMaxSub > 0.8 extremely good model MaxSub 0.208 MaxSub 0.055  (2) ProQJPred LGscore LG score > 1.5 fairly good modelLG score > 2.5 very good modelLG score > 4 extremely good model LGscore 2.914 LGscore 2.231 MaxSub MaxSub > 0.1 fairly good modelMaxSub > 0.5 very good modelMaxSub > 0.8 extremely good model MaxSub 0.219 MaxSub 0.046  (3) Rampage tool Favoured region residuesAllowed region residuesOutlier region residues  156 (79.2%)26 (13.2%)15 (7.6%) 152 (77.2%)24 (12.2%)21 (10.7%)The predicted 3D structure ofD.andersoni p36 protein (Figures 4(a) and 4(b)) is a ball-like structure comprised of 1 alpha-helix and several antiparallel beta-strands. The region predicted as a likely conserved antigenic region “74⋯107” inD. andersoni p36 protein is not only located in between the alpha-helix and beta-strands but also occurs within the potentially groove region of the predicted 3D structure and further has its loop exposed on the protein surface (Figure 4(c)). Ligands bind in the largest cleft in over 83% of the proteins [51]; thus presence of the predicted conserved antigenic region within this potential groove may be associated with immunosuppressive function ofD. andersoni p36 protein, as internal cavities in proteins are important structural elements that may produce functional motions such as ligand binding [52].Figure 4
(a, b)D. andersoni p36 protein predicted 3D structure ribbon and space field model; (c) predicted antigenic region “74–107,” in 3D structure ofD. andersoni p36 protein. (d) Topology ofD. andersoni p36 protein showing the likely predicted conserved exposed loop.Yellow: predicted conserved antigenic region “74–107”; red: α-helix secondary structure; purple: β-strands secondary structure. ↑: predicted exposed loop region “87–94”(“DKGMLSPF”) inD. andersoni p36, showing conservation in alignment of tick p36 proteins.
(a) (b) (c) (d)Potentially exposed loop region “87⋯94” (Figure4(d)) in predicted 3D structure ofD. andersoni p36 protein coincides with its likely conserved alignment region “107⋯115” after cleavage of signal peptide at amino acid position 21-22. This suggested loop region might be associated with binding site ofD. andersonip36 protein. The ligands predicted with potential to bind on this site include fatty acid glycerol and sugars like lactose. The hydroxyl group of polar amino acid residue serine (S), hydrophobic amino acid residue leucine (L), and charged amino acids lysine (K) and aspartic acid (D) found in this region could, respectively, have a role in binding of these ligands [53]. Immunomodulator ligands predicted with potential of binding at this site include fatty acid glycerol and sugars like lactose. There is need for future studies to evaluate whether immunomodulator ligands have a role in suppression of select T-cell receptor (TCR) induced signaling events inD. andersoni p36 protein mode of action [44, 45].Collectively results from this in silico study provide further insight into potential characters of p36 protein, which is vital in exploiting the proteins as targets for developing improved next-generation cross-protective tick control approaches. In an effort to determine exact role of these proteins in tick feeding process, it is necessary for future laboratory and animal studies to confirm these preliminary predictive findings.


## 3.1. Identification and Phylogenetic Analysis of p36 Proteins from Ixodid Ticks

The study identified 32 homologs ofD. andersoni p36 protein among 6 ixodid (hard) tick species (Table 1). These included p36 genes reported in earlier studies fromR. appendiculatus,A. variegatum,H. longicornis, andRhipicephalus haemaphysaloidestick species as well as those found by this study inAmblyomma sculptum andAmblyomma aureolatum. Among these homologs, 4 co-orthologs which are potential orthologs ofD. andersoni p36 protein were identified inR. appendiculatus species (Table 1). Occurrence of p36 protein across a range of tick species may be related to a biological function for this protein in tick feeding [36]. Several p36 immunosuppressant protein sequences were found in a single tick species suggesting functional and structural redundancy in which a tick expresses multiple similar proteins in minute quantities during feeding [37]. Such redundancy may render saliva proteins less immunogenic, as reported with cystatins [38].Table 1
Tick proteins related toD. andersoni p36 protein.
Tick species NCBI accessionnumber Sequence similarity searches Reference Blastp homology search OrthoMCL Search Protein description% identityAlignmentE ValueBit scorelengthaa D. andersoni AAF03683.1 p 36 ∗ 100 220 1.00 E - 165 459 Reference Bergman et al., 2000 R. appendiculatus JAP82151.1 Da-p36 family member 37.72 228 2.00 E - 034 124 Co-ortholog De castro et al., 2016 R. appendiculatus JAP81510.1 Da-p36 family member 37.8 209 3.00 E - 034 123 Co-ortholog De castro et al., 2016 R. appendiculatus JAP87204.1 Da-p36 family member 37.81 201 3.00 E - 033 120 Co-ortholog De castro et al., 2016 R. appendiculatus JAP86350.1 Da-p36 family member 35.82 201 6.00 E - 032 116 Co-ortholog De castro et al., 2016 A. variegatum BAD11807.1 Da-p36 35.04 234 1.00 E - 029 111 In-paralog Roller et al., 2004 R. h. haemaphysaloides ABB90890.1 Rhh-ISP partial 36.71 158 2.00 E - 027 103 In-paralog Xiang et al., 2005 A. sculptum JAU03129.1 Hypothetical protein partial 35.06 231 1.00 E - 026 103 In-paralog Eliane et al., 2016 R. appendiculatus JAP81944.1 Da-p36 family member 32.3 226 2.00 E - 024 97.4 In-paralog De castro et al., 2016 R. appendiculatus JAP88013.1 Da-p36 family member partial 31.58 228 2.00 E - 024 97.4 In-paralog De castro et al., 2016 A. sculptum JAU02613.1 Hypothetical protein partial 27.65 217 2.00 E - 016 74.3 In-paralog Eliane et al., 2016 R. appendiculatus JAP85022.1 Hypothetical protein 25.11 231 7.00 E - 016 72.8 In-paralog De castro et al., 2016 A. sculptum JAU02539.1 partial Da-p36 family member 32 175 2.00 E - 015 70.9 In-paralog Eliane et al., 2016 A. variegatum DAA34595.1 Da-p36 like 27.95 229 3.00 E - 015 70.9 In-paralog Ribeiro et al., 2011 A. aureolatum JAT98922.1 Hypothetical protein partial 31.65 218 4.00 E - 015 70.5 In-paralog Martins et al., 2016 A. aureolatum JAT98921.1 Hypothetical protein 30.19 212 3.00 E - 013 65.5 In-paralog Martins et al., 2016 R. appendiculatus JAP85729.1 Da-p36 family member 26.24 221 4.00 E - 013 65.1 In-paralog De castro et al., 2016 R. appendiculatus JAP85564.1 Da-p36 family member 25.47 212 2.00 E - 012 63.5 In-paralog De castro et al., 2016 R. appendiculatus JAP82143.1 Da-p36 family member 23.31 236 2.00 E - 011 60.1 In-paralog De castro et al., 2016 R. appendiculatus JAP86306.1 Da-p36 family member 25.74 237 3.00 E - 011 60.1 In-paralog De castro et al., 2016 R. appendiculatus JAP81863.1 Da-p36 family member 27.14 210 6.00 E - 011 59.3 In-paralog De castro et al., 2016 A. variegatum DAA34748.1 Da-p36 like 29.24 171 1.00 E - 010 57.8 In-paralog Ribeiro et al., 2011 R. appendiculatus JAP78061.1 Da-p36 family member 26.23 244 3.00 E - 009 54.3 In-paralog De castro et al., 2016 R. appendiculatus JAP86680.1 Da-p36 family member 27.72 202 7.00 E - 009 53.5 In-paralog De castro et al., 2016 R. appendiculatus JAP88255.1 Da-p36 family member 26.73 202 2.00 E - 008 52 In-paralog De castro et al., 2016 R. appendiculatus JAP85730.1 Da-p36 family member 24.82 141 2.00 E - 008 51.2 In-paralog De castro et al., 2016 H. longicornis BAG11660.1 Isp-p36 31.78 107 1.00 E - 007 50.1 In-paralog Nakajima et al., 2008 R. appendiculatus JAP81735.1 Da-p36 family member 24.58 240 6.00 E - 004 38.9 In-paralog De castro et al., 2016 R. appendiculatus JAP86324.1 Da-p36 family member 24.24 198 0.001 38.1 In-paralog De castro et al., 2016 A. sculptum JAU02519.1 Hypothetical protein partial 33.7 92 0.001 36.6 In-paralog Eliane et al., 2016 A. variegatum DAA34145.1 ISP-p36 partial 28.95 76 0.002 36.6 In-paralog Ribeiro et al., 2011 R. appendiculatus JAP81446.1 Da-p36 family member 25.74 237 0.011 35 In-paralog De castro et al., 2016 R. appendiculatus JAP86032.1 Da-p36 family member 25.18 139 0.019 34.3 In-paralog De castro et al., 2016 a aAmino acid; ∗reference p36 protein in D. andersoni.The tick p36 proteins have 3 potential common motifs designated as 1, 2, and 3 with motif 2 being the only one conserved among p36 proteins (Figure1). Motif 2 is located between amino acid positions “107–127” in the referenceD. andersoni p36 protein. This motif 2 may be associated with a functional domain, possibly a role in immunomodulatory activity of tick p36 proteins [39]. The 3 common motifs were not found in the motif database and could be representing an orphan protein family [40].Figure 1
(a)Occurrence of tandem motifs among p36 proteins. Motif 2 is conserved across all homologs; (b)motifs sequence logo analysis.
(a) (b)Alignment of tick p36 proteins revealed a conserved region occurring between amino acid positions “107–115” (“IDKGMLSPF”) in the referenceD. andersoni p36 protein (Figure 2). This region that coincides with location of conserved motif 2 has polar amino acid residue serine (S) and charged residues lysine (K) and aspartate (D), which are associated with potential active sites [41]. Phylogenetic tree (Figure 3) showed that, among homologs with higher amino acid percentage similarity andE-scores,D. andersoni was closely related to homologs fromR. haemophysaloides andR. appendiculatus as compared to homolog fromA. variegatum indicating more recent ancestry betweenDermacentor andRhipicephalusthan withAmblyomma genera as inferred by phylogeny [42].Figure 2
Multiple alignment of p36 homologous amino acid sequences showing likely conservation region. In the case of referenceD. andersoni p36 protein, the conserved region “IDKGMLSPF” is located at positions “107–115.” (:) and (.): marks conservation between groups of strongly or weakly similar properties, respectively.Note. Amino acids colour according to physicochemical properties: red is for small hydrophobic, blue for acidic, magenta for basic, and green for hydroxyl/sulfhydryl/amine amino acid residues. Highlighted region shows conservation in tick p36 proteins.Figure 3
Phylogenetic relatedness between p36 proteins. Bootstrap resampling (1000 replicates) was employed to validate the robustness of the groupings yielded.


## 3.2. Identification and Characterization of Antigenic Regions in the p36 Proteins

Most tick p36 proteins were predicted as secretory with signal peptide cleavage site at position 21-22 (Supplementary TableS1 and Figure S1). Secretory proteins are favoured candidates for vaccine development as they are easily accessible microbial antigens to the immune system [43].D. andersoni p36 protein and most p36 variants were predicted as antigenic with several homologs having antigenicity score above 0.7000 (Table 2, Supplementary Table S1), surpassing the vaxijen tool threshold of 0.5000. JAP81944.1, a homolog inR. appendiculatus had antigenicity score of 0.7701, comparably higher than that of Bm86 (0.7681), the constituent antigen of Tickgard and Gavac™ commercial tick vaccines. Whether this theoretically predicted immunogenicity can confer protection against tick infestation there is need to be evaluated empirically through an immunization/tick challenge set up.Table 2
Conserved motif 2 of tick p36 proteins mapped as a potential antigenic/binding site region.
Tick species NCBI accession number Antigenic score Conserved Motif 2 location Antigenic region antigenic peptide tool/SVM Trip tool Mapped immunogenic segments of Motif 2 Epitopia tool Mapped Binding sites of Motif 2 Sprint pep tool Predicted ligands for Motif 2 Coach tool D. andersoni AAF03683.1 0.5880 107–127 95–128 IDKGMLSPFNLSATVKFPLIP IDKGMLSPFNLSATVKFPLIP Lactose, Glycerol, NAG-(4-1)GAL, Sucrose  R. appendiculatus JAP81944.1 0.7701 117–137 108–137 IDNGIKTPFHLKAVFSFPITG IDNGIKTPFHLKAVFSFPITG -  R. appendiculatus JAP88013.1 0.7379 113–133 104–133 IDNGIKTPFHLKAVFSFPITG IDNGIKTPFHLKAVFSFPITG -  R. appendiculatus JAP81510.1 0.7258 102–122 94–133 IDDSMYSPFNIMTTVAFPLIG IDDSMYSPFNIMTTVAFPLIG B-Octylglucoside  R. appendiculatus JAP86350.1 0.7072 78–98 74–110 IDYGIYSPFNLVTPVQFPLMG IDYGIYSPFNLVTPVQFPLMG Alpha-D-Mannose, Alpha-D-Lactose, B-Octylglucoside Bold sections: tick p36 conserved region residues mapped as potentially antigenic/binding sites.The potentially conserved motif 2 in p36 protein was predicted as a likely epitope-rich antigenic region with binding residues for glycerol and lactose ligands which are associated with an immunomodulatory role [44, 45]. To facilitate tick feeding a single tick saliva protein ligand may bind receptors on several immune cell types in the vertebrate host; alternatively, multiple tick saliva proteins may bind to a common receptor [37].


## 3.3. 3D Structure ofD. andersoni p36 Protein

D. andersoni p36 protein has an instability index of 35.53 and GRAVY score of −0.324 classifying it as a stable, globular protein [46]. The protein’s high aliphatic index of 86.41 is associated with increase in thermostability of globular protein [47]. The stable secondary structures alpha-helix (α) and beta-sheets (β) comprised approximately 55% ofD. andersoni p36 protein amino acid sequence (Supplementary Figure S2). The predicted conserved immunogenic region “74–107” in processed secretoryD. andersoni p36 protein had several segments within loop regions where epitopes are generally found [48]. The combination of α-helixes and β-structures through loops with specific geometric arrangements with respect to each is responsible in forming conserved structural motifs [49, 50].Based on Verify 3D [34] scores of the 10 models designated as 1, 2, 3, 4, 5, 6, 7, 8, 9, and 10 generated forD. andersoni p36 protein; models 2 and 9 were selected for further validation as they passed tool limit of 80% of the amino acids residues scoring >=0.2 in the 3D/1D profile (Supplementary Table S2). Comparison of validation scores of the selected models 2 and 9 (Table 3, Supplementary Figures S3 and S4) identified model 2 as the best 3D structure ofD. andersoni p36 protein.Table 3
Validation of 3D structures for models 2 and 9 ofD. andersoni p36 protein.
Number Validation tool Parameter monitored Limit Results Model 2 Model 9 (1) ProQPsiPred LGscore LG score > 1.5 fairly good modelLG score > 2.5 very good modelLG score > 4 extremely good model LGscore 2.797 LGscore 2.366 MaxSub MaxSub > 0.1 fairly good modelMaxSub > 0.5 very good modelMaxSub > 0.8 extremely good model MaxSub 0.208 MaxSub 0.055  (2) ProQJPred LGscore LG score > 1.5 fairly good modelLG score > 2.5 very good modelLG score > 4 extremely good model LGscore 2.914 LGscore 2.231 MaxSub MaxSub > 0.1 fairly good modelMaxSub > 0.5 very good modelMaxSub > 0.8 extremely good model MaxSub 0.219 MaxSub 0.046  (3) Rampage tool Favoured region residuesAllowed region residuesOutlier region residues  156 (79.2%)26 (13.2%)15 (7.6%) 152 (77.2%)24 (12.2%)21 (10.7%)The predicted 3D structure ofD.andersoni p36 protein (Figures 4(a) and 4(b)) is a ball-like structure comprised of 1 alpha-helix and several antiparallel beta-strands. The region predicted as a likely conserved antigenic region “74⋯107” inD. andersoni p36 protein is not only located in between the alpha-helix and beta-strands but also occurs within the potentially groove region of the predicted 3D structure and further has its loop exposed on the protein surface (Figure 4(c)). Ligands bind in the largest cleft in over 83% of the proteins [51]; thus presence of the predicted conserved antigenic region within this potential groove may be associated with immunosuppressive function ofD. andersoni p36 protein, as internal cavities in proteins are important structural elements that may produce functional motions such as ligand binding [52].Figure 4
(a, b)D. andersoni p36 protein predicted 3D structure ribbon and space field model; (c) predicted antigenic region “74–107,” in 3D structure ofD. andersoni p36 protein. (d) Topology ofD. andersoni p36 protein showing the likely predicted conserved exposed loop.Yellow: predicted conserved antigenic region “74–107”; red: α-helix secondary structure; purple: β-strands secondary structure. ↑: predicted exposed loop region “87–94”(“DKGMLSPF”) inD. andersoni p36, showing conservation in alignment of tick p36 proteins.
(a) (b) (c) (d)Potentially exposed loop region “87⋯94” (Figure4(d)) in predicted 3D structure ofD. andersoni p36 protein coincides with its likely conserved alignment region “107⋯115” after cleavage of signal peptide at amino acid position 21-22. This suggested loop region might be associated with binding site ofD. andersonip36 protein. The ligands predicted with potential to bind on this site include fatty acid glycerol and sugars like lactose. The hydroxyl group of polar amino acid residue serine (S), hydrophobic amino acid residue leucine (L), and charged amino acids lysine (K) and aspartic acid (D) found in this region could, respectively, have a role in binding of these ligands [53]. Immunomodulator ligands predicted with potential of binding at this site include fatty acid glycerol and sugars like lactose. There is need for future studies to evaluate whether immunomodulator ligands have a role in suppression of select T-cell receptor (TCR) induced signaling events inD. andersoni p36 protein mode of action [44, 45].Collectively results from this in silico study provide further insight into potential characters of p36 protein, which is vital in exploiting the proteins as targets for developing improved next-generation cross-protective tick control approaches. In an effort to determine exact role of these proteins in tick feeding process, it is necessary for future laboratory and animal studies to confirm these preliminary predictive findings.


## 4. Conclusion

The p36 immunosuppressive proteins from ticks exhibit antigen traits worth evaluating in future experimentalin vitro andin vivo trials. This includes potential conservation across several tick species and presence of a likely conserved antigenic region that may be bound by immunomodulator ligands such as glycerol and lactose. A further study is necessary on suitability of this potentially conserved region in development of a multi/chimeric antitick vaccine that incorporates critical antigenic regions. The predicted 3D model ofD. andersoni p36 protein may be used as a template to model structures of other orphan proteins related to p36. This work is a step towards developing cross-protective next-generation antitick vaccines, as the results expand our knowledge of p36 tick saliva protein and lay ground for future studies to determine their exact role in tick feeding process, which is useful in designing blockade approaches targeting these proteins.



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*Source: 7963401-2018-04-08.xml*