PEDS Advance Access originally published online on September 13, 2006
Protein Engineering Design and Selection 2006 19(11):503-509; doi:10.1093/protein/gzl037
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Improving solubility and refolding efficiency of human VHs by a novel mutational approach
1 Institute for Biological Sciences, National Research Council of Canada Ottawa, Ontario, Canada K1A 0R6 2 Biotechnology Research Institute, National Research Council of Canada Montréal, Québec, Canada H4P 2R2
3To whom correspondence should be addressed. E-mail: jamshid.tanha{at}nrc-cnrc.gc.ca
| Abstract |
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The antibody VH domains of camelids tend to be soluble and to resist aggregation, in contrast to human VH domains. For immunotherapy, attempts have therefore been made to improve the properties of human VHs by camelization of a small set of framework residues. Here, we have identified through sequence comparison of well-folded llama VH domains an alternative set of residues (not typically camelid) for mutation. Thus, the solubility and thermal refolding efficiency of a typical human VH, derived from the human antibody BT32/A6, were improved by introduction of two mutations in framework region (FR) 1 and 4 to generate BT32/A6.L1. Three more mutations in FR3 of BT32/A6.L1 further improved the thermal refolding efficiency while retaining solubility and cooperative melting profiles. To demonstrate practical utility, BT32/A6.L1 was used to construct a phage display library from which were isolated human VHs with good antigen binding activity and solubility. The engineered human VH domains described here may be useful for immunotherapy, due to their expected low immunogenicity, and in applications involving transient high temperatures, due to their efficient refolding after thermal denaturation.
Keywords: human VH/immunogenicity/mutation/phage display library/solubility and refolding
| Introduction |
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Although the utility of VHs (i.e. IgG heavy chain variable domains) as recombinant antibodies was demonstrated in 1989 (Ward et al., 1989
Camelization involving mutation of the residues at positions 44, 45 and 47 in human VHs to those commonly found in VHHs has generated soluble human VH proteins (Davies and Riechmann, 1994
; Tanha et al., 2001
). This strategy, however, does not always result in soluble VHs (Martin et al., 1997
; Voordijk et al., 2000
) and it is becoming clear that residues at other positions and in the CDR3 sequence also play a role in VH/VHH solubility (Spinelli et al., 1996
; Reiter et al., 1999
; Tanha et al., 2002
; Vranken et al., 2002
; Dottorini et al., 2004
). In addition, it is not known whether camelization would also generate VHs with good thermal refolding efficiencies. Such refoldable VHs would have high efficacy in settings where they experience transient denaturing temperatures (Holt et al., 2003
).
We recently showed that several VHs, derived from llama IgGs, had characteristics associated with camelid VHHs in that they were highly soluble and demonstrated reversible thermal denaturation, despite the absence of camelid residues at positions 37, 44, 45 and 47 (Tanha et al., 2002
; Vranken et al., 2002
) or a W103R mutation (Conrath et al., 2001
). Based on framework region (FR) sequence comparison of these VHs and the human VH3 family consensus sequence (Riechmann and Muyldermans, 1999
), to which the llama VHs had showed the highest sequence homology, five amino acid substitutions, E6A (primer-forced mutation), S74A, R83K, A84P and L108Q, were proposed to be responsible for the high solubility and refolding efficiency of these llama VHs. Here we show that VH mutations, involving the above five substitutions, can be used to create human VH proteins with improved solubility and thermal refolding efficiency and good antigen-binding activity.
| Materials and methods |
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Construction of BT32/A6.L1 and BT32/A6.L2 VHs
Standard PCR, which utilized mutagenic primers, was employed to construct BT32/A6.L1 and BT32/A6.L2 from the human antibody BT32/A6 (Tanha et al., 2001
). BT32/A6.L1 has five mutations with respect to BT32/A6 (S23A, S82aN, V93A, E6A, T108Q) and BT32/A6.L2 has three additional mutations with respect to BT32/A6.L1 (S74A, R83K, A84P) (Figure 1). The mutants were cloned in pSJF2 expression plasmid (Tanha et al., 2003
), followed by transformation of Escherichia coli strain TG1 using standard cloning techniques (Sambrook et al., 1989
). Clones harboring the BT32/A6.L1 and BT32/A6.L2 genes were identified by PCR and DNA sequencing.
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Library construction and panning
To construct the BT32/A6 library, the BT32/A6 gene was used as the template in PCR to amplify a shorter fragment using FR1- and FR3-specific primers. The product was gel purified using the QIAquick Gel ExtractionTM kit (QIAGEN Inc., Mississauga, ON, Canada) and extended by PCR using the FR1-specific and 5'-GCCCCAGATATCAAA[(A/C)NN]20TTTCACACAGTAATA-3' primers. The resultant PCR fragments with randomized CDR3s were purified using the QIAquick PCR PurificationTM kit (QIAGEN Inc.) and the full-length VH genes were constructed by PCR using the FR1-specific primer and a primer that added the FR4 codons. In the case of the BT32/A6.L1 library, the BT32/A6.L1 gene was used as the initial template, and CDR3 was randomized using the primer 5'-CCCTTGGCCCCAGATATCAAA[(A/C)NN]6GTAATAACCACTACTATC-3'. Cloning of the library VH genes in a phage vector, transformation, library size determination, and phage propagation and purification were performed as described (Tanha et al., 2002
). The integrity of the library was confirmed by batch sequencing of VH genes. Panning and subsequent screening of the phage clones by enzyme-linked immunosorbent assays (ELISA) and DNA sequencing were performed as described (Tanha et al., 2002
). For panning with human alpha-thrombin, the thrombin active site was blocked with an excess amount of D-Phe-Pro-Arg-CH2Cl (PPACK) (Calbiochem, Mississauga, ON, Canada). Specific elution of phages that bound to the fibrinogen-recognition site of thrombin was carried out by competitive binding with the hirudin-derived peptide hirudin5465 at 1 mM concentration (Bachem, King of Prussia, PA). Subcloning of the VH fragments from the phage vector into pSJF2 expression plasmid for expression purposes was performed as described (Tanha et al., 2003
).
Protein analyses
VHs were expressed and purified (Tanha et al., 2001
) and their concentrations were determined by OD280 measurements using molar absorption coefficients calculated for each protein (Pace et al., 1995
). Gel filtration chromatography using a Superdex 75 column (GE Healthcare, Baie d'Urfè, QC, Canada) was performed as described (Deng et al., 1995
). Tms and thermal refolding efficiencies were determined by performing circular dichroism (CD) experiments using a Jasco J-600 spectropolarimeter that was connected to Neslab RTE-110 water bath. Tms were determined at a protein concentration of 2 µg/ml as described for PTH50 (Zhang et al., 2004
). Refolding experiments were performed in 10 mM sodium phosphate buffer pH 7.0 using circular cuvettes with 1 cm pathlengths. Spectra were recorded and processed as described for Tm measurements (Zhang et al., 2004
).
To determine the refolding efficiency, RE, protein samples were equilibrated at 30°C (native) then at 85°C (fully unfolded) for 20 min and the spectra were obtained in each instance. The samples were cooled to room temperature for 70 min, re-equilibrated to 30°C and the spectrum was obtained. The RE was calculated from
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The binding kinetics for the interaction of the purified FlagL1 VH to immobilized anti-FLAG M2 monoclonal antibody (Sigma Oakville, ON, Canada) were determined by surface plasmon resonance using a BIACORE 3000 biosensor system (Biacore, Inc., Piscataway, NJ). A total of 1900 resonance units of M2 and 598 resonance units of ovalbumin as a reference surface were immobilized on a research grade CM5 sensor chip (Biacore). Immobilizations were carried out at antigen concentrations of 20 µg/ml in 10 mM acetate buffer pH 4.5, using the amine coupling kit supplied by the manufacturer. FlagL1 was subjected to Superdex 75 size exclusion column chromatography to remove any trace of aggregates prior to the binding analysis. All measurements were carried out at 25°C in 10 mM HEPES buffer pH 7.4, containing 150 mM NaCl, 3 mM EDTA and 0.005% P20 at a flow rate of 40 µl/min. Surfaces were regenerated by washing with running buffer. Data were evaluated using the BIAsevaluation 4.1 software (Biacore, Inc).
Fibrinogen clotting assays
Fibrinogen clotting assays were performed with 0.1% bovine plasma fibrinogen (Sigma, Oakville, ON, Canada) in 50 mM TrisHCl, pH 7.6, 100 mM NaCl, 0.1% poly(ethylene glycol) 8000, at 37°C. Assay mixtures contained different concentrations of VH and were incubated at 37°C for 2 min. The reaction was initiated by the addition of human
-thrombin (Haematologic Technologies Inc., Essex Junction, VT) to a final concentration of 0.4 units/ml. Optical absorbance of the assay mixtures was monitored at 420 nm on a SpectroMax spectrophotometer to follow the progression of the clotting reaction.
NMR spectroscopy
15N-labeled VHs were produced in bacterial cultures grown in M9 medium containing 1.0 g/l of [15N]ammonium sulfate and 2.0 g/l of glucose, supplemented with 1 mM MgSO4, 0.15 mM CaCl2, 0.00005% vitamin B1 and 100 µg/ml ampicillin. Purified proteins were concentrated and exchanged into PBS buffer, pH 6.5 by ultrafiltration. Protein samples contained
0.08 mM of uniformly 15N-labeled protein and 10% D2O. NMR experiments were performed at 298 K on a Bruker Avance-500 NMR spectrometer equipped with a 5 mm triple-resonance CryoProbe. Two-dimensional 1H15N HSQC spectra were acquired using solvent suppression via the WATERGATE method (Sklenar et al., 1993
). NMR data were processed and analyzed using the Bruker XWINNMR software package. For HSQC titration experiments, aliquots of PPACK-thrombin at a concentration of 3.5 mg/ml were added to the VH protein samples.
| Results |
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It was recently shown that a set of llama VHs demonstrated high solubility and reversible thermal denaturation (Tanha et al., 2002
Solubility was assessed in terms of VH oligomerization state by size exclusion chromatography. Identical concentrations of BT32/A6, BT32/A6.L1 and BT32/A6.L2 were analyzed. The results clearly show that the mutations significantly decreased the aggregation of BT32/A6 (Figure 2a). Compared to the wild type, BT32/A6.L1 and BT32/A6.L2 exist primarily as monomeric proteins and the multimeric and aggregated forms observed with BT32/A6 are absent or present in much reduced amounts. For the wild-type VH, the monomer fraction is 51.3% of the total protein, while for BT32/A6.L1 and BT32/A6.L2 the monomeric fractions increase to 87 and 90%, respectively. Compared to BT32/A6.L1, BT32/A6.L2 contained less aggregated material, indicating that the three additional mutations in BT32/A6.L2 further improved VH solubility. On a non-reducing SDSPAGE, all three VHs ran as single bands with the same mobility expected for a monomer, demonstrating that aggregate formation was purely mediated by non-covalent interactions without any involvement of disulfide linkages (data not shown).
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The effect of the amino acid substitutions on the refolding efficiency and thermal stability of BT32/A6 was investigated by CD. As shown in Figure 2b, a clear stepwise increase in refolding efficiency with the addition of the BT32/A6.L1 and BT32/A6.L2 mutation sets was observed with the wild-type VH having the lowest value (13%), BT32/A6.L1 being intermediate (44%) and BT32/A6.L2 having the highest value (74%). As controls, BT32/A6.ERI, a camelized derivative of BT32/A6 with G44E/L45R/Y47I mutations (Figure 1), and PTH50, a llama VHH (Zhang et al., 2004
To assess its suitability as library scaffold, BT32/A6.L1 was used to construct a synthetic phage display library in which CDR3 residues were randomized. The choice of BT32/A6.L1 as opposed to BT32/A6.L2 as the library scaffold was based on the fact that while BT32/A6.L1 was not quite as soluble as BT32/A6.L2, it had fewer of its original residues replaced with non-human residues. Consequently, being more human and thus potentially less immunogenic, BT32/A6.L1 should be more favorable for immunotherapy. A reference library based on the BT32/A6 scaffold was also constructed. To assess the integrity of the libraries, colony PCR and DNA sequencing of the library clones were performed. In the instance of the BT32/A6 library, out of 36 colonies analyzed by PCR and agarose gel electrophoresis, 16 did not have insert, 5 had truncated inserts and 15 had full-length inserts with authentic open reading frames as determined by DNA sequencing. For the BT32/A6.L1 library, 38 out of the 40 colonies analyzed had complete VH sequences with 2 having no VH. After normalization for full-length VHs, the sizes of both libraries were determined to be 2.5 x 108.
In the case of the BT32/A6 library, up to four rounds of panning under different conditions were performed against two protein targets including anti-FLAG M2 a monoclonal antibody which recognizes the FLAG motif XYKXXD (Tanha et al., 2001
). For each target, PCRs on 150 colonies from various rounds showed enrichment for truncated VHs. The predominance of the truncated VHs over full-length VHs is thought to be due to their growth advantage. This predominance is further accentuated by the instability of the full-length VHs which compromises their functionality and hence selection during the binding steps of panning.
By contrast, the library based on BT32/A6.L1 was very stable as there was enrichment for full-length VH binders during panning against two single-chain antibodies H11 and Yst9.1 (Reilly et al., 2001
; Tanha et al., 2002
), M2 monoclonal antibody and human thrombin with a blocked active site. Following three rounds of panning against the two single-chain antibodies, more than 90% of the phage clones tested positive in phage ELISA. The binding, measured in terms of OD450, was 0.41.7 for the positive clones compared to 0.0300.040 for the phage clones displaying no VH. Batch sequencing revealed more than a dozen different VH binders in each instance with several VH sets having the same motif (Table I). For example, the sequence motif SRWSS/EG exists in the first four Yst9.1 binders and the sequence FSSP is part of the paratope of the first five H11 binders in Table I.
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In the case of M2, 12 different VH binders with the expected XYKXXD recognition motif were identified (Tanha et al., 2001
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In the case of thrombin, 64% (general elution) and 36% (specific elution) of the third round clones tested were positive in ELISA. Of the five different VH binders that were identified and subsequently expressed as soluble VHs, four were obtained by specific elution (Figure 4a, PEPC1-4). These had at least two acidic residues separated by bulky hydrophobic residues in their CDR3s, a sequence feature characteristic of protein cofactors or inhibitors targeting the fibrinogen-recognition exosite of thrombin (Rose and Di Cera, 2002
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| Discussion |
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Our work shows that the properties of a typical human VH domain (based on engineering consensus framework residues of the human antibody BT32/A6) can be transformed by two single mutations in each of FR1 and FR4. We thereby conferred on a human VH favorable properties typically associated with camelid VHHs, namely, good solubility and high thermal refolding efficiency. VHs with these properties are desirable in immunotherapeutics as homing agents to target disease molecules as well as in contexts involving transient denaturing temperatures. The gain in VH solubility was neither at the expense of expression yield, as both mutated VHs maintained a high level expression of the parent VH, nor at the expense of stability, as was shown by Tm measurements. In fact, the mutated VHs had slightly higher Tms than the wild-type VH. This is in sharp contrast to a previous example where VH solubilization by camelization was accompanied by a drastic decrease in Tm (Davies and Riechmann, 1996a
Our strategy may provide an alternative to camelization in instances in which camelization fails (Martin et al., 1997
; Voordijk et al., 2000
), and also provide stable VH scaffolds for synthetic protein libraries. Synthetic libraries constructed by randomizing one CDR are better suited as a source of peptidomimetics than camelid VHH libraries (Davies and Riechmann, 1996b
). Indeed, VH hits specific for human thrombin showed characteristic binding sequences common among many natural thrombin-binding proteins.
In the case of BT32/A6, BT32A6.L1 and BT32A6.L2, higher refolding efficiency appears to correlate with slight increases in Tm but this correlation does not hold true for the llama VHH which has the lowest Tm but has by far the highest refolding efficiency. This, as mentioned previously, is in agreement with the finding that the VHHs are characterized by high thermal refolding efficiencies but not always by high Tms (Ewert et al., 2002
). The mutations in BT32A6.L1 and BT32A6.L2 must have a stabilizing effect on the VH fold resulting in somewhat improved Tms. However, the dramatic increases in refolding efficiencies of the mutated VHs relative to BT32A6 suggest that, more importantly, the mutations must stabilize folding intermediates which lead to the native structure. It seems that for the llama VHH used in this study, by contrast, the residues resulting in high thermal refolding do not confer high Tms. Based on the finding that the mutated BT32/A6.ERI with camelid residues 44E, 45R and 47I had only a modest improvement in thermal refolding over BT32/A6 one may conclude that the camelid residues at the above-mentioned positions do not play a significant role in thermal refolding of VHHs. On the other hand, this may be a rather simplistic view of the situation since the camelid residues can improve the thermal refolding properties of some VHHs depending on the sequence context.
In conclusion, there appear to be several strategies for improving solubility and/or refolding characteristics. For example, mutations introduced into the CDRs have proved effective in increasing solubility (Jespers et al., 2004a
) and/or refolding (Jespers et al., 2004b
). Our work has shown that several FR residues (E6A, S74A, R83K, A84P and L108Q), identified earlier from a set of llama VHs (Tanha et al., 2002
) can confer high thermal refolding efficiencies on human VHs, and that a library comprising only two of these mutations (E6A and L108Q) can lead to the isolation of VH domains with excellent thermal refolding properties and antigen-binding activities.
| Acknowledgements |
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We thank Doris Bilous for oligonucleotide synthesis, Anna Cunningham and Joe Michniewicz for DNA sequencing and Tomoko Hirama for Biacore analysis. We thank Drs Darren Fast, Joycelyn Entwistle, Keith Lewis and Howard Kaplan for helpful discussions. We acknowledge the technical assistance of Ginette Dubuc. This is National Research Council of Canada Publication 42510.
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Received July 26, 2006; accepted August 10, 2006.
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