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Journal of Virology, May 2008, p. 4853-4861, Vol. 82, No. 10
0022-538X/08/$08.00+0 doi:10.1128/JVI.02388-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Julie E. Burns,1*
Wenke Zhang,2,
Hannah F. Walker,1
Stephanie Allen,2
Alfred A. Antson,3 and
Norman J. Maitland1
YCR Cancer Research Unit, Department of Biology (Area 13), University of York, Heslington, York, YO10 5DD United Kingdom,1 Laboratory of Biophysics and Surface Analysis, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD United Kingdom,2 York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 5DD United Kingdom3
Received 5 November 2007/ Accepted 15 February 2008
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E2 proteins are
45-kDa nuclear phosphoproteins with a tripartite secondary structure. The structure of the intact E2 protein closely resembles that of other mammalian transcription factors, consisting of a DNA-binding/dimerization domain (DBD) connected by a flexible linker to a multiple-protein-binding transactivation domain (TAD). The three-dimensional structures of the C-terminal DBD (11, 16, 17) and N-terminal TAD (1, 5, 15, 30, 45) of several E2 proteins have been reported, both alone and in complex, revealing a tight dimer of the DBD bound to DNA and a characteristic L-shaped TAD structure. In the case of HPV-16, two TAD domains form a dimer; this additional dimerization interface has been proposed to link two E2 dimers bound via the DBD to two distant E2BS within the URR (5). Such interactions would induce a loop within the viral promoter (Fig. 1), supporting the model proposed by Knight et al. (21), who showed that full-length wild-type bovine papillomavirus type 1 (BPV-1) E2 protein, and not the truncated C-terminal E2 protein, formed stable DNA loops, visible with electron microscopy.
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FIG. 1. Structure of HPV-16 E2 protein. Schematic representation of E2-mediated DNA loop formation showing possible N-terminal (E2NT) interactions between E2 molecules (shown in yellow and blue) bound through the C termini (E2CT) at different E2BS in DNA. (Adapted from reference 5 with permission).
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FIG. 2. Computer modeling of the N-terminal dimerization interfaces of wild-type and mutant HPV-16 E2 proteins. Potential amino acid interactions in the TAD dimerization domain of the wild-type (A), R37A (B), E80A (C), and A69Q E2 proteins (D). Dotted lines represent potential hydrogen bonding between residues of two E2 TAD molecules (colored blue and red). Fourteen bonds can potentially be formed in the wild-type E2 dimer interface, six in the R37A mutant, and eight in the E80A mutant. The A69Q mutant is not predicted to disrupt hydrogen bonding in the interface but to cause steric hindrance to the opposing loop structure. (E) Apparent molecular mass (MW) of wild-type (WT) and R37A E2 proteins at various concentrations at 18,000 rpm. The R37A mutant appears to be monomeric at all concentrations. The wild-type protein is a mixture of monomeric and dimeric forms which may contain oligomers higher than the dimer. The wild type's curves cover the same molecular-mass range at different concentrations and do not overlap, suggesting that the mixture is not in equilibrium under these conditions.
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Soluble, recombinant, full-length E2 or CT proteins were expressed in Escherichia coli BL21(DE3) pLysS by induction with 1 mM isopropyl-β-D-thiogalactopyranoside for 3 h at 25°C, purified by nickel affinity followed by heparin-binding chromatography (modified from reference 29), and used immediately or snap-frozen and stored at –80°C. The final purified proteins were checked by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting with rabbit primary antibody anti-E2SCT (described in reference 40). The E2NT protein was expressed and purified as described in reference 9, dialyzed into 20 mM Tris-HCl, pH 8.0, 0.2 mM EDTA, 300 mM NaCl, 2.5 mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP), snap-frozen, and stored at –80°C.
Cell culture. HeLa cells were grown in monolayer culture in Dulbecco's modified Eagle's medium plus 10% fetal calf serum (D10 medium) at 37°C and 5% CO2. C-33A cells were cultured in D10 medium supplemented with 10 mM HEPES. LNCaP cells (derived from a human prostate carcinoma) were maintained in monolayer culture in RPMI medium plus 10% fetal calf serum.
Transcriptional transactivation assays. The response plasmid p2x2E2BS:SV40min:EGFP was previously constructed by the ligation of a 513-bp fragment containing the 4E2BS and minimal simian virus 40 promoter from pGL2:2x2xE2BS:SV40min:luc (22) into pEGFP-1 (Clontech) (32).
For transactivation assays, cells were passaged 1:2 2 days before transfection, and six-well plates were seeded with 1.5 x 105 to 1.8 x 105 cells per well on the following day. After 24 h, cells were transfected with an E2 expression plasmid (pLNCX-E2 or pTriEx-E2) and the E2 response plasmid p2x2E2BS:SV40min:EGFP, using Fugene6 transfection reagent (Roche). Cells were observed by fluorescence microscopy and harvested after 48 h for analysis of enhanced green fluorescent protein (EGFP) expression by flow cytometry.
In vivo HPV DNA replication. Transient replication assays were carried out as described by Sakai et al. (28). C-33A cells were split 1:2 2 days before transfection and seeded on the following day into 10-cm-diameter plates at a density of 6 x 105 cells per plate. After 24 h, cells were cotransfected by using a calcium phosphate transfection kit (Invitrogen) with 1 µg of plasmid p16ori containing the HPV-16 replication origin, 5 µg of the HPV-16 E1 expression plasmid pCMV-E116, and 100 ng of the HPV-16 E2 expression plasmid pLNCX:E2. Seventy-two hours after transfection, low-molecular-weight DNA was extracted and digested with 10 U of DpnI and/or 10 U of XmnI overnight. Digested DNAs were separated on agarose gels, transferred to positively charged nylon membranes (Roche), and probed by using a 32P-radiolabeled, 700-bp, ori-containing HPV-16 fragment released from PvuII-digested p16ori.
Analytical ultracentrifugation. Sedimentation analyses were carried out in an Optima XL-I ultracentrifuge (Beckman-Coulter, CA), using scanning UV optics. Three concentrations of recombinant E2NT were loaded into cells containing 12-mm path length, six-channel Epon centerpieces with quartz windows. The solvent was 20 mM Tris-HCl, pH 8.0, 0.2 mM EDTA, 300 mM NaCl, 2.5 mM TCEP. Data were obtained at rotor speeds of 18,000 and 25,000 rpm, and the time to equilibrium was typically 10 to 12 h. All runs were carried out at 20°C, and all radial scans were at a wavelength of 280 nm. Molecular weights were estimated by using the Beckman ultracentrifuge software.
EMSA. Complementary 20-mer oligonucleotides, including E2BS 4 (most distal to the P97 promoter of HPV-16; E2BS4 sense, 5'-TTCAACCGAATTCGGTTGCA-3', and E2BS4 antisense, 5'-TGCAACCGAATTCGGTTGAA-3'), were end-labeled with biotin using a biotin 3'-end DNA-labeling kit (Perbio) and annealed. Binding reactions were carried out by using a LightShift chemiluminescent electrophoretic mobility shift assay (EMSA) kit (Perbio) according to the manufacturer's instructions. Twenty-microliter reaction mixtures containing 1x binding buffer (10 mM Tris, 50 mM KCl, 1 mM dithiothreitol, pH 7.5), 2.5% glycerol, 0.05% NP-40, 25 to 60 ng (0.5 to 1.33 pmol) of purified protein, and 50 fmol labeled, double-stranded oligonucleotide were incubated for 20 min at room temperature. Reaction mixtures lacking protein or containing cold competitor (10 pmol unlabeled oligonucleotide) were included as controls. Reaction products were separated on 8% native polyacrylamide gels and transferred to positively charged nylon membrane for chemiluminescent detection.
AFM of DNA-protein complexes. (i) DNA template. In order to generate the template for DNA looping, a fragment from the HPV-16 URR containing E2BS 3 and 4 was amplified by PCR using the primers 5'-GTGTGTTTGTATGTATGGTA-3' (nucleotides 7239 to 7258 in the HPV-16R sequence) and 5'-TACGCCCTTAGTTTTATACA-3' (nucleotides 15 to 34 in the HPV-16R sequence). The PCR product was gel purified by using GeneClean (Q-BIOgene) according to the manufacturer's instructions.
(ii) Protein preparation. Proteins used for AFM studies were cleaved overnight with enterokinase (pET30) or thrombin (pET15b) to remove the N-terminal His tag, using a recombinant enterokinase or recombinant thrombin kit (Novagen) according to manufacturer's protocols. Cleavage was monitored by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
(iii) DNA binding. Binding reaction mixtures containing 50 ng (0.11 pmol) of double-stranded DNA template, 0.55 pmol of cleaved protein, 1x binding buffer from a LightShift chemiluminescent EMSA kit, 2.5% glycerol, and 0.05% NP-40 were incubated at 37°C for 30 min. Samples were kept on ice for 30 min to a few hours until they were immobilized on a NiCl2-treated, freshly cleaved mica surface (Agar Scientific) as described below.
(iv) AFM imaging. Imaging experiments were carried out using a multimode AFM with a Nanoscope IIIa controller (Veeco, CA), using a tip holder for tapping-mode imaging in air. To enable imaging, 5 to 10 µl of the protein-DNA complex solution was deposited on NiCl2-treated mica and incubated at room temperature for 30 seconds, followed by three gentle rinses with deionized water (100 µl/rinse). The sample was then dried under a gentle flow of dry N2, attached to a magnetic sample puck, and positioned in the AFM sample stage for imaging. Rectangular silicon tapping-mode cantilevers (Olympus) with resonant frequencies in the range of 280 to 360 kHz were employed during the experiments. The scanning frequencies were typically 3 Hz per line. The AFM images were analyzed by using the instrument analysis software or SPIP (Image Metrology A/S, Denmark).
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In order to assess whether mutant E2 could self-interact, wild-type and R37A E2 N-terminal truncated proteins were expressed in E. coli, purified by immobilized metal-ion affinity chromatography and ion exchange chromatography, and analyzed by analytical ultracentrifugation. The results presented in Fig. 2E show that the R37A mutant exists in solution as monomers, unlike the wild-type protein, which shows both monomeric and dimeric forms, although the mixture was not in equilibrium under the conditions used. Similar results were obtained at 25,000 rpm (data not shown). The solvent density and partial specific volume of the protein were calculated as 1.0113 and 0.7306, respectively, using the program SEDNTERP according to the method of Laue et al. (23).
E2 N-terminal dimerization disruption affects transactivation. For measurement of their transactivation activities, mutant E2 genes were cloned into the expression vectors pTriEx and pLNCX and cotransfected into the human epithelial cell lines HeLa, C-33A, and LNCaP together with an E2-responsive EGFP reporter vector. After optimization of the relative dosage of E2 and target plasmids in each cell type (data not shown), a standard transactivation assay was carried out in LNCaP epithelial cells, in which E2 cytotoxicity was lowest in our cell bank. Forty-eight hours after transfection, the EGFP fluorescence of the cells was visualized by inverted phase fluorescence microscopy, as shown in Fig. 3A. Overall transfection efficiencies of approximately 50% were achieved (measured by transfection of a cytomegalovirus-EGFP construct, not shown). The cells were harvested, and the relative amounts of EGFP fluorescence were quantified by fluorescence-activated cell sorter analysis (Fig. 3B). The results confirmed the ability of wild-type E2 to transactivate the minimal promoter, with EGFP expression increased almost 70-fold compared to basal levels. A complete abrogation of transactivation was observed with the R37A and A69Q mutants. Although the E80A mutant showed increased transactivation (about fivefold) in comparison to that of the other two mutants, it was less than 7% of that achieved using wild-type E2. When the expression vector pTriEx was used, similar transactivation levels were obtained, as shown in Fig. 3B.
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FIG. 3. In vitro transcriptional transactivation of a synthetic E2-responsive promoter by E2 mutants. (A) EGFP expression in LNCaP cells 48 h after cotransfection with pLNCX-E2 expression and reporter plasmids. Cells shown in the panel labeled "no E2" were transfected with reporter vector and empty expression plasmid only. (B) Fluorescence-activated cell sorter quantification of E2-mediated transactivation 48 h posttransfection. Means and standard deviations of the results of three experiments using pLNCX (black) and pTriEx (gray) E2 expression plasmids are shown. Results were normalized to "basal expression" (i.e., that of cells transfected with empty expression plasmid), set at a value of 1. WT, wild type.
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N-terminal dimerization disruption does not affect replication. In general, papillomavirus DNA replication requires both the full-length E2 protein and the E1 protein. While E1 is recognized as the major papillomavirus viral replication protein, it is widely accepted that E2 plays an important auxiliary role (43). In order to assess the capacities of the mutant E2 proteins to replicate viral DNA, transient replication assays were carried out in C-33A cells, as described above. As shown in Fig. 4, wild-type, R37A, A69Q, and E80A E2 proteins were replication competent, while no replication was observed with E39A mutant E2. This mutant was previously established as replication defective (28) and was used in our study as a negative control.
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FIG. 4. In vitro HPV DNA replication in the presence of HPV-16 E2 and E1. Replication assays were performed as described in Materials and Methods. Low-molecular-weight DNA was digested with XmnI (X) or XmnI/DpnI (XD), and the products probed for HPV-16 ori. The lane labeled "ori" contained only plasmid p16ori. The band at 4 kb represents linearized plasmid p16ori. The presence of this band in XD lanes represents newly replicated, DpnI-resistant plasmid. WT, wild type.
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FIG. 5. DNA-binding capacities of recombinant E2 proteins. Binding reactions were performed, visualized by EMSA as described in Materials and Methods, and separated on an 8% native acrylamide gel. +, lane contained E2 protein; –, lane contained no E2 protein; CT, C terminus; WT, wild type.
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The DNA template was generated by PCR and comprised a 700-bp HPV-16 URR fragment (nucleotides 7239 to 34 of the HPV-16 genome) containing the two E2BS (3 and 4) most distal to the P97 promoter (Fig. 6A). Purified proteins were incubated with the DNA template, immobilized, and imaged. Two hundred DNA molecules were analyzed for each protein examined.
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FIG. 6. DNA-looping abilities of wild-type and mutant HPV-16 E2 proteins. (A) Diagram of the HPV-16 URR. The template for AFM was generated by PCR amplification of the region between the arrows, containing E2BS 3 and 4. (B) Predicted E2-DNA structures and measurements. E2 is represented schematically as TAD (gray ovals) linked to DBD (dark circles) (upper schematic) or as gray ovals (lower schematic). (C) Large-area AFM image views of DNA structures complexed with E2 proteins. The scale bars represent 160 nm. The Z ranges for the images shown are as follows: wild type (WT), Z range of 2 nm; R37A mutant, Z range of 2.5 nm; A69Q mutant, Z range of 3 nm; E80A mutant, Z range of 2 nm; and C terminus (CT), Z range of 3 nm. (D) Zoomed images of the representative structures observed for the DNA-E2 protein complexes (images of various dimensions). Arrows indicate the positions of E2 binding to the DNA template (image of R37A is a three-dimensional representation rather than a planar view as for the other images). (E) Zoomed (100 x 100 nm) images and measurements of three DNA loops formed by wild-type E2 protein. (F) Results of analysis of 200 E2-DNA molecules. *, P value of <0.001 using Fisher's exact test. WT, wild type; C-term, C terminus.
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DNA looping is mediated by the N-terminal dimerization interface of HPV-16 E2. The identification of a second dimerization interface located within the E2 N-terminal domain suggested that looping may result from interactions between DNA-bound E2 dimers (5) (Fig. 1). To test this hypothesis, we evaluated the abilities of R37A, A69Q, E80A, and C-terminal E2 proteins to form DNA loops by using AFM as described above. R37A E2 protein was completely defective in forming DNA loops (Fig. 6C). This result was not due to a binding deficiency, since all the proteins bound to E2BS DNA (Fig. 5) and protein-DNA complexes were observed with AFM (Fig. 6D). The A69Q and E80A E2 proteins both showed a reduced ability to form DNA loops compared with that of wild-type E2 (Fig. 6C): loops were observed in only 2% and 1% of the analyzed molecules, respectively (Fig. 6F), showing a statistically significant difference (P < 0.001, using Fisher's exact test) in comparison to the number of loops formed by wild-type E2. These proteins were also observed bound to the DNA template (Fig. 6D). As expected, an N-terminally deleted C-terminal fragment of E2 was unable to form DNA loops while retaining the ability to form protein-DNA complexes, visualized by using AFM (Fig. 6C and D).
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Recently, Sanders et al. (30) demonstrated that the BPV-1 E2 protein also dimerizes through the TAD. Although the residues important for HPV-16 TAD dimerization are highly conserved, the BPV-1 interaction is mediated through redox interactions involving a different interface and residues that are not conserved between BPV and HPV E2 proteins. Nevertheless, these results support the hypothesis of N-terminal dimerization as a more-general mechanism to regulate papillomavirus E2 activity.
There is an accumulated literature reporting the effects of single-residue mutations on the transactivation and replication functions of the E2 TAD (reviewed in reference 8). However, many of these amino acid changes are predicted to disrupt the overall protein structure, leading to inconclusive results. Information derived from the three-dimensional structure of the N-terminal TAD of the HPV-16 E2 protein and computational modeling allowed us to identify important residues in the dimerization interface. In the HPV-16 E2 TAD dimer, arginine 37 (R37) makes several hydrogen bonds with glutamic acid 80 (E80) and threonine 81 (T81) of a separate E2 molecule (Fig. 2A) (5). We replaced R37 and E80 with alanine (R37A and E80A, respectively) in order to abolish those interactions. These changes were predicted to cause destabilization of the dimer interface (Fig. 2B and C) and minimal perturbation of the protein conformation, since the R37 side chain is exposed and alanine is compatible with all secondary structures (13). Alanine 69 is a highly conserved residue, with all papillomavirus E2 proteins having glycine or alanine at this position (http://hpv-web.lanl.gov). A69 was mutated to glutamine (A69Q) to evaluate the replacement of a nonpolar, small amino acid with a polar side-chain amino acid, and as shown in Fig. 2D, the glutamine side chain is predicted to interfere with dimer formation due to steric hindrance.
It has been suggested that mutations which reduce or eliminate one function but not another should not disrupt protein structure extensively. All three mutants were able to support the replication of a plasmid containing an HPV-16 origin of replication (Fig. 4), consistent with previous reports for R37A and the analogous HPV-18 Q80A mutant (15, 28) and confirming that the mutant E2 proteins have no major structural alterations.
For the transactivation function of E2, our results showed that the R37A mutation has a major effect on transactivation by HPV-16 E2, as previously demonstrated (28). Alanine substitutions for this invariant amino acid in BPV-1 and HPV-11 and -31 E2 proteins have shown similar results (3, 12, 41). The replacement of glutamine 80 with alanine in HPV-18 (15) resulted in a 50% reduction in transactivation. In our work, the replacement of glutamic acid 80 with alanine resulted in an even more striking reduction in transactivation. Replacing A69 with glutamine (A69Q) severely affected E2-mediated transactivation.
It had been previously reported that the full-length wild-type BPV-1 E2 protein formed stable DNA loops that were visible by electron microscopy and that the TAD was necessary for this looping (21). Antson et al. suggested that the loop formation may be mediated by TAD dimerization forming tetramers between E2 molecules bound as dimers to widely separated E2BS in the URR of the virus genome (5) (Fig. 1). Such a structure could bring tissue-specific enhancers into close proximity to the core transcription complex, as reported for other transcriptional regulators (27). The redox-dependent TAD dimerization since reported for BPV-1 E2 (30) has been proposed as an intradimeric, and not as a tetrameric, interaction. However, tetrameric forms in BPV E2 are not ruled out and are likely to be the structural mechanism by which this virus induces DNA loops (21).
Using AFM, we found that the HPV-16 E2 protein indeed formed DNA loops with an HPV-16 URR fragment containing E2BS 3 and 4 and that the loop formation required the TAD. When mutant E2 proteins were tested for their ability to form DNA loops, TAD dimerization interface mutant E2 proteins were completely or mostly defective in forming DNA loops in comparison to loop forming by wild-type E2 (P < 0.001). This was not due to an inability to bind specifically to DNA. Since truncated C-terminal E2 or mutant E2 proteins, presumably defective in TAD dimerization, were unable to form DNA loops, we conclude that the E2 N-terminal dimerization must be responsible for the DNA looping.
A recent study has shown that HPV-11 E2 also forms loops with URR fragments containing E2BS, with a frequency similar to that in our results (36). As with BPV-1 and HPV-16, this study found that the full-length protein was necessary for loop formation, and the results suggested that the N-terminal TAD was responsible. It was suggested that ori DNA remodeling by E2 could facilitate the binding of the E1 protein and melting of DNA during viral replication, while the formation of long-distance loops may inhibit this process. Although the URR fragment we used did not include the promoter-proximal E2BS 1 and 2, this model is not inconsistent with our results in which mutants which failed to form DNA loops were still competent for E1-dependent replication.
The results of this work suggest that N-terminal dimerization may play a role in regulating the transactivation function of the HPV-16 E2 protein, possibly via DNA looping. It would not be surprising if the E2 protein, as a transcriptional regulator, employs the DNA-looping mechanism to regulate gene transcription. It is believed that this mechanism is widely used in gene regulation (7, 44), particularly by transcriptional enhancers (31), bringing distally bound transcription factors close to the site of transcription initiation. Furthermore, it has been reported that multiple transcription factors function by oligomerizing and self-associating to form DNA loops (20, 39, 42, 47).
During the course of this investigation, E2 was reported to interact directly with the cellular bromodomain protein Brd4 (2). Brd4, besides tethering the viral genome to mitotic chromosomes in BPV-1 (6, 46), was proposed as the major cellular partner required for E2 transcriptional activation in a number of papillomaviruses, using either a heterologous or a homologous promoter in transactivation assays (19, 24, 34, 35). However, the results of a more-recent study suggested that HPV-18 and -11 E2-mediated repression of the HPV promoter does not require Brd4 (33). Although we have not assessed the ability of our mutants to bind Brd4, the R37A mutant and other mutants with mutations in the dimer interface fail to interact with cellular Brd4 (2, 6, 34, 35). Since the transactivation activity was assessed in vivo, it is likely that the lack of transactivation may be due to an inability to interact with cellular Brd4. DNA looping, however, was studied in vitro in the absence of Brd4 or any other proteins.
The participation of the N-terminal dimerization in DNA looping provides more insight into the mechanisms of HPV-16 E2 function. Ultimately, analysis of the crystal structures of these mutants is still necessary in order to fully confirm that the dimerization disruption is indeed occurring, as well as examination of the interaction of Brd4 with residues E80 and A69 and its consequences for loop and complex formation.
Elena E. Hernandez-Ramon was funded by the Consejo Nacional de Ciencia y Tecnologia, Mexico, and by the Secretaria de Educacion Publica, Mexico. Wenke Zhang was funded by the Biotechnology and Biological Sciences Research Council.
Published ahead of print on 12 March 2008. ![]()
Present address: Genomic Medicine Unit, Hospital General de México, Dr. Balmis 148, Col. Doctores, Del. Cuauhtémoc, México D.F., CP 06726 Mexico. ![]()
Present address: State Key Lab for Supramolecular Structure and Materials, Jilin University, 2699 Qianjin Street, Changchun, 130012 People's Republic of China. ![]()
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