Selection, characterization, and thermal stabilization of llama single domain antibodies towards Ebola virus glycoprotein
© The Author(s) 2017
Received: 17 August 2017
Accepted: 28 November 2017
Published: 12 December 2017
A key advantage of recombinant antibody technology is the ability to optimize and tailor reagents. Single domain antibodies (sdAbs), the recombinantly produced variable domains derived from camelid and shark heavy chain antibodies, provide advantages of stability and solubility and can be further engineered to enhance their properties. In this study, we generated sdAbs specific for Ebola virus envelope glycoprotein (GP) and increased their stability to expand their utility for use in austere locals. Ebola virus is extremely virulent and causes fatal hemorrhagic fever in ~ 50 percent of the cases. The viral GP binds to host cell receptors to facilitate viral entry and thus plays a critical role in pathogenicity.
An immune phage display library containing more than 107 unique clones was developed from a llama immunized with a combination of killed Ebola virus and recombinantly produced GP. We panned the library to obtain GP binding sdAbs and isolated sdAbs from 5 distinct sequence families. Three GP binders with dissociation constants ranging from ~ 2 to 20 nM, and melting temperatures from ~ 57 to 72 °C were selected for protein engineering in order to increase their stability through a combination of consensus sequence mutagenesis and the addition of a non-canonical disulfide bond. These changes served to increase the melting temperatures of the sdAbs by 15–17 °C. In addition, fusion of a short positively charged tail to the C-terminus which provided ideal sites for the chemical modification of these sdAbs resulted in improved limits of detection of GP and Ebola virus like particles while serving as tracer antibodies.
SdAbs specific for Ebola GP were selected and their stability and functionality were improved utilizing protein engineering. Thermal stability of antibody reagents may be of particular importance when operating in austere locations that lack reliable refrigeration. Future efforts can evaluate the potential of these isolated sdAbs as candidates for diagnostic or therapeutic applications for Ebola.
Camelid single domain antibodies (sdAbs, also referred to as nanobodies or VHH) and shark-derived sdAbs (termed VNAR) are recombinantly expressed variable domains derived from the heavy-chain-only antibodies found in camelids and sharks [1–5]. Each sdAb contains three variable complementarity determining regions (CDRs) and four relatively well conserved framework regions (FRs). SdAbs constitute the smallest naturally occurring antigen binding domains and offer many advantages. Their superior thermal stability and ability to recognize hidden epitopes combined with specificity and binding affinity comparable to conventional antibodies (Abs) make sdAbs an attractive alternative to Abs [6–9]. Importantly, sdAbs are amenable to protein engineering to improve their properties. While sdAbs are generally thermal stable and most refold and recover the majority of their secondary structure after heat denaturation, sdAbs are not heat proof. They can, however, be engineered to increase their melting temperature . Furthermore, sdAbs can be engineered to tailor them for integration into specific applications [6, 11]. These properties make sdAbs ideal reagents for a wide range of uses including detection of, or therapeutic response to, infectious diseases and bio-threat agents [6–9, 11, 12].
An important target for sdAb development is the Ebola virus. Ebola virus is a member of Family Filoviridae, along with the Marburg viruses. Genus Ebola virus includes four species, Zaire ebolavirus (EBOV), Sudan ebolavirus, (SUDV) Tai Forest ebolavirus (TAFV) and Bundibugyo ebolavirus (BDBV) originally described in Africa plus Reston ebolavirus (RESTV) from the Philippines. With the exception of Reston virus, these viruses cause severe fatal viral hemorrhagic fever due to the systemic infection and replication upon entry into the human body and if untreated result in mortality rates of up to 90%. The incubation period for EBOV infection lasts 5–7 days and in most of patients symptoms appear within 21 days after the exposure. In some cases the infection of Ebola viruses can be detected as early as 2 days post exposure by reverse transcription polymerase chain reaction (RT-PCR) . In addition, enzyme-linked immunosorbent assays (ELISAs) are used for the detection of Ebola specific IgM and IgG antibodies and viral antigens. Viral particles detected by antibodies can be traced in blood from day 3 up to day 7–16 following the beginning of symptoms. While there are a number of promising leads, currently there is no licensed vaccine nor an approved treatment available for human use (http://www.who.int/mediacentre/factsheets/fs103/en/); .
The cause of the extreme virulence by Ebola virus infection is still not well established. However current data suggests that the interaction of glycosylated envelope protein (glycoprotein) with the immune system plays an important role in the extraordinary pathogenicity of this virus. The Ebola virus genome consists of a non-segmented, negative sense RNA, approximately 19 kb in size, which encodes seven structural proteins and two glycoproteins (GPs), the envelope glycoprotein (GP) and a secretory GP (sGP) [15, 16]. Transcriptional editing of the GP gene results in production of a transmembrane-linked GP with a length of 676 amino acids and a secreted soluble non-structural sGP with a length of 364 amino acids . Both GP and sGP share approximately 300 N-terminal amino acids; sGP is detected in high concentrations in the blood of acutely infected patients. The role of sGP is not well known yet, but likely it is involved in limiting neutrophil activation by binding to host receptors and inhibiting the neutralizing activity of anti-GP antibodies by decoying them. Most Ebola virus GP contains a convertase furin cleavage site, which results in two subunits, GP1 and GP2 in the native GP . GP1 and GP2 form heterodimers on the virions. The surface subunit (GP1) is involved in receptor binding and the transmembrane subunit (GP2) mediates the virus host membrane fusion. Ebola virus GP is responsible for the entry of viruses to the target cells and thus is considered the most important protein for pathogenesis. It is the sole protein on the viral surface and serves as the primary target of neutralizing antibodies.
Several promising therapeutic antibodies specific against GP, including humanized mouse antibodies (Zmapp), bi-specific antibodies and other related monoclonal antibodies aiming to neutralize Ebola viruses by inhibiting viral entry to host cells have been or are under development [19–21]. SdAbs represent attractive alternatives to these conventional antibodies.
Both llama- and shark-derived sdAbs specific for the EBOV nucleoprotein (NP) have been described for the detection of EBOV [22, 23]. However, sdAbs against EBOV GP have not yet been developed. In this study, a combination of killed EBOV and recombinant EBOV GP was used to immunize a llama and an immune sdAb library was developed for biopanning against EBOV GP. Specific GP binders were selected and characterized for binding to GP and EBOV virus like particles (VLPs). The sequences of the EBOV GP binding sdAbs were modified to improve their physical properties and the detection capability for GP and VLPs.
Results and discussion
Library construction and biopanning
Ideally an immune sdAb phage display library captures the repertoire of variable regions from the heavy-chain-only antibodies of an immunized animal. A library of phage displayed sdAbs derived from a llama immunized with both killed EBOV and recombinant EBOV GP was constructed. As described in the methods, the variable domains amplified from heavy-chain-only antibodies were cloned into the phage display vector pECAN 21 and the ligated vectors were subsequently transformed into E. coli through electroporation. Twenty colonies were randomly picked from the plates and sequenced. Approximately 90%, 18 out of 20 clones, had unique and full length sequences. In addition, the library was subject to deep sequencing and ~ 1,180,000 sequences were recovered. A random sample of 100 sequences were checked for copy number and of these, 93% were present in the library as a single copy. Library size was estimated using the number of transformants in combination with the percentage of unique sequences. From this calculation it was estimated that the constructed EBOV GP immune phage display library contained 1.8 × 107 unique representatives, a large enough collection of variable domains for subsequent rounds of biopanning and selection.
For each round of biopanning, we used approximately 5 × 1011 phage to ensure multiple copies of each sdAb sequence were included. Three rounds of panning were performed and resulted in 10- and 24-fold enrichment in phage titers relative to the respective previous rounds, round 2 (R2) and round 3 (R3), as indicated in Additional file 1: Figure S1. Approximately 198 colonies from R2 and R3 were subjected to monoclonal phage ELISA (data not shown). Forty clones with absorbance ratios (EBOV GP/BSA) between 4 and 80 were sequenced; the thirty-four unique sequences were grouped into sequence families based on CDR homology and are shown in Additional file 1: Figure S2.
Characterization of initially selected sdAb
Binding affinity and melting temperature (Tm) for EBOV GP binding sdAb
We examined the ability of the 10 selected binders to bind immobilized GP. The on-rate and off-rate (ka and kd respectively) were measured using the ProteOn XPR36, a surface plasmon resonance (SPR) based biosensor (Additional file 1: Figure S3; Table 1) and the dissociation constant (KD) determined for each putative GP binder. Measurements were performed in duplicate and standard deviations from the calculated curve fit were obtained. EBOV-GP-A8 has the slowest off rate, which results in one of the lowest KD values among the GP sdAbs, displaying ~ 2 nM affinity. Another GP sdAb, EBOV-GP-G6 also exhibited ~ 2 nM affinity for EBOV GP. Clones EBOV-GP-G3 and EBOV-GP-G11, both belonging to the same sequence family, failed to bind GP in these experiments. The other sdAbs had KD values ranging from 11 to 34 nM. The two clones that showed no binding are part of a sequence family that contained five representatives identified through monoclonal phage ELISA. Differences in antigens attached versus adsorbed to a surface can affect the availability of binding sites. Thus it seems more likely that their epitope on GP is obscured during the covalent immobilization process as opposed to being false positives. Using SPR binding competition for GP, it was observed that EBOV-GP-A8 competed with EBOV-GP-G6, EBOV-GP-H7, EBOV-GP-D1, EBOV-GP-B5, and EBOV-GP-B11; but did not show competition with EBOV-GP-E7 or EBOV-GP-C12 (Additional file 1: Figure S5).
Sequence modifications of three GP binding sdAbs
The two sdAbs with the best binding characteristics, EBOV-GP-A8 and EBOV-GP-G6 along with the sdAb with the highest Tm, EBOV-GP-H7, were selected for sequence modification to improve their thermal stability. Our approach to thermal stabilization is to utilize a process that combines a number of strategies including addition of a disulfide bond and point mutations, to achieve the end result of a construct with an improved Tm. We use the IMGT numbering scheme  to indicate specific positions within each sdAb. The antigen receptor numbering and receptor classification tool  was used to number amino acid sequences of the sdAbs and a table of position number and corresponding amino acid for clones EBOV-GP-A8, EBOV-GP-H7 and EBOV-GP-G6 is shown as Additional file 1: Figure S4.
A non-canonical disulfide bond was added to the three sdAbs by incorporating two Cys within FR2 and FR3 at positions 54 and 78 respectively. Previous studies showed that the introduction of a disulfide bond at this location significantly increases Tm, with gains of 4–19 °C and can also increase the proteolytic stability of sdAbs [26–31].
Description of sdAbs and variants
Description of mutations
Disulfide addition: A54C, I78C
FR1 changes: Q5V, A6E
Disulfide addition: A54C, I78C
FR1 changes: Q5V, A6E
Disulfide addition: A54C, I78C
FR1 changes: Q5V, A6E, A13V, G17D
Disulfide addition: A54C, I78C
FR1 changes: Q5V, A6E, A13V, G17D
Unpaired Cys mutated: C106S
The site directed mutagenesis was guided by sequences of sdAbs with high Tms. Previously, we had shown that the introduction of the sequence VE at positions 5 and 6 of an sdAb in combination with 1E or D, and 3Q could lead to an increase in Tm of 5–9 °C [32, 33]. Other researchers examined a large repertoire of sdAb sequences and identified the changes 1E and 5V as stabilizing . Also, prior studies have shown that the addition of negative charges can increase thermal stability and solubility of sdAbs [35, 36].
When examining the sequences of the sdAbs we had noted that EBOV-GP-A8, and its whole sequence family contained an unpaired Cys within FR3. We constructed clone EBOV-GP-A8-fneg+ containing the Cys substitutions at positions 54 and 78 plus the negative changes in FR1 with the additional change, C106S, to eliminate the unpaired non-canonical Cys, which might form an inter-molecular disulfide bridge. Previously, we as well as other researchers have eliminated unpaired Cys within sdAbs with the resulting variants retaining the binding ability of the parental sdAb [37, 38].
We also incorporated a modification of the sdAbs designed to increase their performance in assays. A positively charged tail consisting of a linker and three lysine residues, termed GSKKK (or GS3K), and consisting of the sequence GGGGSGGGGKKK, was genetically fused to the C-terminus of the three sdAbs (Fig. 2d). We hypothesized the tail would serve to increase biotin incorporation or facilitate directional immobilize of the sdAbs.
Characterization of sdAb variants
Comparison of Tm, refolding and binding kinetics for EBOV GP binders and their derivatives
Binding affinity was measured using SPR and compared among parental sdAbs and mutants. Our results indicate that the binding affinity for EBOV-GP-G6-neg+ and -H7-neg+ is 2–5-fold worse than the respective parental sdAbs, while the EBOV-GP-A8-fneg+ has 5-fold better binding affinity than the parental A8 (Table 3). Disulfide bond addition has previously been found to negatively impact the binding affinity of some sdAbs as we observed for EBOV-GP-G6-neg+ and EBOV-GP-H7-neg+ , thus we were pleased that EBOV-GP-A8-neg+ and EBOV-GP-A8-fneg+ both possessed improved affinities relative to the parental EBOV-GP-A8. This difference would suggest that while we found these three sdAbs bind overlapping epitopes by SPR competition (Additional file 1: Figure S5), that their binding interactions with GP are not identical. We found no difference in binding affinity between GSKKK fusions and the neg+ mutants.
Detection of EBOV GP and VLPs
The sdAbs were examined by both sandwich and direct binding assays to determine their ability to bind to EBOV GP and VLPs. Both bead-based MagPlex assays as well as ELISAs were utilized in these experiments. A lysine-containing tail termed GSKKK (GGGGSGGGGKKK) was fused to the C-terminus of the sdAbs aiming to either increase biotin incorporation for use as the detection molecule or to enhance directional immobilization onto the surface to improve the percentage of active antibody attached, with the goal of improving the detection limits for GP/VLP (Fig. 2d) .
The addition of a positive tail was expected to facilitate the directional immobilization of sdAbs onto the negatively charged microsphere surface and thus improve the detection limits in that manner as well , unfortunately, we did not see the GSKKK fusion achieve this result. The cause of this is unclear, but perhaps the sdAb’s binding site on the GP is difficult for the surface immobilized sdAb to access efficiently.
Construction of genetically linked sdAbs (diabodies) has proven a helpful strategy to increase the usefulness of sdAbs [40–42]. Although competition experiments indicate that EBOV-GP-G6, EBOV-GP-H7 and EBOV-GP-A8 bind to the same or overlapping epitopes (Additional file 1: Figure S5), GP is a multimer in solution and on the VLP surface. Incorporating the isolated anti-EBOV GP sdAbs into linked constructs to form homodimers or heterodimers may improve their performance as captures and tracers in sandwich assays and is a strategy that can be investigated in the future.
Cross-reactivity analysis of sdAbs and mutants
The binding of GPs from denatured VLPs, including EBOV, SUDV, MARV, and purified recombinant GPs from EBOV and MARV by the GP sdAb mutants was assessed using western blotting analysis. EBOV-GP-A8-fneg+, EBOV-GP-G6-neg+ and EBOV-GP-H7-neg+ and their GSKKK fusions all bound to GP from denatured EBOV VLPs and recombinant EBOV GP, but not in SUDV VLPs, MARV VLPs or recombinant MARV GP (Additional file 1: Figure S6 and unpublished data).
Although cross-reactive mAbs against conserved GP epitopes among five Ebola virus species were developed , we do not see cross-reactivity of the selected EBOV GP binding sdAbs to SUDV or MARV VLPs using western blot analysis. It is likely that the selected EBOV GP sdAbs bind to an epitope only on EBOV GP (Additional file 1: Figure S6). Polyclonal antibodies against EBOV VLPs show that GPs from denatured VLPs appear as multiple bands due to the extent of glycosylation with sizes that are between 62 and 110 kDa. The recombinant GP exhibits a similar profile except that fewer bands were obtained, with sizes between 60 and 70 kDa on western blots using commercial mouse anti-GP antibody. Our results suggest that the selected GP binders bind preferentially to less glycosylated GP bands with the sizes of 60 and 70 kDa from VLPs, however they also bind the heavily glycosylated GPs with the size more than 100 kDa in purified recombinant GP (Additional file 1: Figure S6).
We prepared an immune phage display library from llamas immunized with killed EBOV and recombinantly produced EBOV GP, and successfully selected sdAbs that bind recombinant EBOV GP with ~ nM binding affinity. These sdAbs also bind to EBOV VLPs specifically. We incorporated changes including a non-canonical disulfide bond and negative charges in FR1 which resulted in Tm increases of at least 15 °C. The elimination of the unpaired non-canonical Cys106 in EBOV-GP-A8-fneg+ dramatically restored its refolding ability, going from 0 to 66%. In addition, the fusion of a C-terminal GSKKK tail increased the detection signals for EBOV VLP/GP approximately 2–25-fold relative to the parental clone when serving as a tracer antibody. We postulate that EBOV-GP-A8-fneg+-GSKKK with a sub-nM affinity to GP, 74 °C Tm and the best VLP binding ability is a prime candidate for further evaluation to determine its utility in diagnostic or therapeutic applications for EBOV.
Antibodies, antigens and reagents
The mouse mAb 4F3 and human mAb KZ52 both recognize EBOV GP and were from IBT Bioservices (Gaithersburg, MD). Recombinant GP without transmembrane domain (from EBOV and Marburg virus) as well as the EBOV, SUDV, and Marburg VLPs used in the western blotting experiment were also from IBT Bioservices. Killed EBOV was acquired from the (now defunct) Critical Reagents Program. In addition, the following reagent was obtained through BEI Resources, NIAID, NIH: Zaire Ebola virus Mayinga, Gamma-Irradiated, NR-31807.
Most reagents were purchased from Sigma-Aldrich (St Louis, MO), VWR, or Thermo Fisher Scientific. Enzymes and cloning reagents were purchased from New England Biolab (Ipswich, MA) unless specified.
Immunization and construction of phage display library
A llama was immunized 5 times, 14 days apart, with 100 μg killed EBOV from the Department of Defense Critical Reagents Program followed 21 days later by one immunization of killed EBOV from BEI Resources and finally 14 days later boosting the animal twice (14 days apart) with recombinant EBOV GP. Peripheral blood lymphocytes in the buffy coat were isolated using a Ficoll separation method and the total RNA was isolated using QIAamp RNA Blood Mini kit (Qiagen Inc, Valencia, CA) according to manufacturer’s protocol. cDNA was obtained by reverse transcribing the total RNA using superscript RTIII and oligo-dT (both from Life Technologies, Grand Island, NY) according to manufacturer’s protocol. The heavy chain variable domain fragments were amplified from PCR reaction using degenerated primers  and our previously published modified protocol .
The immune library derived from a llama immunized with killed EBOV and recombinant GP was obtained by cloning the amplified variable domain fragments into the phage display vector, pECAN21 [7, 8]. Gel purified variable domain PCR fragments and pECAN21 DNA cut with SfiI (New England Biolab Inc, Ipswich, MA) were ligated overnight at 15 °C with a 3:1 ratio of insert to vector. The ligation mixture was then transformed to XL1 Blue cells (Agilent Technologies Inc, Clara, CA) using electroporation. Phage displaying sdAbs were prepared from the library according to the previous protocol . Representative clones were sequenced to assess the library quality and diversity. Library sequencing was performed by Eurofins Genomics and analysis of the library sequences was as previously described .
Biopanning, selection and sequence analysis of EBOV GP potential binders
Panning was carried out using a procedure similar to previous work [7, 45]. The recombinant GP at the concentration of 10 µg/mL was coated onto 4 wells of a 96-well plate at 4 °C overnight. The coated wells were then washed with PBS supplemented with 0.05% Tween 20 (PBST) and incubated with phage displaying sdAbs amplified from immunized phage display library. Following extensively washing wells with PBST and PBS, the binding phages were then eluted by 100 mM triethylamine, which was subsequently neutralized by adding 1 M Tri–HCl, pH 8.0. The eluted phage titer was determined by infecting the log phase XL1 Blue and referred to as R1 eluted phage. The eluted phage were also grown and replicated in XL1 blue to obtain higher titer of amplified phage, which was referred as R1 amplified phage. R1 amplified phage were then used to repeat the above panning procedure once to obtain R2 eluted phage and R2 amplified phage, and twice to obtain R3 eluted phage and R3 amplified phage. Bacterial colonies were obtained by infecting XL1 blue with R2 and R3 eluted phage and individual colonies were inoculated into wells in a 96-well plate. Approximately 198 colonies were grown to conduct monoclonal phage ELISA. Binding was assessed using the target GP as well as an irrelevant antigen (BSA). Colonies giving a higher absorbance at 450 nm on the target versus irrelevant antigen were selected and grown for plasmid purification. Plasmid DNA was sent out for sequencing (Eurofins Genomics, Louisville, KY). Amino acid sequences were obtained and aligned using multalin (http://multalin.toulouse.inra.fr/multalin/) to compare the variations in the complementarity determine regions (CDRs) .
Expression and purification of potential binders
Representative sdAb genes from each sequence family were subcloned into a periplasmic expression vector, pET22b, for protein preparation and transformed into Turner (DE3) E. coli strain (EMD Millipore, Billerica, MA). The expression and purification procedure was performed according to the previously published protocol [48, 49]. Following IMAC extraction, sdAbs were further purified from other protein contaminates or aggregates through gel filtration chromatography using a Superdex 75 10/300 GL column (GE Healthcare) on a BioLogic DuoFLow chromatography system (Bio-Rad). Monomeric sdAb concentration was determined using BCA protein kit (Pierce) or a NanoDrop 1000 instrument.
Modification of GP binders
DNA fragments encoding modified amino acid sequences were synthesized by Eurofins Genomics and later subcloned into pET22b expression vector for further expression and purification. To construct sdAb-GSKKK fusion, NcoI-NotI SdAb fragments were ligated into GSKKK-pET22b plasmids cut with NcoI and NotI. The sequences were verified by Sanger sequencing and transformed into Tuner (DE3). Sequence modified proteins and fusions were subsequently purified according to the above section.
Measurement of Tm by circular dichroism (CD) and fluorescent dye melt assay
Protein samples were diluted to 22 µg/mL in deionized water and placed in a quartz cuvette with 1 cm path length. CD was measured at an ultraviolet wavelength between 200 and 210 nm using a Jasco J-815 Spectropolarimeter. Samples were heated from 25 to 95 °C at a rate of 2.5 °C/min. A cooling stage at the same rate was used to assay the amount of refolding after denaturation. The Tm is taken to be the inflection point of the S-shaped denaturation curve. The refolding ability is calculated as the change in CD magnitude upon cooling divided by the change in magnitude upon heating, expressed as a percentage.
The Fluorescent dye-based melting assay was performed as described previously . Each of the sdAbs was diluted to a concentration of 500 µg/mL in a final volume of 20 µL PBS and Sypro Orange dye was added a dilution of 1:1000. Samples were measured in triplicate using a StepOne Real-Time PCR machine (Applied Biosystems, Foster City, CA). The heating program was run in continuous mode from 25 to 99 °C at a heating rate of 1% (~ 2 °C/min), and data was recorded using the ROX filter. The melting point was determined to be the peak of the first derivative of the fluorescence intensity. Each measurement was performed in triplicate, all three replicates giving essentially identical values for the melting temperature.
Surface plasmon resonance (SPR)
Surface plasmon resonance affinity and kinetics measurements were performed using the ProteOn XPR36 (Bio-Rad). Lanes of a general layer compact (GLC) chip were individually coated with GP or left uncoated initially and then coated with GP for additional tests. Immobilization of the proteins was performed using dilution to 20 µg/mL in 10 mM acetate buffer pH 5.0 and attached to the chip following the standard 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride (EDC)/N-hydroxysulfosuccinimide (sulfo-NHS) coupling chemistry available from the manufacturer. Binding kinetics of each sdAb was tested at 25 °C by flowing six concentrations typically varying from 3000 to 0 nM at 100 μL/min for 90 s over the antigen coated chip and then monitoring dissociation for 600 s. Following each run, the chip was regenerated by flowing 0.085% phosphoric acid (~ pH 3.0) across the surface for 18 s. Data analysis was performed with ProteOn Manager 2.1 software, corrected by subtraction of the zero antibody concentration column as well as interspot correction. The standard error on the fits was less than 10%. Binding constants were determined using the Langmuir model built into the analysis software. The competition experiments were performed by flowing EBOV-GP-A8 over three of the sensor chip’s six lanes to saturate those spots. Then three other sdAbs were flowed over two lanes each, one previous saturated with EBOV-GP-A8 and one unreacted. The amount of signal differential resulting is indicative of the amount of binding inhibition, see Additional file 1: Figure S5.
MagPlex sandwich immunoassays
MagPlex assays were performed essentially as described previously . Briefly, MagPlex beads were coated with the desired monoclonal Abs or sdAbs using the recommended two step EDC/sulfo-NHS chemistry. The biotin-labeled sdAbs (Bt-sdAbs) were prepared by using a 10-fold molar excess of NHS-LC-LC-biotin, after 30 min the excess biotin was removed using a Zeba spin 7 K desalting column (ThermoFisher). The protein-coated MagPlex beads (~ 100/set) were mixed with various concentrations of GP or EBOV VLPs diluted into PBSTB (PBS + 0.05% Tween (PBST) and 1 mg/mL bovine serum albumin (BSA)) in the wells of a 96-well polystyrene round bottom microtiter plate. After 30 min the beads were washed by placing the plate on a 96f magnet (BioTek, Winooski, VT) and washing three times with PBST. The beads were then incubated with the 1 µg/mL Bt-sdAb as indicated. After 30 min the beads were washed 3 times and then, to complete the fluorescent sandwich assay, the beads were incubated for 30 min with 2.5 µg/mL streptavidin conjugated phycoerythrin (SAPE, Columbia Biosciences, Frederick, MD). After a final wash, the binding was measured on the MAGPIX instrument (Luminex Corp., Austin, TX). The median value obtained by the evaluation of ≥ 50 microspheres for each set plotted, and error bars plotted as the standard error of the mean (SEM), which is typically less than ± 10% the mean.
Enzyme-linked immunosorbent assay (ELISA)
Mouse monoclonal Ab, 4F3 was coated onto wells in a 96-well plate at the concentration of 2 µg/mL at 4 °C overnight. Next day, wells were washed with 3× PBST and blocked with PBST supplemented with 2% milk powder (2% MPBST) at room temperature (RT) for 1 h, followed by the addition of EBOV VLP at various concentrations of 2, 5, 10, 20, and 40 µg/mL at RT for 1 h. Bt-sdAbs were then subsequently added onto wells at the concentration of 2 µg/mL at RT for 1 h after washing wells with PBST and PBS. Horseradish peroxidase (HRP) conjugated Streptavidin was then added into wells at the concentration of 1 µg/mL at RT for 1 h. Peroxidase substrate, SureBlue TMB-1 component (KPL, Gaithersburg, MD) was added to each well and the reaction was stopped by the addition of 1 M HCl according to the manufacturer’s protocol before measuring the absorbance at 450 nm.
Approximately 5 µg of EBOV VLP containing GP, NP and VP40 (IBT Bioservices, Gaithersburg, MD) and 5 μg of EBOV rGPdTM in 15 µL of 1× LDS sample buffer supplemented with 1× reducing agent was loaded onto pre-casted 4–12% BIS–TRIS NuPAGE gel in 1× MES-SDS running buffer, followed by applying electric current through the gel to separate the proteins by size. SeeBlue plus 2 prestained standard was loaded in separate lane as a size marker. Following the manufacturer’s protocol, separated proteins on the gel were then transferred to a PVDF membrane on ice. The blot was then washed with 1× TBST (10 mM Tris pH 7.5, 150 mM NaCl and 0.01% Tween 20), and was subsequently blocked with 5% milk in 1× TBST (TBSTM) at room temperature (RT) for 1 h. Approximately 1–5 µg/mL of primary antibody was then added to the blot at RT for 1 h before washing with TBSTM for 15 min three times. Horseradish peroxidase conjugated secondary antibody at a concentration of 1–2 µg/mL was then added onto the blot at RT for 1 h, followed by washing with TBST for 15 min three times. The luminescent substrate was then applied to the blot and incubated for 5 min and the images were captured by using a GEL doc XR + system.
JL designed, performed the experiments and wrote the manuscript; DZ and LCSL performed the experiments and edited the manuscript; EG designed and performed the experiments and edited the manuscript; GA designed and performed the experiments and wrote the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Availability of data and materials
All data generated or analyzed during this study are included in this published article and its additional files are available from the corresponding author on reasonable request.
Consent for publication
Ethics approval and consent to participate
This work was funded by the Joint Science and Technology Office and DTRA J9 Chemical and Biological Technologies Department, Project Number HDTRA1518114 and ONR/NRL Base Funding, WU# MA-236-018-6703.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
- Hamers-Casterman C, Atarhouch T, Muyldermans S, Robinson G, Hamers C, Songa EB, Bendahman N, Hamers R. Naturally occurring antibodies devoid of light chains. Nature. 1993;363:446–8.View ArticleGoogle Scholar
- Greenberg AS, Avila D, Hughes M, Hughes A, McKinney EC, Flajnik MF. A new antigen receptor gene family that undergoes rearrangement and extensive somatic diversification in sharks. Nature. 1995;374:168–73.View ArticleGoogle Scholar
- Arbabi Ghahroudi M, Desmyter A, Wyns L, Hamers R, Muyldermans S. Selection and identification of single domain antibody fragments from camel heavy-chain antibodies. FEBS Lett. 1997;414:521–6.View ArticleGoogle Scholar
- Nuttall SD, Krishnan UV, Doughty L, Nathanielsz A, Ally N, Pike RN, Hudson PJ, Kortt AA, Irving RA. A naturally occurring NAR variable domain binds the Kgp protease from Porphyromonas gingivalis. FEBS Lett. 2002;516:80–6.View ArticleGoogle Scholar
- Dooley H, Flajnik MF, Porter AJ. Selection and characterization of naturally occurring single-domain (IgNAR) antibody fragments from immunized sharks by phage display. Mol Immunol. 2003;40:25–33.View ArticleGoogle Scholar
- Wesolowski J, Alzogaray V, Reyelt J, Unger M, Juarez K, Urrutia M, Cauerhff A, Danquah W, Rissiek B, Scheuplein F, et al. Single domain antibodies: promising experimental and therapeutic tools in infection and immunity. Med Microbiol Immunol. 2009;198:157–74.View ArticleGoogle Scholar
- Goldman ER, Anderson GP, Liu JL, Delehanty JB, Sherwood LJ, Osborn LE, Cummins LB, Hayhurst A. Facile generation of heat-stable antiviral and antitoxin single domain antibodies from a semisynthetic llama library. Anal Chem. 2006;78:8245–55.View ArticleGoogle Scholar
- Liu JL, Anderson GP, Delehanty JB, Baumann R, Hayhurst A, Goldman ER. Selection of cholera toxin specific IgNAR single-domain antibodies from a naive shark library. Mol Immunol. 2007;44:1775–83.View ArticleGoogle Scholar
- Muyldermans S. Nanobodies: natural single-domain antibodies. In annual review of biochemistry, vol. 82. Palo Alto: Annual Reviews; 2013. p. 775–97.Google Scholar
- Goldman ER, Liu JL, Zabetakis D, Anderson GP. Enhancing stability of camelid and shark single domain antibodies: an overview. Front Immunol. 2017;8:865.View ArticleGoogle Scholar
- de Marco A. Biotechnological applications of recombinant single-domain antibody fragments. Microb Cell Fact. 2011;10:44.View ArticleGoogle Scholar
- Eyer L, Hruska K. Single-domain antibody fragments derived from heavy-chain antibodies: a review. Vet Med. 2012;57:439–513.Google Scholar
- Towner JS, Rollin PE, Bausch DG, Sanchez A, Crary SM, Vincent M, Lee WF, Spiropoulou CF, Ksiazek TG, Lukwiya M, et al. Rapid diagnosis of Ebola hemorrhagic fever by reverse transcription-PCR in an outbreak setting and assessment of patient viral load as a predictor of outcome. J Virol. 2004;78:4330–41.View ArticleGoogle Scholar
- Rewar S, Mirdha D. Transmission of Ebola virus disease: an overview. Ann Glob Health. 2014;80:444–51.View ArticleGoogle Scholar
- Volchkov VE. Processing of the Ebola virus glycoprotein. Curr Top Microbiol Immunol. 1999;235:35–47.Google Scholar
- Volchkova VA, Klenk HD, Volchkov VE. Delta-peptide is the carboxy-terminal cleavage fragment of the nonstructural small glycoprotein sGP of Ebola virus. Virology. 1999;265:164–71.View ArticleGoogle Scholar
- Takada A, Kawaoka Y. The pathogenesis of Ebola hemorrhagic fever. Trends Microbiol. 2001;9:506–11.View ArticleGoogle Scholar
- Volchkov VE, Feldmann H, Volchkova VA, Klenk HD. Processing of the Ebola virus glycoprotein by the proprotein convertase furin. Proc Natl Acad Sci USA. 1998;95:5762–7.View ArticleGoogle Scholar
- Frei JC, Nyakatura EK, Zak SE, Bakken RR, Chandran K, Dye JM, Lai JR. Bispecific antibody affords complete post-exposure protection of mice from both Ebola (Zaire) and Sudan viruses. Sci Rep. 2016;6:19193.View ArticleGoogle Scholar
- Qiu X, Alimonti JB, Melito PL, Fernando L, Stroher U, Jones SM. Characterization of Zaire ebolavirus glycoprotein-specific monoclonal antibodies. Clin Immunol. 2011;141:218–27.View ArticleGoogle Scholar
- Lee JE, Fusco ML, Hessell AJ, Oswald WB, Burton DR, Saphire EO. Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor. Nature. 2008;454:177–82.View ArticleGoogle Scholar
- Sherwood LJ, Hayhurst A. Ebola virus nucleoprotein C-termini potently attract single domain antibodies enabling monoclonal affinity reagent sandwich assay (MARSA) formulation. PLoS ONE. 2013;8:e61232.View ArticleGoogle Scholar
- Goodchild SA, Dooley H, Schoepp RJ, Flajnik M, Lonsdale SG. Isolation and characterisation of Ebola virus-specific recombinant antibody fragments from murine and shark immune libraries. Mol Immunol. 2011;48:2027–37.View ArticleGoogle Scholar
- Lefranc MP, Pommie C, Ruiz M, Giudicelli V, Foulquier E, Truong L, Thouvenin-Contet V, Lefranc G. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev Comp Immunol. 2003;27:55–77.View ArticleGoogle Scholar
- Dunbar J, Deane CM. ANARCI: antigen receptor numbering and receptor classification. Bioinformatics. 2015;32:298–300.Google Scholar
- Hagihara Y, Mine S, Uegaki K. Stabilization of an immunoglobulin fold domain by an engineered disulfide bond at the buried hydrophobic region. J Biol Chem. 2007;282:36489–95.View ArticleGoogle Scholar
- Saerens D, Conrath K, Govaert J, Muyldermans S. Disulfide bond introduction for general stabilization of immunoglobulin heavy-chain variable domains. J Mol Biol. 2008;377:478–88.View ArticleGoogle Scholar
- Hussack G, Riazi A, Ryan S, van Faassen H, MacKenzie R, Tanha J, Arbabi-Ghahroudi M. Protease-resistant single-domain antibodies inhibit Campylobacter jejuni motility. Protein Eng Des Sel. 2014;27:191–8.View ArticleGoogle Scholar
- Hussack G, Hirama T, Ding W, MacKenzie R, Tanha J. Engineered single-domain antibodies with high protease resistance and thermal stability. PLoS ONE. 2011;6:e28218.View ArticleGoogle Scholar
- Shriver-Lake LC, Goldman ER, Zabetakis D, Anderson GP. Improved production of single domain antibodies with two disulfide bonds by co-expression of chaperone proteins in the Escherichia coli periplasm. J Immunol Methods. 2017;443:64–7.View ArticleGoogle Scholar
- Chan P-H, Pardon E, Menzer L, De Genst E, Kumita JR, Christodoulou J, Saerens D, Brans A, Bouillenne F, Archer DB, et al. Engineering a camelid antibody fragment that binds to the active site of human lysozyme and inhibits its conversion into amyloid fibrils. Biochemistry. 2008;47:11041–54.View ArticleGoogle Scholar
- Shriver-Lake LC, Zabetakis D, Goldman ER, Anderson GP. Evaluation of anti-botulinum neurotoxin single domain antibodies with additional optimization for improved production and stability. Toxicon. 2017;135:51–8.View ArticleGoogle Scholar
- Liu JL, Goldman ER, Zabetakis D, Walper SA, Turner KB, Shriver-Lake LC, Anderson GP. Enhanced production of a single domain antibody with an engineered stabilizing extra disulfide bond. Microb Cell Fact. 2015;14:158.View ArticleGoogle Scholar
- Kunz P, Flock T, Soler N, Zaiss M, Vincke C, Sterckx Y, Kastelic D, Muyldermans S, Hoheisel JD. Exploiting sequence and stability information for directing nanobody stability engineering. Biochimica et Biophysica Acta (BBA)-General Subjects. 2017;1861:2196–205.View ArticleGoogle Scholar
- Dolk E, van der Vaart M, Hulsik DL, Vriend G, de Haard H, Spinelli S, Cambillau C, Frenken L, Verrips T. Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo. Appl Environ Microbiol. 2005;71:442–50.View ArticleGoogle Scholar
- Turner KB, Zabetakis D, Goldman ER, Anderson GP. Enhanced stabilization of a stable single domain antibody for SEB toxin by random mutagenesis and stringent selection. Protein Eng Des Sel. 2014;27:89–95.View ArticleGoogle Scholar
- Turner KB, Liu JL, Zabetakis D, Lee AB, Anderson GP, Goldman ER. Improving the biophysical properties of anti-ricin single-domain antibodies. Biotechnol Rep. 2015;6:27–35.View ArticleGoogle Scholar
- Ben Abderrazek R, Vincke C, Hmila I, Saerens D, Abidi N, El Ayeb M, Muyldermans S, Bouhaouala-Zahar B. Development of Cys38 knock-out and humanized version of NbAahII10 nanobody with improved neutralization of AahII scorpion toxin. Protein Eng Des Sel. 2011;24:727–35.View ArticleGoogle Scholar
- Raphael MP, Christodoulides JA, Byers JM, Anderson GP, Liu JL, Turner KB, Goldman ER, Delehanty JB. Optimizing nanoplasmonic biosensor sensitivity with orientated single domain antibodies. Plasmonics. 2015;10:1649–55.View ArticleGoogle Scholar
- Conrath KE, Lauwereys M, Wyns L, Muyldermans S. Camel single-domain antibodies as modular building units in bispecific and bivalent antibody constructs. J Biol Chem. 2001;276:7346–50.View ArticleGoogle Scholar
- Glaven RH, Anderson GP, Zabetakis D, Liu JL, Long NC, Goldman ER. Linking single domain antibodies that recognize different epitopes on the same target. Biosensors. 2012;2:43.View ArticleGoogle Scholar
- Hultberg A, Temperton NJ, Rosseels V, Koenders M, Gonzalez-Pajuelo M, Schepens B, Ibanez LI, Vanlandschoot P, Schillemans J, Saunders M, et al. Llama-derived single domain antibodies to build multivalent, superpotent and broadened neutralizing anti-viral molecules. PLoS ONE. 2011;6:e17665.View ArticleGoogle Scholar
- Hernandez H, Marceau C, Halliday H, Callison J, Borisevich V, Escaffre O, Creech J, Feldmann H, Rockx B. Development and characterization of broadly cross-reactive monoclonal antibodies against all known Ebolavirus species. J Infect Dis. 2015;212(Suppl 2):S410–3.View ArticleGoogle Scholar
- Vu KB, Ghahroudi MA, Wyns L, Muyldermans S. Comparison of llama VH sequences from conventional and heavy chain antibodies. Mol Immunol. 1997;34:1121–31.View ArticleGoogle Scholar
- Liu JL, Zabetakis D, Goldman ER, Anderson GP. Selection and evaluation of single domain antibodies toward MS2 phage and coat protein. Mol Immunol. 2013;53:118–25.View ArticleGoogle Scholar
- Turner KB, Naciri J, Liu JL, Anderson GP, Goldman ER, Zabetakis D. Next-generation sequencing of a single domain antibody repertoire reveals quality of phage display selected candidates. PLoS ONE. 2016;11:e0149393.View ArticleGoogle Scholar
- Corpet F. Multiple sequence alignment with hierarchical-clustering. Nucleic Acids Res. 1988;16:10881–90.View ArticleGoogle Scholar
- Conway JO, Sherwood LJ, Collazo MT, Garza JA, Hayhurst A. Llama single domain antibodies specific for the 7 botulinum neurotoxin serotypes as heptaplex immunoreagents. PLoS ONE. 2010;5:e8818.View ArticleGoogle Scholar
- Goldman ER, Brozozog-Lee PA, Zabetakis D, Turner KB, Walper SA, Liu JL, Anderson GP. Negative tail fusions can improve ruggedness of single domain antibodies. Protein Expr Purif. 2014;95:226–32.View ArticleGoogle Scholar
- Duhoo Y, Roche J, Trinh TTN, Desmyter A, Gaubert A, Kellenberger C, Cambillau C, Roussel A, Leone P. Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis. Acta Crystallogr Sect F. 2017;73:286–93.View ArticleGoogle Scholar