Cloning, Expression, Purification, and Characterization of a Novel Esterase from Lactobacillus plantarum
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Protein Expression and Purification 59 (2008) 203–214 www.elsevier.com/locate/yprep
Cloning, expression, purification, and characterization of a designer protein with repetitive sequences Silke Gerber a, Kristin Kirchhof a,c, Jörg Kressler b, Christian E.H. Schmelzer a, Carmen Scholz c,*, Thomas C. Hertel a, Markus Pietzsch a,* a
Department of Pharmacy, Faculty of Natural Sciences I, Martin-Luther-University Halle-Wittenberg, Biozentrum, Weinbergweg 22, 06099 Halle (Saale), Germany b Department of Chemistry, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany c Department of Chemistry, University of Alabama in Huntsville, 301 Sparkman Drive MSB 333, Huntsville, AL 35899, USA Received 20 December 2007, and in revised form 30 January 2008 Available online 15 February 2008
Abstract An artificial protein containing alternating hydrophilic–hydrophobic blocks of amino acids was designed in order to mimic the struc ture of synthetic multiblock copolymers. The hydrophobic block consisted of the six amino acids Ala Ile Leu Leu Ile Ile (AILLII) and the hydrophilic block of the eight amino acids Thr Ser Glu Asp Asp Asn Asn Gln (TSEDDNNQ). The coding DNA sequence of the cluster was inserted into an commercial pET 30a(+) vector using a two step strategy. The expression of the artificial protein in Escherichia coli was optimized using a temperature shift strategy. Only at cultivation temperature of 24 °C after induction expression was observed, whereas at 30 and 37 °C no target protein could be detected. Cells obtained from a 15 L bioreactor cultivation of E. coli were disintegrated by mechan ical methods. Interestingly, glass bead milling and high pressure homogenization resulted in a diVerent solubility of the target protein. The further purification was carried out by aYnity chromatography using the soluble homogenized protein. Extreme conditions (6 M urea, 0.5 M NaCl) were applied in order to prevent aggregation to insoluble particles. The designer protein showed an extremely high tendency to form dimers or trimers caused by intermolecular interactions which were even not broken under the conditions of SDS–polyacrylamide gel electrophoresis, rendering the behavior during purification diVerent from proteins usually found in nature. The protein preparation was not completely pure according to SDS–PAGE stained by Coomassie blue or silver. In MALDI-TOF-MS, nano-ESI qTOF-MS of the entire protein preparation and nano-ESI-MS after digestion by trypsin and chymotrypsin impurities were not detectable. © 2008 Elsevier Inc. All rights reserved. Keywords: Artificial protein; Hydrophilic hydrophobic copolymer; Expression; Purification; Characterization
Controlling the spatial arrangement of polymers is highly desirable but techniques are rather limited for conventional polymers. Conventional flexible polymers adopt a random coil structure when in solution or melted. In the solid state, tacticity, chirality and intermolecular forces determine the secondary structure of polymers. Typically, polymer helices crystallize into lamellae separated by amorphous regions being indistinct in their secondary and tertiary structure * Corresponding authors. Fax: +1 256 824 6349 (C. Scholz), +49 (0)345 55 27260 (M. Pietzsch) E-mail addresses: cscholz@chemistry.uah.edu (C. Scholz), markus. pietzsch@pharmazie.uni-halle.de (M. Pietzsch). 1046-5928/$ - see front matter © 2008 Elsevier Inc. All rights reserved. doi:10.1016/j.pep.2008.01.022
[1]. Conventional polymers are used as either completely amorphous or semi-crystalline materials. The degree of crys tallinity of polymeric materials can be controlled by the pro cessing parameters. However, since these polymers consist of only one type of monomer, or possibly up to four diVerent monomers in copolymers, and have a rather broad polydis persity, it is virtually impossible to achieve a specific tertiary structure. In an eVort to obtain polymer constructs of a cer tain three-dimensional structure, amphiphilic block copoly mers [2] or dendrimers [3,4] are used to induce self-assembly into nano- and micro-sized three-dimensional objects or to induce a certain spatial arrangement.
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Nature’s way of gaining control over the tertiary struc ture of a polymer is to have a variety of chemically diVerent monomer units that are arranged in a distinct, predetermined sequence. Thus, proteins are obtained which usually consist of up to 20 chemically diVerent monomer units (essential amino acids) that are linked via peptide bonds according to a genetically determined sequential order. Proteins are charac terized by identical molecular weights for all polymer chains, i.e. a polydispersity index of 1.0, and a unique spatial arrange ment that is adopted by all polymer chains. Such a strict con trol over the primary and resulting secondary and tertiary structure can only be achieved by biological means, following a genetic blueprint for the assembly of the macromolecule. The versatility and unique functions of proteins, for instance, the powerful catalytic activity of enzymes, is based upon the amino acid sequence and derived distinct secondary and ter tiary structure. Thus, the amino acid sequence ultimately determines the spatial arrangement of a natural macromole cule and ultimately decides its biological function. Advances in molecular biology allow the use of such strictly controlled and biologically derived systems for the synthesis of macromolecules that are chemically related to proteins and polypeptides but have no biological functions. These macromolecules are studied and produced for ultimate materials applications. Recombinant DNA technology has been used for the synthesis of peptides outside of their nat ural realm, that is, naturally occurring proteins have been synthesized in new host systems [5–7]. In another approach, polypeptides were synthesized that contained non-natural amino acid building blocks [8–10]. With the work presented here, we took yet another route to the synthesis of non-natural polypeptides. Inspired by work on ethylene oxide—propylene oxide block copolymers [11–16], we synthesized a non-natural polypeptide by means of recombinant DNA technology. The only governing ele ment in the design of the genetic blueprint for this polypep tide was the idea to generate alternating hydrophobic and hydrophilic peptide blocks within this macromolecule. The project described here is driven by the fact that the material properties of conventional polyamides are limited due to the random character of polycondensation processes that are necessary to link amino acids, lactames, or diacids and diamines [17]. It is assumed that the tailored synthesis of multiblock copolymers having blocks with hydrophobic and hydrophilic amino acid sequences, respectively, may yield new and unique material properties. With the current work we show feasibility for using recombinant DNA technolo gies to produce polypeptide materials that are not derived from or structurally similar to any naturally occurring pep tides or proteins. Materials and methods Materials Unless otherwise stated all chemicals were of analytical grade and were purchased from Sigma Aldrich, Taufkir
chen, Germany. The protein marker (PageRuler Protein Ladder) used for SDS–PAGE was purchased from Fermen tas (St. Leon-Rot, Germany). Yeast extract was purchased from Deutsche Hefewerke (Marl, Germany), Benzonase from Merck (Darmstadt, Germany) and skim milk powder from Applichem (Darmstadt, Germany). Deionized water was used throughout the experiments. Sterilization of cultivation media was carried out at 121 °C at 1 bar for 30 min. Chromatography equipment and materials were purchased from GE Healthcare, Freiburg, Germany. Bacterial strains Escherichia coli BL21Gold(DE3) was purchased from Stratagene (Amsterdam, The Netherlands). Vector and nucleotide inserts The vector pET-30a(+) (Novagen, Merck KGaA Darms tadt, Germany) was modified via cutting BamHI and Hin dIII restriction sites (indicated in small letters, see below) in order to introduce a SpeI/BcuI restriction site (indicated in bold letters, see below) to which later the DNA coding for the amphiphilic block copolymer units were introduced. The following DNA fragment was inserted to pET-30a(+): Top strand: 59-ga tcc AAA AAG AAA GCT ATC CTG CTG ATC ATT A|CT AGT GAA GAC GAC AAC AAC CAG AAA AAG AAA a-39 Bottom strand: 39-g TTT TTC TTT CGA TAG GAC GAC TAG TAA TGA TC|A CTT CTG CTG TTG TTG GTC TTT TTC TTT ttc ga-59 The oligonucleotides for the inserts encoding for the tar get protein were synthesized by MWG Biotech (Ebersberg, Germany) and introduced into the modified vector using the SpeI/BcuI restriction site. Due to one maintained SpeI/BcuI site in the resulting vector sequence it is possible to intro duce several inserts. Top strand: 59-CT AGC GAA GAC GAC AAC AAC CAG GCT ATC CTG CTG ATC ATT A-39 Bottom strand: 59-CT AGT AAT GAT CAG CAG GAT AGC CTG GTT GTT GTC GTC TTC G-39 After the insertion of the first sequence the 59 end becomes a hybrid SpeI site (ACT AGC), which still encodes for Thr and Ser, respectively, but is not cleavable any more by SpeI. The 39 side retains cleavability by SpeI (ACT AGT). Addi tional repeat blocks can be added through this restriction site. Construction of plasmid pBP68 Standard methods of recombinant DNA technology were used as published by Sambrock et al. [18]. Small scale preparations of plasmids used for restriction enzyme analy sis were prepared by a modified alkaline lysis method [19]. For nucleotide sequencing, plasmid DNA was prepared by the Qiawell Plasmid Kit (QIAGEN GmbH, Hilden, Germany). Restriction enzymes were purchased either from
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Roche Diagnostics, Promega or New England BioLabs and used as recommended by the manufacturer. DNA restric tion fragments used in the cloning experiments were puri fied from 1% (w/v) low-melting-point agarose gels (FMC SeaPlaque GTG Biozym Diagnostik, Hessisch Oldendorf, Germany), and the DNA fragment was eluted from the aga rose by heating to 65 °C followed by phenol extraction and ethanol precipitation [18]. Ligation of DNA was performed with T4 DNA ligase (New England BioLabs, Roche Diag nostics) and competent E. coli JM109 were transformed by the method of Chung et al. [20] (GenBank Accession No. EF523820). Preparation of competent cells and transformation Preparation of electrocompetent cells of E. coli BL21Gold(DE3) (Stratagene) and transformation via elec troporation were carried out following the protocol in the Qiagen Bench guide [21]. For cloning experiments, Nova Blue competent cells (Novagen) were used. A 1 lL aliquot of the ligated product was introduced into 40 lL of competent NovaBlue cells (approximately 2 £ 1011 cells per mL). Cells were grown on LB medium containing kanamycin and clones containing the insert were identified by colony PCR. Positive clones were identified by sequenc ing after plasmid preparation using the “QIAprep Miniprep Kit” (Qiagen, Valencia, CA, USA). Fermentation and induction Shake flask cultivation of E. coli. Single colonies of BL21 DE3 pBP68 grown on LBkan solid medium were used to inoculate precultures of 7 mL LBkan liquid medium con taining 20 lg/mL of Kanamycin. After overnight growth at 37 °C at 200 rpm in an incubator shaker, 500 mL LBkan were inoculated with 5 mL (1%) preculture and grown to an OD600 between 0.5 and 0.6 after inoculation at 37 °C and 80 rpm (rotary shaker). A 5 mL aliquot of sterile 100 mM IPTG solution (final concentration 1 mM) was added and the cultivation was continued in diVerent experiments at temperatures of 24, 30, and 37 °C, respectively. One cultiva tion was carried out without induction. Optical density at 600 nm was measured at time intervals of 1 h and 1/OD sam ples were prepared in order to harvest comparable amounts of biomass. The volume to be centrifuged was calculated fol lowing the following equation: vcentr = 1 mL/OD600 (for example: samples with an OD600 of 0.5, centrifuge 2.0 mL; samples with an OD600 of 5.0, cen trifuge 0.2 mL). Centrifugation was carried out for 3 min at 16,100g at 4 °C. Cell pellet and supernatants were stored at ¡25 °C. For large volumes, cells were harvested by centrifu gation (Eppendorf ZK 630, 6000g, 30 min, 4 °C) and stored at ¡25 °C. Fed-batch bioreactor cultivation. The cultivation of E. coli BL21 DE3 pBP68 was carried out according to the fed-batch method described by Yee and Blanch [22] using a complex medium [23]. Two precultures were used. A 25 mL aliquot of preculture I was inoculated by a single colony of BL21 DE3
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pBP68. After growth for 8 h at 37 °C with shaking at 80 rpm, 500 mL LBkan were inoculated with 5 mL (1%) preculture I and grown overnight at 37 °C and 80 rpm in a rotary shaker (preculture II). A 12 L volume of fermentation medium (see below) was inoculated with 500 mL preculture II and cells grown at 37 °C, with stirring at 300 rpm and an air flow rate of 4.0 stdL/min. During fermentation, the pH was controlled using phos phoric acid and NaOH solutions, respectively. After 2, 3.5 and 5 h, silicone oil was added via a hose pump to diminish the foam. After 5.5 h at an OD600 of 15 the temperature was low ered to 24 °C. Then, 12 mL of sterile 1 M IPTG solution were added (final concentration 1 mM). After 6.5 h, feeding was started using a feeding solution that is specified below with a constant feed rate of 3 g/min which was increased to 5 g/min after 8 h fermentation. In total, 700 mL of feeding solution were added to the reactor. Samples were taken at regular intervals, diluted to 1/OD and analyzed for BP68 using the inclusion bodies (IB) isolation method [24]. After 9.5 h the fermentation broth was cooled to 16 °C and the cells harvested by 6000g centrifugation at 4 °C for 30 min (Eppendorf ZK 630, Hamburg, Germany). The bio mass was resuspended in 0.9% NaCl solution, centrifuged again, and stored at ¡25 °C. Cultivation medium For the preparation of 12 L complex medium, 600 g yeast extract (50 g/L), 60 g glucose (5 g/L), and 6 g NH4Cl (0.5 g/L) were dissolved in 11 L deionized water in a Biostat C bio reactor (Braun Melsungen, Germany) and sterilized. After sterilization, evaporated water (approximately 1 kg) was replenished with sterile water. Solutions of 132 g K2HPO4·3 H2O in 500 mL and 8.16 g MgSO4·7 H2O in 500 mL water were prepared. After separate sterilization, these solutions were added to the bioreactor (final concentrations of K2HPO4·3 H2O and MgSO4·7 H2O were 11 and 0.68 g/L, respectively). The pH was adjusted to 7.0 using 10% NaOH. Feeding solution The feeding solution contained 25% (v/v) glycerol and 30% (w/v) yeast extract in water and was sterilized sepa rately. Isolation of inclusion bodies The isolation of inclusion bodies (IB) was carried out according to the literature [24] with some modifications. All steps were carried out at 4 °C. In order to isolate inclu sion bodies, wet biomass corresponding to 1/OD was resus pended in 950 lL buVer 1 (0.1 M Tris–HCl, 1 mM EDTA, and pH 7.1) in a 2 mL Eppendorf tube. Then, 0.5 g glass 1 Abbreviations used: IB, inclusion bodies; SDS, sodium dodecylsulfate; PPL marker, prestained protein marker; RT, room temperature.
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beads (d = 0.25–0.5 mm) were added. A 74 lL volume of a lysozyme solution in water (stock solution: 6.75 mg/mL) was added and the solution shaken vigorously for 10 min using a mixer mill (Retsch MM2, Haan, Germany). Then, 69 lL of a 90 mM MgCl2 solution, pH 8.0 (final concen tration 3 mM) and 5 lL benzonase solution (final concen tration 10 lg/mL) were added and the homogenate incu bated at 25 °C for 45 min to hydrolyze the polynucleotides. Finally, 740 lL solution 2 (60 mM EDTA, 1.5 M NaCl, 6% (v/v) Triton X-100, pH 7.0 with NaOH) were added and incubated for 30 min at 4 °C to solubilize the membrane lip ids. After centrifugation at 16,100g at 4 °C for 10 min, the supernatant was removed and the pellet resuspended in 1.5 mL solution 2 and incubated for 30 min following cen trifugation as before. The supernatant was discarded. The pellet (IB and glass beads) was resuspended in 1.5 mL buVer (0.1 M Tris–HCl, 20 mM EDTA, pH 7.0) and centrifuged again for 10 min. The supernatant was aspirated and the residue was resuspended in a twofold concentrated SDS sample buVer (2£ SDS SB) to a total weight of 2.175 g (con sisting of 0.5 g glass beads, approximately 1.1 g Eppendorf tube, and 0.575 g 2£ SDS SB). The 2£ SDS SB contained 100 mM Tris–HCl, pH 8.0, 2.5% SDS, 0.05% (w/v) bromo phenol blue, 10% (v/v), 7 M urea and 1% (v/v) 2-mercap toethanol [24]. After holding the samples for 4 min at 99 °C, they were analyzed by SDS–PAGE. Cell disintegration Technical cell disintegration by glass bead milling (DynoMill) A 25 g sample of frozen cells (E. coli BL21 DE3, pBP68) was dissolved in 100 mL of 50 mM Tris–HCl buVer, pH 8.0. Using a 150 mL batch glass chamber and 177 g glass beads (d = 0.3–0.4 mm), this cell suspension was disintegrated using a glass bead mill (DynoMill, W.A. Bachofen, Switzerland) at 3097 rpm and 4 °C for 20 min. The cell suspension was filtered using a glass frit (porosity 2). The glass beads were washed consecutively using a total of 200 mL of the disinte gration buVer. After centrifugation at 6000g for 30 min, the pellet was washed using 100 mL of 50 mM Tris–HCl buVer, pH 8.0 and centrifuged again in order to remove adsorbed soluble protein. The supernatant of the first centrifugation was centrifuged at a higher force (16,100g, 30 min) in order to get a clear solution. Washed pellet and supernatant were ana lyzed by SDS–PAGE. Comparable protein concentrations between supernatant and pellet fractions were prepared by resuspending the precipitated protein in the starting volume using SDS sample buVer. Technical cell disintegration by high pressure homogenization A 100 g sample of frozen cells (E. coli BL21 DE3, pBP68) was dissolved in 500 mL of 50 mM Tris–HCl, (pH 8,0, 4 °C) and disintegrated by eight passages at 500 bar using a high pressure homogenizer (APV 200, Manton Gaulin, Albertsl und, Denmark). After each passage, the suspension was
allowed to cool to 4 °C before the next disintegration cycle. Centrifugation and SDS–PAGE analysis were performed as described previously for the glass bead mill. Protein purification by preparative aYnity chromatography Unless otherwise stated, all purification steps were per formed at room temperature (20 °C) using an Äkta Purifier 100 (GE Healthcare, Freiburg, Germany). The elution pro file of the protein was determined at wavelengths of 230, 240, and 280 nm, respectively. A 150 mL sample after high pressure homogenization was applied to an aYnity column packed with Streamline Che lating Ni–NTA support (column: XK 50/20; CV: 300 mL; Flow rate for sample application: 3.0 mL/min (up-flow direc tion); Flow rate for washing and elution: 10.0 mL/min (downflow direction); Equilibration buVer: 20 mM Tris–HCl with 500 mM NaCl, 6 M urea, pH 8.0 and 5 mM imidazole; Elu tion buVer: 20 mM Tris–HCl with 500 mM NaCl, 6 M urea, pH 8.0 and 1 M imidazole). Sequential elution was carried out at steps of 100 mM, 150 mM, and 1 M imidazole. Frac tions of 15 mL volume were collected and assayed for BP68 using Western blotting with 17 fractions containing BP68 finally being pooled (255 mL). In order to remove the salts, the 255 mL pooled fractions were dialyzed using a dialysis tube with a cut oV of 8000 Da and a diameter of 32 mm (7 Spectrapor, Spectrum Labo ratories Inc., Rancho Dominguez, USA) against 2 L pure deionized water. The water was replaced three times. After complete removal of salts, the BP68 containing solution was lyophilized and the residue weighed. Analytical methods SDS–PAGE Polyacrylamide gel electrophoresis (PAGE) was per formed according to the method of Laemmli [25] using a Mighty Small apparatus from Hoefer (Amersham Biosci ences, Freiburg, Germany). Gels were either stained with Coomassie Blue according to the method of Fairbanks et al. [26] or by silver accord ing to Blum et al. [27]. In the latter case, methanol was used instead of ethanol in the fixing solution. After staining, the gels were dried between two cellophane sheets fixed in a frame. Quantitative analysis of the stained gels was carried out using a GeneGenius device (Syngene, Cambridge, United Kingdom) and the GeneSnap and GeneTools software. The amount of insoluble and soluble pro-MTG was determined by integration of the peak areas of the corresponding bands by choosing “lowest slope” as the integration algorithm pro vided by the software. Western blotting and detection of BP68 using anti-His antibodies The detection of the Histidine-tags of BP68 was per formed by Western blotting using an anti-His-antibody (monoclonal anti-polyhistidine clone His-1, H 1029, Sigma, Steinheim, Germany).
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The proteins separated using SDS–PAGE were trans ferred electrophoretically to a PVDF membrane (Millipore PVDF/Immobilon-P Transfer membrane, Roth, Steinfurt, Germany) using the semi-dry electrophoretic transfer cell and a power supply purchased from BioRad (Munich, Germany) according to the manufacturer’s manual. The PVDF membrane was cut to the size of the SDSgel, activated by incubation for 10 min in 100% methanol, washed with deionized water for 5 min and equilibrated as the SDS-gel in semi-dry transfer buVer (50 mM Tris, 40 mM glycine, 3.75% (w/v) sodium dodecylsulfate (SDS), pH 9.2 § 0.2, 20% (v/v) methanol). The electrophoretic trans fer using one SDS-gel was performed at 15 V (constant) and 0.44 A for 20 min. Correct transfer was verified by checking the prestained protein marker (PPL marker). The binding of the primary antibody was detected by a peroxidase labeled second antibody (anti-mouse-IgG peroxidase conjugate produced in goat, A2304, Sigma, Steinheim, Germany). All incubation and washing steps were performed at room tem perature (RT) using an innOva 4230 shaker (New Brunswick Scientific Inc., Edison, USA). After transfer, the PVDF mem brane was incubated for 1 h at RT in 5% (w/v) skim milk powder in PBS-T buVer (0.1% (v/v) Tween 20 in 1000 mL PBS, pH 7.5). The membrane was washed two times for 10 s with PBS-T buVer and incubated for 1 h in a 1:10,000 diluted solution of the anti-His antibody in PBS-T buVer. The mem brane was washed two times for 10 s using PBS-T buVer and incubated in PBS-T buVer 1 £ 15 and 3 £ 5 min before incu bating for 50 min in a 1:10,000 diluted solution in PBS-T of the peroxidase labeled antibody. The PVDF membrane was incubated 1 £ 15 and 3 £ 5 min. The detection of the bound antibodies was performed using the ECL-plus kit according to the protocol of the manufacturer (Amersham Bioscience, Uppsala, Sweden). The X-ray film (Kodak X-Omat AR,
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Sigma, Steinheim, Germany) was exposed for 30 s to 2 min in a dark room. Characterization of BP68 using MALDI mass spectrometry MALDI experiments were carried out on a delayed extrac tion TOF mass spectrometer Voyager-DE PRO (Applied Biosystems, Foster City, CA, USA) equipped with a pulsed nitrogen laser (k = 337 nm, 3 ns pulse width, 20 Hz repetition rate). The supernatant of an acetonitrile/0.1% TFA (1:1, v/v) solution saturated with sinapinic acid was used as matrix solution. This solution was mixed with the sample solution (1 mg/mL in the same solvent system) 9:1 (v/v) and then dried in a stream of air at a temperature of 35 °C on the flat surface of a stainless steel plate. Measurements were per formed operating in the positive ion linear mode at a total acceleration voltage of 25 kV, grid voltage set to 90%, 0.15% guide wire voltage and an extraction delay of 300 ns. A low mass gate was set to m/z 1000 to prevent detector saturation from matrix cluster peaks. The instrument was externally calibrated using calibration mixture 3 of the Sequazyme Pep tide Standards Kit (Applied Biosystems). Characterization of BP68 using FT-IR spectroscopy The Infrared spectrum of the protein was obtained on pressed protein-containing KBr tablets. A Bruker Tensor 37 MIR Spectrometer was used. Results and discussion In order to produce a peptide related to block copolymers a synthetic oligonucleotide was designed coding for an alter nating modular structure of hydrophobic and hydrophilic blocks of amino acids. The artificial protein named BP68 was expressed in E. coli, purified and characterized.
Fig. 1. Cloning strategy of BP68. (A) Designed primary sequence of the modular structure of alternating hydrophilic and hydrophobic elements and related DNA sequence (one insert). (B) Restriction enzymes used in the construction of the expression plasmid. First, a SpeI restriction site was introduced into the cloning vector pET30a(+) by using BamHI and HindIII restriction sites. The flanking regions introduced contribute a hydrophobic and a hydrophilic blocks. Between these blocks, the first insert (AB) was introduced. The second insert was introduced in the same way at the remaining SpeI restriction site. (C) Amino acid sequence of the final construct of BP68 containing two inserts, regular letters: protein sequences provided by the pET-30a(+) vector, let ters in italics: amino acids introduced in the first cloning step, introducing the SpeI restriction site; underlined letters: hydrophobic sequences, bold letters: hydrophilic sequences.
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Design of the artificial protein and construction of the expression plasmid The nucleotide sequence was designed in an attempt to mimic amphiphilic block copolymers. Aside from their inherent biocompatibility, artificial “blocked” proteins pro vide another major advantage over regular synthetic block copolymers, this is, the potential of having a multitude of alternating hydrophilic and hydrophobic blocks. Typically, synthetic block copolymers are limited in their number of individual blocks by the synthesis technique. Although diblock copolymers are prevalent, triblock copolymers are accessible by a “from the inside out” approach, and pentablock copolymers have been synthesized in some instances [28]. However, a multitude of fault-free alternating blocks of exactly defined and reproducible block length and chemi cal composition can only be achieved by recombinant DNA techniques. The BP68 expression plasmid pBP68 was constructed by cloning a first DNA fragment coding for a part of the desired protein sequence into the pET-30a(+) vector using BamHI and HindIII restriction sites as described in Mate rial and methods. The SpeI/BcuI restriction site which was thereby introduced to the vector was used to insert two repet itive sequences (inserts) in a sequential manner. The plasmid itself provides an N-terminal and a C-terminal His-tag use ful for easy purification as well as several potential protease cleavage sites.
The correct sequence was verified by sequencing. In Fig. 1B, the incorporation of one insert consisting of the hydrophilic module A and the hydrophobic module B (Fig. 1A) into the modified vector is shown schematically. The final gene prod uct carrying two inserts is called BP68 in the following and is shown in Fig. 1C. The designed protein consists of 111 amino acids and has a calculated molecular weight of 12360.8 g/mol. Secondary structure Using the open source protein structure prediction pro gram PSIPRED the secondary structure of the designed pro tein was calculated [29].
Fig. 3. Localization of BP68 after expression in E. coli; Western blot using an anti-His antibody, 10 lL sample per lane; 1/OD samples of E. coli BL21 DE3 pBP68 cells grown at 37 °C before and at 24 °C after induction (sam ples taken after 2, 3, 3.5 and 4 h after induction), S, soluble fraction; P, insoluble fraction; M, marker. Outside the area shown in the gel there was no other band visible.
Fig. 2. Prediction of the secondary structure of the designed protein BP68 by PSIPRED [29]. Conf: confidence of prediction: 0 = min, 9 = max; Pred (upper line): prediction of secondary structure elements: black arrows indicate beta strands, grey boxes with vertical sectioning indicate helical structures; Pred (lower line): prediction of secondary structure: “H” indicates helical, “C” coiled, and “E” beta strand structure elements, respectively; AA, amino acid sequence.
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As can be seen from the results of in-silico folding shown in Fig. 2, the hydrophobic block of the artificial protein is forming strands. The flanking regions contributed by the cloning vector contribute regions which are able to form helical structures. Investigations on the expression of the artificial protein BP68 Due to the ease of transformation, cloning and high cell density cultivation, E. coli is by far the most widely used microorganism for the production of recombinant proteins and enzymes. In order to over-express BP68, E. coli strain BL21Gold(DE3) was transformed with the expression plas mid pBP68. The expression strain was cultivated at 37 °C in a 2-L shaking flask containing LB medium and kanamy cin at 37 °C. Protein expression was induced by IPTG after cooling to 24 °C. Use of temperature shift strategy combines the advantages of fast growth with reduced expression rates, which may lead to reduced inclusion body (IB) formation
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[30–32]. Samples were taken up to 4 h after induction and analyzed for BP68 expression by SDS–PAGE and Western blotting. To determine the amount of soluble and insoluble BP68, 1/OD samples were collected and lysed by small scale glass bead milling. After centrifugation, the pellet represents the insoluble fraction and the supernatant represents the solu ble fraction of BP68. A 10 lL sample of each fraction was analyzed by SDS–PAGE (Fig. 3). Unfortunately, staining of BP68 with Coomassie or sil ver showed only minor bands (see Fig. 8). Therefore, the detection of BP68 was performed by using an anti-His-tag specific antibody. Interestingly, several unexpected bands were detected. As can be seen from Figs. 3 and 4, there are major bands related to BP68 migrating at a MW equivalent to 24 kDa and one minor band of 36 kDa besides several thin bands. The monomeric BP68 exhibits a MW of exactly 12,361 Da. Obviously, even under the harsh conditions of SDS–PAGE, there is a strong interaction between diVerent
Fig. 4. Influence of the temperature after induction on the expression of BP68; (A) Growth curves of induced E. coli BL21 DE3 pBP68 cultivated until induc tion at 37 °C and at diVerent temperatures after induction (24, 30, 37 °C), the moment of induction was set to time zero; (B) Western blot using an anti-His antibody. Samples are taken after 1–4 h after induction, disintegrated and the insoluble fractions were analyzed for inclusion bodies containing BP68. Ten microliters of sample per lane. Nc, negative control, not induced; S, supernatant after cell disintegration (induced, growth after induction at 24 °C, 4 h).
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molecules of BP68 resulting in distinct bands of double and triple molecular weight. In addition, lysozyme used for cell disintegration is detected in Fig. 4. The target protein was produced mainly as the insoluble protein found in the pellet (Fig. 3). In order to investigate whether the production of the tar get protein could be increased at higher temperatures, the cultivation was repeated and the temperature after induc tion was varied. After initial growth at 37 °C until an OD of approximately 0.6 was reached, the temperature was adjusted to 24, 30 or 37 °C, respectively. Protein production was induced by the addition of IPTG, then 1/OD samples were taken and analyzed for inclusion body formation by SDS–PAGE (Fig. 4). As shown in Fig. 4, significant amounts of the target pro tein BP68 were obtained only at an induction temperature of 24 °C. Cell growth at induction temperatures of 30 or 37 °C did not yield any substantial amount of BP68 in the pellet. Interestingly the lysozyme used for cell disintegration was also stained with the anti-His-antibody. Using a minimal medium under optimal production conditions did not lead to the formation of BP68 (results not shown). Therefore, the mass production of BP68 using high cell density fed-batch cultivation was carried out in a complex medium. The temperature was lowered from 37 to 24 °C before induction. Mass production of BP68 using high cell density fed-batch cultivation In order to obtain enough biomass for the purification of BP68, a fed-batch fermentation was carried out using a com plex medium. The airflow was maintained at 4.0 stdL/min
throughout the fermentation. The stirrer speed was increased manually in order to maintain pO2 above 20%. The pH was controlled at 7.0 § 0.1. The temperature was lowered to 24 °C after reaching an OD600 of 15 after 5.5 h. Then, 12 mL of sterile 1 M IPTG solution were added (final concentration 1 mM). After 6.5 h the pO2 began to rise and feeding was started with a constant feed rate of 3 g/min. The time profiles of the measured parameters are shown in Fig. 5A. Samples were taken and analyzed oZine for the biomass content and the expression of BP68. In Fig. 5B, the Western blot of the samples after induction is shown. At the time of induction, no BP68 was detected. Approximately 1–3 h after induction, BP68 was detected as inclusion bodies, as observed in the shake flask experiments. Again, dimeric and trimeric aggre gates were detected. After 3 h of induction (total cultivation time 8.5 h) the biomass was harvested, washed and stored at ¡25 °C. This gave 460 g wet biomass, corresponding to a concentration of 38 g/L. Purification of BP68 Mechanical disintegration of E. coli using a glass bead mill or high pressure homogenization In order to scale up cell disintegration, both a technical glass bead mill and a high pressure homogenizer were used as described in Materials and methods. As can be seen from the SDS–PAGE shown in Fig. 6, glass bead milling resulted mainly in insoluble BP68 pro tein present in the pellet fraction. High pressure homogeni zation, on the other hand, resulted mainly in soluble target protein (Fig. 6B, lane 3). This result is caused either by the diVerent disintegration principles of glass bead milling and high pressure homogenization or by the higher local temper
Fig. 5. Fed-batch cultivation of E. coli BL21 DE3 pBP68 using a complex medium. (A) temperature and biomass vs. cultivation time, arrows indicate the time of induction and start of the fed-batch; (B) Western blot using an anti-His antibody of IB preparations of 1/OD samples taken at the indicated time (lane 1, time of induction; 2–4, induction time of 1, 2, 3 h), 10 lL sample per lane.
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Fig. 6. Cell disintegration of E. coli BL21 DE3 pBP68 using (A) a glass bead mill, and (B) an high pressure homogenizer (Western blot using an anti-His antibody, 10 lL sample per lane). P, pellet; S, supernatant after centrifuga tion at 16.100 g; IB, control prepared by inclusion body preparation using the enzymatic lysis procedure using lysozyme.
atures obtained with high pressure homogenization. The insoluble protein after glass bead milling was soluble in 50 mM Tris–HCl-buVer, (pH 8.0) containing 6 M urea (data not shown). As a result, the following purification steps using aYnity chromatography were performed using the homogenized soluble BP68. Purification of BP68 Basic binding studies were carried out in small scale in order to determine optimal conditions for aYnity chroma tography thus producing suYcient amounts of BP68 for subsequent characterization. Cell disintegration using the high pressure homogenizer was repeated using a cell concen tration of 230 g of E. coli wet mass dissolved in 1000 mL of
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Tris–HCl-buVer. A 150 mL sample of the BP68-containing cell homogenate supernatant was applied to the preparative Ni-NTA column as described in the Material and methods section. In order to ensure that BP68 did not precipitate during the chromatographic separation, 6 M urea was added to all solvents used. Also, 0.5 M sodium chloride was present in order to reduce ionic interactions with the elution per formed by a step gradient of imidazole. The developed chro matogram and the SDS–PAGE analysis of the fractions are shown in Figs. 7 and 8, respectively. As discussed before, BP68 could not easily be detected using staining with Coomassie brilliant blue or silver. The BP68 is also not visible at 280 nm due to the lack of aromatic amino acids in the sequence. Therefore the elution profile was measured at 230 nm. With the Western blot shown in Fig. 8C, it was again possible to detect the fractions containing BP68. At these high concentrations, it was also possible to observe some bands in the silver stained (Fig. 8B) and more faintly in the Coomassie stained SDS–PAGE (Fig. 8A). At molecular weights higher than 40 kDa there are other protein bands visible in the silver and Coomassie stained gels which do not react in the Western blot and therefore the target protein cannot be considered as pure. A more precise calculation is not reasonable, since the detection sensitivity of proteins by silver and Coomassie in PAGE depends on the type of pro tein ([33] and supporting information) and would be only possible, if the calibration would be carried out with BP68 itself. In order to get some more information about the purity of BP68, mass spectrometry was carried out (results see below).
Fig. 7. Preparative scale purification of BP68 using nickel chelate aYnity chromatography. Sample: Clarified lysate from E. coli containing BP68-His fusion protein after high pressure homogenization and centrifugation. Sample volume: 150 mL; fraction volume: 15 mL. Sequential elution was carried out at steps of 100 mM, 150 mM and 1 M imidazole. The box indicates the fractions analyzed by SDS–PAGE and Western blotting (see Fig. 8).
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Fig. 8. SDS–PAGE of the fractions obtained after Ni-aYnity chromatography of BP68 shown in Fig. 7 stained by Coomassie (A), silver (B), and Western blotting using an anti-His antibody (C) (10 lL applied to each lane). R, reference BP68 (IB preparation of 4 h induced cells grown at 37 °C and at 24 °C after IPTG addition); N, negative control of uninduced E. coli (1/OD sample), Sp, sample; F, flow through; M, marker.
The fractions containing BP68 were pooled and dia lyzed and subsequently lyophilized. Altogether, 15 mg protein was isolated from 150 mL disintegrated cell suspen sion which contained 34.5 g cell wet mass (CWM). With a CWM to cell dry mass (CDM) relation of 4:1 and a total protein concentration of 50% of the CDM (as determined for E. coli), the total amount of protein can be calculated to be approximately 4.3 g. Hence, the obtained yield of 15 mg corresponds to about 0.35% of the total protein, which is comparable low. Since only one chromatographic step was used and no BP68 loss was detected throughout the purification, that is, in the cell disintegration or in the flow through of the column, or during dialysis, obviously the expression in the host organism is the limiting step for a higher yield. In optimal E. coli expression systems, yields of a target protein of up to 40–50% of the total cell protein have been reported [30].
Characterization of the purified BP68 with two inserts MALDI mass spectrometry MALDI-TOF measurements were carried out as described in Materials and methods to investigate the purity and to confirm the integrity of the produced protein. From the spectrum shown in Fig. 9 it can be seen that (i) no impurities were detectable besides a minor abundant impurity with a molecular mass of 11,185 g/mol. Only peaks for the singly and doubly charged molecule ions of the target protein BP68 are present. Moreover, also the singly charged BP68 dimer, trimer, and tetramer were detected with small and decreasing intensities. (ii) The measured mass of 12,364 g/ mol agrees with the calculated average mass of 12,360.8 g/ mol within the error limitations of the instrument. Further more, this result was verified by static nanoelectrospray qTOF mass spectrometry. The deconvolution of the multiple
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Fig. 9. Positive ion MALDI-linTOF spectrum of isolated BP68 (solution of 1 mg/mL in ACN/0.1% TFA). The asterisk denotes the position of the sinapinic acid adduct of the protein. The analyte was prepared, using the dried droplet method, by mixing the sample with sinapinic acid.
charges of BP68 resulted in an even more precise mass of 12,359.88 § 1.5 g/mol (data not shown). In a third approach, using static nano-ESI-MS after digestion with trypsin and chymotrypsin, only peptides of BP68 were detected and iden tified with a sequence coverage of 50% (data not shown). In conclusion, experiments performed using two diVerent ionization methods (MALDI, nano-ESI) before and after proteolytic cleavage did not result in the detection of any con taminating protein or peptide apart from the one mentioned above. This result however, does not provide evidence that the target protein BP68 is completely pure. Like other tech niques, mass spectrometry is not a universal method and proteinogenic impurities might not be detectable because of low ionization eYciencies, low concentration, and/or sup pression eVects.
Conclusions
IR spectrum and solubility of BP68 The FT-IR spectrum of BP68 was recorded in the wave number range from 500 to 4000 cm¡1 (data not shown). The spectrum shows a number of unambiguous peaks that char acterize this protein. There is a broad band between 3000 and 3500 cm¡1 which corresponds to the OH groups of the amino acids serine and threonine [34]. In the same range, the N–H stretching vibration related to the amide bond system appears. Additionally, the asymmetric stretching vibration of the primary amino group of lysine appears in this region. Fur thermore, the two characteristic amide bands arising from the peptide linkage in proteins occur at 1658 and 1534 cm¡1 [35]. The protein BP68 is not soluble or swellable in water. The only solvent that could be used is trifluoroacetic acid. Triflu oroacetic acid is known to break strong hydrogen bonds in polyamides and is therefore frequently used as a good sol vent for poly (amino acids) or polyamides.
Acknowledgment
An artificial protein containing alternating hydrophilic– hydrophobic blocks of amino acids was synthesized. The protein was overproduced in E. coli, purified, and charac terized. However, the yield from the fermentation process was too small to carry out extensive application testing as biomedical material. In further studies, the expression level of the target protein and therefore, the concentration of the starting material have to be optimized. The designer pro tein forms dimers or trimers caused by intermolecular inter actions which were not broken even under the conditions of SDS–polyacrylamide gel electrophoresis, rendering the behavior during purification diVerent from proteins usually found in nature.
Carmen Scholz is deeply indebted to Dr. David Kaplan at the Tissue Engineering Resource Center, (NIH-P41) at the Department of Biomedical Engineering at Tufts Univer sity, Medford, MA, for providing an opportunity to gather hands-on experience in the field of recombinant polymers and for inspiring this entire project. References [1] G. Strobl, The Physics of Polymers, Springer, Berlin, 2007. [2] P. Alexandris, B. Lindman, Amphiphilic Block Copolymers, Elsevier, Amsterdam, 2000. [3] S.D. Hudson, H.-T. Jung, V. Percec, W.-D. Cho, G. Johansson, G. Ungar, V.S.K. Balagurusamy, Direct visualization of individual cylin drical and spherical supramolecular dendrimers, Science 278 (1997) 449–452.
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[4] J.M.J. Frechet, D.A. Tomalia, Dendrimers and Other Dendritic Poly mers, VCH-Wiley, Weinheim, 2002. [5] D.L. Kaplan, Spiderless spider webs, Nat. Biotechnol. 20 (2002) 239– 240. [6] R. Martin, L. Waldmann, D.L. Kaplan, Supramolecular assembly of collagen triblock peptides, Biopolymers 70 (2003) 435–444. [7] C. Wong, D.L. Kaplan, Genetic engineering of fibrous proteins: spi der dragline silk and collagen, Adv. Drug Deliv. Rev. 54 (2002) 1131– 1143. [8] M.T. Krejchi, E.D. Atkins, A.J. Waddon, M.J. Fournier, T.L. Mason, D.A. Tirrell, Chemical sequence control of beta-sheet assembly in macromolecular crystals of periodic polypeptides, Science 265 (1994) 1427–1432. [9] W. Shen, R.G.H. Lammertink, J.K. Sakata, J.A. Kornfield, D.A. Tir rell, Assembly of an artificial protein hydrogel through leucine zipper aggregation and disulfide bond formation, Macromolecules 38 (2005) 3909–3916. [10] E. Dessipiri, D.A. Tirrell, Trifluoroalanine N-carboxy anhydride: a reactive intermediate for the synthesis of low surface energy polype tides, Macromolecules 27 (1994) 5463–5470. [11] J.H. Lee, J. Kopecek, J.D. Andrade, Protein-resistant surfaces prepared by PEO-containing block copolymer surfactants, J. Biomed. Mater. Res. 23 (1989) 351–368. [12] M.J. Bridgett, M.C. Davies, S.P. Denyer, Control of staphylococcal adhesion to polystyrene surfaces by polymer surface modification with surfactants, Biomaterials 13 (1992) 411–416. [13] N.F. Owens, D. Gingell, P.R. Rutter, Inhibition of cell adhesion by a synthetic polymer adsorbed to glass shown under defined hydrody namic stress, J. Cell Sci. 87 (1987) 667–675. [14] J.S. Tan, P.A. Martic, Protein adsorption and conformational change on small polymer particles, J. Colloid Interface Sci. 136 (1990) 415– 431. [15] J. Lee, P.A. Martic, J.S. Tan, Protein adsorption on pluronic copoly mer-coated polystyrene particles, J. Colloid Interface Sci. 131 (1989) 252–266. [16] M. Amiji, K. Park, Prevention of protein adsorption and platelet adhe sion on surfaces by PEO/PPO/PEO triblock copolymers, Biomaterials 13 (1992) 682–692. [17] M.I. Kohan, Nylon Plastics Handbook, Hanser Gardner Pub., Munich, 1995. [18] J. Sambrock, E.F. Fritsch, T. Maniatis, Molecular Cloning—A Labora tory Manual, Cold Spring Harbor Laboratory Press, USA, 1989.
[19] T. Kieser, Factors aVecting the isolation of cccDNA from Streptomy ces lividans and Escherichia coli, Plasmid 12 (1984) 19–36. [20] C.T. Chung, S.L. Niemela, R.H. Miller, One-step preparation of com petent Escherichia coli: transformation and storage of bacterial cells in the same solution, Proc. Natl. Acad. Sci. USA 86 (1989) 2172–2175. [21] Qiagen, Bench guide: Competent Cells and Transformation, Qiagen, Hilden, Germany, 2001. [22] L. Yee, H.W. Blanch, Recombinant protein expression in high cell density fed-batch cultures of Escherichia coli, Biotechnology (NY) 10 (1992) 1550–1556. [23] H.E. Reiling, H. Laurila, A. Fiechter, Mass-culture density cultivation of Escherichia coli B/R in minimal and complex media, J. Biotechnol. 2 (1985) 191–206. [24] R. Rudolph, H. Lilie, In vitro folding of inclusion body proteins, FASEB J. 10 (1996) 49–56. [25] U.K. Laemmli, Cleavage of structural proteins during the assembly of the head of bacteriophage T4, Nature 227 (1970) 680–685. [26] G. Fairbanks, T.L. Steck, D.F. Wallach, Electrophoretic analysis of the major polypeptides of the human erythrocyte membrane, Biochem istry (Mosc.) 10 (1971) 2606–2617. [27] H. Blum, H. Beier, H.J. Gross, Improved silver staining of plant pro teins, RNA and DNA in polyacrylamide gels, Electrophoresis 8 (1987) 93–99. [28] V. Abetz, Block Copolymers I, Springer, Berlin, 2005. [29] L.J. McGuYn, K. Bryson, D.T. Jones, The PSIPRED protein structure prediction server, Bioinformatics 16 (2000) 404–405. [30] F. Baneyx, Recombinant protein expression in Escherichia coli, Curr. Opin. Biotechnol. 10 (1999) 411–421. [31] S. Jana, J.K. Deb, Strategies for eYcient production of heterologous proteins in Escherichia coli, Appl. Microbiol. Biotechnol. 67 (2005) 289–298. [32] C. Marx, T. Hertel, M. Pietzsch, Soluble expression of a pro-transglu taminase from Streptomyces mobaraensis in Escherichia coli, Enzyme Microb. Technol. 40 (2007) 1543–1550. [33] C. Winkler, K. Denker, S. Wortelkamp, A. Sickmann, Silver- and Coomassie-staining protocols: detection limits and compatibility with ESI MS, Electrophoresis 28 (2007) 2095–2099. [34] B.C. Smith, Infrared Spectral Interpretation: A Systematic Approach, CRC Press, Boca Raton, Florida, 1999. [35] D.C. Lee, P.I. Haris, D. Chapman, R.C. Mitchell, Determination of protein secondary structure using factor analysis of infrared spectra, Biochemistry (Mosc.) 29 (1990) 9185–9193.
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