Proteinase K-catalyzed synthesis of linear and star oligo(l-phenylalanine) conjugates

Article abstract of DOI:10.1021/bm4009974

Chemoenzymatic synthesis of peptides is a green and clean chemical reaction that offers high yields without using organic synthesis and serves as an alternative to traditional peptide synthesis methods. This report describes the chemoenzymatic synthesis of oligo(l-phenylalanine) mediated by proteinase K from Tritirachium album, which is one of the most widely used proteases in molecular biological studies. The synthesized linear oligo-phenylalanine showed a unique self-assembly in aqueous solutions. To further functionalize linear oligo(l-phenylalanine) as a low-molecular-weight gelator, it was cosynthesized with tris(2-aminoethyl)amine to obtain star-oligo(l-phenylalanine), which was bioconjugated to demonstrate its self-assembly into fluorescent fibers. The self-assembled fibers of star-oligo(l-phenylalanine) formed fibrous networks with various branching ratios, which depended on the molecular weights and molecular aspect ratios of star-oligo(l-phenylalanine). This is the first study to demonstrate that proteinase K is a suitable enzyme for chemoenzymatic cosynthesis of oligopeptides and star-shaped heteropeptides.

Full text of DOI:10.1021/bm4009974

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Article
Proteinase K-catalyzed synthesis of linear
and star oligo-L-phenylalanine conjugates
Jose M. Ageitos, Peter James Baker, Michihiro Sugahara, and Keiji Numata
Biomacromolecules, Just Accepted Manuscript • DOI: 10.1021/bm4009974 • Publication Date (Web): 03 Sep 2013
Downloaded from http://pubs.acs.org on September 9, 2013
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Proteinase K-catalyzed synthesis of linear and star
oligo-L-phenylalanine conjugates
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Jose M. Ageitos, Peter J. Baker, Michihiro Sugahara, Keiji Numata*
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Enzyme Research Team, Biomass Engineering Program Cooperation Division, RIKEN Center
for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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ABSTRACT
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Chemo-enzymatic synthesis of peptides is a green/clean chemical reaction that offers high yields
without using organic synthesis, and serves as an alternative to traditional peptide synthesis
methods. This report describes the chemo-enzymatic synthesis of oligo-L-phenylalanine
mediated by proteinase K from Tritirachium album, which is one of the most widely used
proteases in molecular biological studies. The synthesized linear oligo-phenylalanine showed a
unique self-assembly in aqueous solutions. To further functionalize linear oligo-L-phenylalanine
as a low-molecular-weight gelator, it was co-synthesized with tris(2-aminoethyl)amine to obtain
star-oligo-L-phenylalanine, which was bioconjugated to demonstrate its self-assembly into
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10 fluorescent fibers. The self-assembled fibers of star-oligo-L-phenylalanine formed fibrous
11 networks with various branching ratios, which depended on the molecular weights and molecular
12 aspect ratios of star-oligo-L-phenylalanine. This is the first study to demonstrate that proteinase
13 K is a suitable enzyme for chemo-enzymatic co-synthesis of oligopeptides and star-shaped
14 hetero-peptides.
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KEYWORDS. Chemo-enzymatic synthesis; oligo-phenylalanine; proteinase K; star peptide;
16 tris(2-aminoethyl)amine.
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Introduction
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Peptides are an emerging class of functional biopolymers with unique chemical, physical, and
biological properties that are not demonstrated by synthetic polymers. Peptides are short linear
chains of amino acids linked together in either repetitive or non-repetitive motifs. Among several
technologies used for peptide synthesis, solid phase and recombinant syntheses are the most
commonly used.1, 2 In solid-phase peptide synthesis, protected amino acid are bonded to other
amino acids through a process that requires multiple steps of protecting and de-protecting the
carboxyl and amine groups of amino acids; nevertheless, this technique can control the
composition and length of the peptides being synthesized. However, a lack of stereoselectivity
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10 and the use of strongly polluting agents are limitations of the method.3 Recombinant expression
11 allows peptide synthesis to be scaled up easily, but microorganisms often poorly express
12 repetitive peptides,2 especially cationic or hydrophobic peptides.4
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An alternative approach is chemo-enzymatic synthesis,1, 2 wherein an enzyme is used as a
14 catalyst to produce peptide bonds. Enzymes enable selective reactions to occur because their
15 active sites are stereoselective and have specific affinities for substrates.5 Proteases (peptidase)
16 are one of the most studied enzymes for peptide synthesis because they can act on the
17 polypeptide backbone.6 Peptides can be synthesized chemo-enzymatically using 2 approaches.
18 The first approach is thermodynamically controlled synthesis (TCS), which represents the
19 reverse reaction of hydrolysis. Proteases are enzymes that hydrolyze peptide bonds, but the
20 hydrolysis reaction can be reversed.1, 2 The reverse reaction is induced most conveniently by
21 using organic solvents6 that increase the solubility of products and limits hydrolysis, but an
22 excess of organic co-solvents can inactivate enzymes.6, 7 Because the reversal of hydrolysis with
23 organic solvents is carried out in absence of water or with as little water as possible,7 the reaction
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equilibrium is changed.1 However, any type of protease can be used in TCS because the protease
serves as a mold with affinity for the substrate and reduces the energy needed for the process.2
TCS requires large amounts of enzymes, but the yields are lower than those with other
alternatives6 such as kinetically controlled synthesis (KCS).1, 2, 5, 6 In the case of KCS, activated
amino acids are used, often with a modified ethyl or methyl ester as the carboxylic end. After the
first enzymatic step, which is similar to esterase activity, the enzyme forms a covalent
intermediate complex with the substrate (ES complex. Scheme I), allowing the amine group of
the other amino acid to act as a nucleophile. The enzyme functions as a transferase, and after
aminolysis has generated a peptide bond, the product is released. If water acts as a nucleophile,
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10 hydrolysis occurs and terminates the reaction. Because a covalent ES complex must be formed,
11 only serine and cysteine proteases can be used for this strategy.1 The proteases used most
12 commonly in chemo-enzymatic synthesis of polypeptide are papain, bromelain, and
13 chymotrypsin.2, 5, 8 Unlike with TCS, with KCS the yield and efficiency of synthesis are affected
14 by the type of enzyme, or conditions of synthesis, 1, 9 indicating that the search for new enzymes
15 for use as catalysts is critical for developing chemo-enzymatic synthesis of polypeptides.
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Proteinase K (pro K) (EC 3.4.21.64) from Tritirachium album is one of the most widely used
17 proteases in molecular biology.10 This serine protease works in broad pH and temperature ranges,
18 being able to operate on substrates and under conditions not suitable for other enzymes.11 Pro K
19 shows affinity for aromatic or hydrophobic residues, and its hydrolytic activity is promoted
20 strongly by long N-terminal regions of peptide substrates.11 Pro K can hydrolyze numerous
21 peptide substrates, and even some non-proteins such as Poly(l-lactic acid),12 which made us
22 consider that peptides can be co-synthesized with non-amino acids using pro K.13 These
23 characteristics make pro K an interesting candidate for the synthesis of star (branched) aromatic
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peptides, which can function as low-molecular-weight gelators (LMWGs). LMWGs are small
molecules that can self-assemble into gels or nanostructures through hydrogen bonding,
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hydrophobic interactions, and π–π stacking in aqueous solutions.14 Phenylalanine-based peptides
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14, 15, 16, 17, 18
have been widely studied as key LMWGs
because these peptides can form
nanostructures or gel-like molecular networks with distinct characteristics depending on the
synthesis conditions.
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Scheme I. Proteinase K-catalyzed oligo-l-phenylalanine synthesis via kinetically controlled
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synthesis (KCS)
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This report describes KCS of oligo-L-phenylalanine [oligo(Phe)] in aqueous solution mediated
11 by pro K. The resultant product self-assembled in amyloid-like fibers, which also form a gel-like
12 fibril network. The self-assembly behavior was controlled by peptide concentration and
13 temperature. To functionalize oligo(Phe) by branching the peptide, it was co-synthesized with
14 Tris(2-aminoethyl)amine (TREN), whose amines acted as nucleophiles (Scheme I). This organic
15 ligand, used traditionally in coordination chemistry, can increase the flexibility and alter the
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morphology of peptide structures.19 Oligo(Phe)-TREN conjugates [TREN(Phe)] self-assembled
into fluorescent fibers (Scheme I). We demonstrate that the star structure of peptides
functionalizes LMWGs20 and that pro K is a suitable enzyme for synthesizing peptides precisely
using organic ligands.
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EXPERIMENTAL SECTION
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Materials: L-phenylalanine ethyl ester hydrochloride (L-Phe-Et), L-phenylalanine methyl
ester hydrochloride (L-Phe-Met), and proteinase K (pro K) were purchased from Wako Pure
Chemical Industries (Osaka, Japan). L-Phenylalanine (PheOH), tris(2-aminoethyl) amine
(TREN) and trifluoroacetic acid (TFA) were purchased from Sigma-Aldrich (St. Louis, MO).
10 Standard chemicals were purchased from Wako Chemical Co. (Kanagawa, Japan).
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Proteinase K-Catalyzed Oligo(Phe) Synthesis. Synthesis conditions were determined based
12 on previous protocols 8, 9, 21, 22. Chemoenzymatic reaction at pH 8 is described as a typical
13 example. Standard reactions were carried out with a final volume of 5 mL, 0.6 M L-Phe-Et, 1
14 mg/mL Pro K (21 U/mg) in 0.9 M phosphate buffer in a 25 mL glass reaction tube. The reactions
15 were performed with stirring (1000 rpm) in EYELA ChemiStation (Tokyo, Japan) at 40 °C for 3
16 h. In order to optimize L-Phe-Et ester polymerization conditions with pro K, reactions were
17 carried out by triplicate, varying the amount of L-Phe-Et (0 to 1 M), concentration of enzyme (0
18 to 10 mg/mL, 0 to 210 U/mg), temperature (24 to 60 °C) and pH (6 to 10). Citrate buffer (pH 6;
19 0.9 M), phosphate buffer (pH 8; 0.9 M), Tris(hydroxymethyl)aminomethane-HCl buffer (TRIS)
20 (pH 8; 0.9 M) and sodium carbonate buffer (pH 10; 0.9 M) were used for each reactions at
21 different pH. After the reaction, for inactivation of the enzyme, the reaction mixture was heated
22 at 100 °C for 10 min and cooled to 25 °C. Oligo(Phe) was purified by centrifugation at 12,000 g,
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25 °C for 5 min, pellets were suspended in 10 mL Milli-Q (MQ) water. The resultant solution
was then dialyzed overnight against MQ water using cellulose dialysis membranes
(Spectra/Por® Biotech cellulose ester (CE); MWCO. 100-500 Da; Spectrum Laboratories Inc.,
Rancho Dominguez, CA). The oligo(Phe) solution was frozen at -80 °C and lyophilized.
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Also, a time course study was performed on the pro K-mediated oligo(Phe) synthesis. The
reactions were carried out at 40 °C and were stopped by addition of 1 mL of chilled proteomic
grade acetone at different time points (0 to 180 min). Following, the reaction mixture was
centrifuged at 16,000 g, 25 °C for 5 min. The resultant pellet was dried at 60 °C for a week.
Based on the weight of the dried product, yield of oligo(Phe) in the reaction was calculated.
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Synthesis of TREN Based Peptides. Tris(2-aminoethyl) amine (TREN) was used as
11 nucleophile during the aminolysis extension step in the kinetically controlled peptide reaction
12 (Scheme I). Several ratios of monomer (L-Phe-Et):TREN were assayed (1:6, 1:9, 1:15 and 1:30)
13 in 0.9 M phosphate buffer (pH 8) with 1 mg/mL of pro K. The reactions were performed as
14 described above in oligo(Phe) synthesis.
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Nuclear Magnetic Resonance. 1H NMR, gCOSY (Two Dimensional J-correlation
16 spectroscopy with gradient coherence selection) and gHMBCAD (Two dimensional
17 heteronuclear multiple-bond J-correlation spectroscopy with adiabatic 180° X-nuclei pulses and
18 gradient coherence selection) spectra were recorded on Varian NMR System 500 (500 MHz)
19 spectrometer (Varian Medical Systems, Palo Alto, CA) at 25 °C controlled with VnmrJ. The
20 lyophilized samples were suspended in deuterated dimethyl sulfoxide (DMSOd6) containing 1%
21 Trifluoroacetic acid (TFA) at 10 mg/mL; 256 scans were recorded. Tetramethylsilane (TMS)
22 was used as internal reference at 0.00 ppm. Data were processed and analyzed by ACD/NMR
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Processor Academic Edition, version 12.01 (Advanced Chemistry Development, Inc., Toronto,
On, Canada, www.acdlabs.com, 2010).
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Tris(2-aminoethyl) amine: 1H NMR (500 MHz, DMSO-d6 : 1% CF3COOH, TMS δ ppm):
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2.48 (t, J=5.87 Hz, 6 H); 2.67 (t, J=5.99 Hz, 6 H); 4.25 (s, 9 H).
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Oligo(Phe): 1H NMR (500 MHz, DMSO-d6 : 1% CF3COOH, TMS δ ppm): 1.08 (t, J=7.09 Hz,
3 H) (a); 3.02 - 3.24 (m, 28 H) (b); 4.05 - 4.13 (m, 2 H) (c); 4.16 (t, J=6.97 Hz, 12 H) (d); 4.24 (t,
J=6.72 Hz, 1 H) (d’); 7.10 - 7.45 (m, 66 H) (e); 8.44 (br. s.) (f); 8.67 (br. s.) (f’).
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TREN(Phe) 1:6: 1H NMR (500 MHz, DMSO-d6 : 1% CF3COOH, TMS δ ppm): 2.64 (t,
J=5.87 Hz, 6 H) (t1); 2.92 - 3.00 (m, 6 H) (t2); 3.11 (d, J=6.36 Hz, 16 H) (b); 4.11 - 4.24 (m, 8
10 H) (d); 7.22 - 7.45 (m, 42 H) (e); 7.97 (br. s.) (t3); 8.38 (br. s.) (f).
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TREN(Phe) 1:30: 1H NMR (500 MHz, DMSO-d6 : 1% CF3COOH, TMS δ ppm): 1.08 (t,
12 J=7.09 Hz, 1 H) (a); 2.61 - 2.68 (m, 6 H) (t1); 2.98 (br. s., 6 H) (t2); 3.12 (d, J=6.60 Hz, 45 H)
13 (b); 4.14 (t, J=6.36 Hz, 21 H) (d); 7.11 - 7.52 (m, 119 H) (e); 8.08 (br. s.) (t3); 8.39 (br. s.) (f).
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Fourier Transform Infrared spectroscopy (FTIR). FTIR absorption spectra of lyophilized
15 samples [oligo(Phe) and Phe(TREN)] were collected using a Shimadzu IR- Prestige-21 FTIR
16 spectrometer (Shimadzu, Kyoto, Japan) equipped with a multiple-reflection, horizontal MIRacle
17 ATR attachment from 700 to 2000 cm−1 at 4 cm−1 resolution, using 100 scans. 21
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Optical and Confocal Laser Scanning Microscopy. Self-assembling and fiber formation
19 were monitored by optical microscopy, in these experiments 15 µL of enzymatic reaction or
20 peptide solution (10 mg/mL) were transferred onto a cover slip. Additionally, fixed samples were
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performed as described in literature24, briefly, peptide samples were dissolved in 60% methanol
in water, 10 µL drop of solution was loaded onto a glass slide and dried at 25 °C. The samples
were visualized in a polarized light microscopy (BX51, Olympus, Hamburg, Germany).
Confocal laser scanning microscopy was performed in a LSM 700 (Carl Zeiss Jena, Germany)
with an excitation wavelength of 405 nm and 450 nm of emission.
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Scanning Electron Microscopy. Samples were dissolved at 10 mg/ml in 60% methanol, 10
µL drop of solution was dried in freshly cleaved mica and coated with gold. SEM images were
recorded using a JSM JEOL 6330F scanning electron microscope (JEOL, Tokyo, Japan)
operating at 7 kV.
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Cell cytotoxicity experiments. Human Embryonic Kidney 293 cells (HEK293) (8 × 104
11 cells/mL) were cultured in 96-well micro plates (100 µL/well) and incubated overnight at 37 °C
12 in Dulbecco’s modified Eagle’s medium (D-MEM) without phenol red (Wako Chemical Co.),
13 supplemented with 10% fetal bovine serum, 0.1 mM nonessential amino acids, 1 ng/mL basic
14 fibroblast growth factor, 100 U/mL penicillin, 100 µg/mL streptomycin and 0.25 µg/mL of
15 amphotericin B. Stock solutions of oligo(Phe), Phe(TREN), PheOH dissolved in Dulbecco’s
16 phosphate buffer saline [D-PBS(-)] (pH 7.4) were added to each well with a final concentration
17 0.5 to 50 mM. Control reactions were performed with addition of D-PBS(-). Following
18 incubation for 8 hours at 37 °C, cell viability was evaluated using CellTiter 96® AQueous One
19 Solution Cell Proliferation Assay kit (Promega Corporation, Madison, WI). The cell viability
20 was calculated as follows: [absorbance at 490 nm of the cell culture incubated with
21 sample]/[absorbance at 490 nm of the negative control] x 100. Each experiment was repeated 3
22 times.
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Results and Discussion
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Although pro K is widely used in molecular biology, to our knowledge this is the first time pro
K has been studied for KCS. Optimal conditions for peptide synthesis must be determined to
enhance product yield and to increase the average degree of polymerization (DPavg).21 Previously,
oligo(Phe) was synthesized successfully using bromelain22 (16.6 mg/mL, 125 mM L-
phenylalanine ethyl ester (L-Phe-Et), 0.25 M phosphate buffer, 30% methanol, pH 8, 40 °C, 3 h;
yield 51%, DPavg 8.2) and papain23 (12 mg/mL, 200 mM L-phenylalanine methyl ester (L-Phe-
Met), 1 M phosphate buffer, pH 7, 40 °C, 24 h; yield 60%, DPavg. 6). Pro K-mediated synthesis
of oligo(Phe) here followed KCS (Scheme I). Organic solvents, which are not required for KCS,
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10 were not used in reactions; this was in line with the concept of clean technology, which is one of
11 the main advantages of enzymatic peptide synthesis over solid-phase peptide synthesis.
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Figure 1. Photograph of oligo-phenylalanine synthesized after 3 h (A). Optical microscopy
14 images of fibers in water (B) and under polarized light (C); scale bars represent 100 µm. Oligo-
15 phenylalanine synthesized using proteinase K in 1 h; time-lapse series interval, 10 min (D).
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Effect of pH and temperature in oligo(Phe) synthesis. To clarify the effect of pH on
17 synthesis, reactions were carried out in 0.9 M of these buffers: sodium carbonate (pH 10),
18 sodium phosphate and TRIS-HCl (pH 8), and sodium citrate (pH 6). After incubating for 1 h, the
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reaction mixtures appeared to change, forming a precipitate in the bottom of the tubes that
transformed into a gel-like structure eventually (Figure 1). Negative control samples without pro
K showed no detectable changes, indicating that the precipitation was caused by the enzymatic
reaction. The highest yield was achieved at pH 8 (Figure 2A), and the yield of reactions in
phosphate buffer (65.5% ± 4.2%) was higher than in TRIS buffer (50.5% ± 3.3%). In KCS, yield
and DPavg are affected by the reaction pH,21 because pH affects enzymatic activity and product
solubility concomitantly. Solubility of phenylalanine peptides depends strongly on their self-
assembling properties.24 For example, diphenylalanine (Phe-Phe) starts self-assembling at its
isoelectric point (pH 5.5).25 Because the optimal pH of reactions tends to decrease in KCS,26
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10 alkaline conditions delay the precipitation or self-assembly of products. Figure 2 shows yields at
11 distinct pH values and temperatures. At pH 10, reaction yields were lower and hydrolysis was
12 increased (Figure 2A). Similarly, although increasing the temperature improved product
13 solubility, the yield was diminished and hydrolysis was increased (Figure 2B). The yield and
14 DPavg at 24 °C and 40 °C were not significantly different, but the reaction kinetic was more stable
15 at 40 °C (Figure 2B). Based on these results, phosphate buffer (pH 8) at 40 °C was chosen for
16 further optimization studies.
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Figure 2. Effect of pH (A) and temperature (B) on the yield of oligo-phenylalanine from 0.6
M L-phenylalanine ethyl ester using 1 mg/mL of proteinase K. Error bars represent the standard
deviation of the replicates.
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Effect of enzyme and substrate concentrations on oligo(Phe) synthesis. Unlike in TCS, in
KCS, enzyme/substrate ratios must be finely tuned to maximize product yield.1, 5, 9 Thus,
reactions with several concentrations of pro K were examined (Figure 3A), which showed that
precipitates formed more quickly in reactions with higher concentrations of enzyme.
Additionally, when reaction yields were measured at 3 h and 8 h, the highest concentrations of
10 enzyme (5 and 10 mg/mL) were found to produce lower yields and hydrolyze the product (loss
11 of ester end) (Figure 3A). Pro K appears to be more active than other proteases for KCS of
12 peptides22, 23 because a 10-times lower concentration of the enzyme was required for oligo(Phe)
13 synthesis. However, pro K can hydrolyze products when used at high concentrations, especially
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with lengthy incubation times (Figure 3). The kinetics of the reaction using 0.6 M of L-Phe-Et
and 1 mg/mL of pro K demonstrated that 120 min was the optimal reaction time to achieve the
maximal yield of approximately 65% (Figure 3B). The reaction behavior was similar to that
reported for bromelain-mediated synthesis of oligo-phenylalanine,22 but with pro K the yield was
higher and the reaction time was shorter than with bromelain. Moreover, bromelain required
20% methanol with phosphate buffer for the reaction.22 The effect of substrate concentration was
also studied using 1 mg/mL pro K in reactions (Figure 3C), and the highest yield was obtained
with 0.6 M of L-Phe-Et. Perhaps because of pro K’s strong hydrolytic activity, a higher
concentration of monomer is needed to induce KCS of oligo(Phe) with pro K than with
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10 bromelain22 (0.125 M) or papain23 (0.2 M), but productivity is better in terms of time and reaction
11 volume. Moreover, by using pro K, product purity can be enhanced, because a lesser amount of
12 the enzyme is required for synthesis.
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Effect of monomer type on oligo(Phe) synthesis. Although the substrate affinity of pro K is
14 not fully known, the enzyme shows distinct affinities for substrate in its esterase activity.11 To
15 study pro K’s substrate specificity for monomers in KCS, the yields of L-Phe-Et and L-Phe-Met
16 reactions were evaluated. Reactions were carried out under the optimal conditions defined above,
17 0.6 M of monomer, 1 mg/mL of pro K, 0.9 M phosphate buffer pH 8, for 3 h. L-Phe-Met and L-
18 Phe-Et reactions showed yields of 67.63% ± 4.18% and 65.48% ± 4.15%, respectively, although
19 structural analysis showed that in the L-Phe-Met reactions, approximately 70% of products were
20 hydrolyzed after 3 h. L-Phe-Met has been reported to hydrolyze products,23 but the extent of
21 hydrolysis was not substantial. Thus, with pro K as a catalyst, distinct products (OH or ester end)
22 can be synthesized by selecting methyl or ethyl esters monomers.
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Figure 3. A. Effect of the concentration of proteinase K on the reaction yield at 3 h and 8 h. B.
Time course of reaction using 0.6 M L-phenylalanine ethyl ester in 0.9 M phosphate buffer, pH 8,
containing 1 mg/mL of proteinase K. C. Effect of monomer concentration in the synthesis of
oligo-phenylalanine by proteinase K. Error bars represent the standard deviation of replicates.
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Molecular weight and chemical structure of oligo(Phe). NMR signals were assigned
according to references22 and 2D NMR (gCOSY) (Figure S1A). DPavg was calculated using the
relative integration valuesof N-terminal CHα (d’) and ethyl protons (c and a) to internal chain
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CHα (d), CHβ (b), and the phenyl ring (e).22 Subsequently, the degree of hydrolysis (loss of ester
end) was calculated using the relative integration values of d’ against c and a, and the carboxylic
signals in carbon-proton long-range interactions (gHMBCAD) (Figure S1). The DPavg was 12 ±
0.5 after 3 h for reactions carried out using 0.6 M L-Phe-Et, 1 mg/mL of pro K in phosphate
buffer (pH 8) at 40 °C. Reactions carried out in phosphate buffer with 0.6 M of L-Phe-Met
showed a DPavg of 6.9. Because the L-Phe-Met sample contained a high proportion of hydrolyzed
products as noted above (Scheme I), to avoid overestimating DPavg, in addition to accounting for
methyl and terminal groups, the ratio of the integrated areas of amino ends and chain repetition
must be calculated. The yield obtained was higher than that reported by Schwab et al.,23 although
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10 with similar DPavg. In contrast, the reactions carried out in TRIS buffer did not show substantial
11 hydrolysis, with DPavg values of 4.8 and 4.7 for L-Phe-Met and L-Phe-Et synthesis, respectively.
12 The TRIS buffer appears to limit the solubility of oligo(Phe) and thereby reduce hydrolysis and
13 DPavg. The NMR studies of purified product did not show the contamination of protease,
14 suggesting that the concentration of pro K in purified product was low enough to be ignored
15 when properties of oligo(Phe) and TREN(Phe) were discussed. Matrix-assisted laser desorption-
16 ionization time-of-flight mass spectrometry was not used to determine the molecular weight of
17 oligo(Phe), because this method was reported to detect its fragmented products rather than
18 oligo(Phe), resulting in underestimation of the molecular weight.22
19
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Figure 4. Bars: yields of oligo-phenylalanine:Tris(2-aminoethyl) amine [TREN(Phe)]
polymers with synthesis carried out in 0.9 M phosphate buffer pH 8 with 1 mg/mL of proteinase
K. Line: Average degree of polymerization of polymers (Dpavg). Error bars represents the
standard deviation of replicates.
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Synthesis and structural analysis of TREN-based oligo(Phe). TREN is an organic ligand
that can increase peptide flexibility and, when combined with LMWGs such as oligo(Phe),
produce star peptides with new properties.19, 20 Recently, chemically synthesized Phe-Phe TREN
conjugates were reported to self-assemble into structures with diverse morphologies.19 (Phe-
Phe)3TREN conjugates were synthesized through several steps using protected amino acids and
10 strongly polluting agents,19 and these star peptides self-assembled into branched fibers and
11 spheres.19 Because pro K can act not only on peptides substrates but also polyesters, we sought to
12 use KCS-mediated chemo-enzymatic synthesis with pro K to produce star peptides. TREN-based
13 oligo-Phe synthesis was designed as a co-polymerization process using the conditions optimized
14 for linear polymers. In this process, one of the 3 free amino groups of TREN acts as a
15 nucleophile (Scheme I) for the L-Phe-pro K complex, producing a star peptide. Similarly, free
16 amines of TREN(Phe) act as nucleophiles until the size or molecular interactions changes the
17 solubility. To characterize the mechanism of this reaction, several ratios of TREN and monomer
18 were used (TREN:monomer, 1:6, 1:9, 1:15, 1:30), and reaction yields were found to range from
19 42% to 75% (Figure 4).
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DPavg values of TREN(Phe) peptides were calculated by accounting for the integration values
21 of t1 and t2 signals as 6 H (Experimental Section). The resulting values were divided into the
22 theoretical tri-branch points. As a result, the distinct ratios used in TREN(Phe) synthesis (1:6, 1:9,
23 1:15, 1:30) showed that DPavg values of peptides decreased in relation to the amount of TREN
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(Figure 4). By using TREN, polydispersity of the reaction can be lowered. In the sample with
1:30 ratio, linear and star polymer (methyl signal a) co-existed, suggesting that higher ratios do
not enhance the DPavg of peptides. NMR signals (Figure S2) were assigned as described19, 22, 27 and
according to the study of oligo(Phe) (Figure S1). The shift in TREN signals observed were
similar to that reported for TREN conjugates.19, 27 In gCOSY analysis, the amino signal at 7.89
ppm (t3) was found to correlate with a signal at 2.94 ppm (t2), which in turn is correlated with
2.64 ppm (t1). Additionally, gHMBCAD connected TREN and phenylalanine signals (Figure S2),
and the connection between TREN and oligo(Phe) was confirmed using Fourier transform
infrared spectroscopy (Figure S3), which revealed a peak of 1643 cm-1 that is not present in
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10 oligo(Phe) and was reported for the NCO bond in TREN conjugates.19, 27
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Microscopic observation of oligo(Phe) and TREN(Phe) structures
Oligo(Phe) reactions acquired fibrous scaffold appearance after reaching 40% yield (1 h in
13 standard reaction) (Figures 1D and 3B). Microscopic observation of reaction mixtures showed
14 that the gel was composed of long birefringent fibrils with a diameter of 1 µm (Figure 1).
15 Because self-assembly of phenylalanine peptides24 is affected by the solubility of peptide
16 monomers in solution, the purified product of reactions (white powder) was dissolved in several
17 solvents (water, methanol, and buffers at pH 6, 8, and 10). At pH 6, the samples acquired a
18 crystalline aspect, whereas at alkaline pH, oligo(Phe) showed better solubility. No significant
19 differences in fiber morphology between reactions at different concentrations of enzyme were
20 observed, suggesting that the enzyme did not affect the self-assembling behavior. Purified
21 oligo(Phe) self-assembled into fibers in aqueous solution, and after heating 10 mg/mL at 85 °C,
22 oligo(Phe) formed a gel composed of long, 1-µm-diameter fibers (Figure S4). These fibers can
23 be also observed after drying oligo(Phe) in 60% methanol. Self-assembly was more evident in
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samples with a higher degree of hydrolysis, as with L-Phe-Met or in reactions carried out in
carbonate buffer, which can be explained by the presence of ethyl ends in oligo(Phe) that can
reduce the ionic interactions that occur more favorably with carboxylic ends in fiber formation.17
Samples with ethyl ends tend to form long crystal structures. Moreover, structural configuration
of the fibers can also affect proteolysis: Ryu et al.28 reported that the susceptibility of Phe-Phe
nanotubes to proteolytic attack by pro K changed with their morphology, with nanowires being
more resistant to proteolysis than nanotubes. Our results indicate that oligo(Phe) fibers are not
hollow, being more akin to flat wires than to tubes, and show morphologies that appear in
amyloid peptides29 or pentafluorophenylalanine18 fibers. Because the flat morphology can help
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10 oligo(Phe) resist hydrolysis, the conformation of the peptide could affect the degree of hydrolysis
11 as well as the length of the product.
12
The TREN(Phe) synthesis reaction mixtures showed complex crystals and fibers depending of
13 the TREN:monomer ratio used, resembling oligo(Phe) more in samples with ratios 1:15 and 1:30.
14 Purified samples, which were yellowish white to white powders, formed fibrils water evaporated.
15 Under polarized light, the fibers appeared discontinuous, suggesting a twisted fibril structure
16 (Figure 5A), which was more evident in samples with lower TREN:monomer ratios (1:6 and 1:9).
17 Unlike oligo(Phe) that remained soluble, TREN(Phe), in the 1:6 ratio samples, self-assembled
18 into fibers in 60% methanol after 1 h at 24 °C at 10 mg/mL. Laser scanning microscopy showed
19 that TREN(Phe) fibers auto-fluoresced at 405 nm (Figure 5B), with the fluorescence intensity
20 being proportional to TREN concentrations (data not shown). The observation of fluorescence
21 confirmed the conjugate synthesis of TREN and oligo(Phe).
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Figure 5. Microscopic observation of dry TREN(Phe) samples. A. Optical micrograph under
polarized light. B. Fluorescence micrograph, with excitation at 405 nm.
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Phenylalanine peptides can form multiples structures depending on their concentrations or
reaction conditions used.16, 28 To simplify comparisons of fiber formed by peptides with different
branched structures, only low and high TREN:monomer ratios (1:30 and 1:6) were included.
When samples were dissolved in 60% methanol and allowed to dry immediately, self-assembly
was observed after the solvent evaporated (Figure 6A-C). Oligo(Phe) samples showed radial
growth of straight fibers, 1:30 TREN(Phe) showed branched fibers, and 1:6 TREN(Phe) showed
10 branch structures and spheres (as reported for chemically synthetized (Phe-Phe)3TREN
11 conjugates19). SEM imaging of oligo(Phe) revealed 1-µm-diameter fibers attached to mica,
12 whereas the TREN-based peptides presented fibers 50 nm in diameter that matted into thicker
13 fibers that were 150 nm and 1 µm in diameter (Figure 6D-F). The 50-nm-diameter fibers were
14 similar in size to Phe-Phe nanotubes described previously17, 24, 28, 30 and to other LMWGs,18, 31, 32
15 but their non-hollow, flat structure was unlike the structure of dipeptide nanotubes. Fibers of
16 TREN(Phe) peptides were interconnected and formed complex scaffolds. In agreement with
17 observations using optical microscopy (Figure 6A-C), SEM revealed that TREN enhanced
18 flexibility in the interaction between oligo(Phe) peptides by increasing fiber connections (Figure
19 6D-F). Furthermore, peptides with properties similar to Phe-Phe or longer oligomer could be
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obtained by controlling branching-aspect ratios, which, in turn, can be controlled by the
monomer:TREN ratio in reactions.
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Figure 6. A-C. Dark field microscopy of dry film fibers. A. Oligo(Phe). B. 1:30 TREN(Phe).
C. 1:6 TREN(Phe). D-F. Scan-ning electron micrographs of 60% methanol xerogels. D.
Oligo(Phe). E. 1:30 TREN(Phe). F. 1:6 TREN(Phe).
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Cytotoxicity assays. Because oligo(Phe) and TREN(Phe) formed fibrous structures
resembling amyloid fibers, their potential toxicity was evaluated by incubating Human
Embryonic Kidney 293 (HEK 293) cells for 8 h with several concentrations of oligo(Phe),
10 TREN(Phe), and l-phenylalanine (PheOH). Control experiments were conducted using the same
11 volume of Dulbecco’s phosphate-buffered saline. PheOH has been reported to be cytotoxic at
12 high concentrations.33 The peptides assayed here showed no more toxicity than PheOH. When
13 oligo(Phe) was compared with amyloid peptides (cytotoxic peptide), the cytotoxicity of
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oligo(Phe) was nearly 300-times lower than that of amyloid peptides,34 and 36-times lower than
that of the hydrolyzed products of amyloid peptides.35
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Figure 7. HEK 293 cell viability after 8 h in the presence of several concentrations of l-
phenylalanine (PheOH), oligo-phenylalanine [oligo(Phe)], oligo-phenylalanine:TREN
[TREN(Phe)], and negative control (C). Error bars represents the standard deviation of replicates
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These results demonstrate that phenylalanine-based peptides can be used for at least 8 h in
biological environments without producing high toxicity. The low cytotoxicity observed with
TREN(Phe) peptides is similar that reported for polyphenylalanine-grafted hyperbranched
10 polyethylenimine in gene transfection,36 which opens up possibilities for new applications of
11 these polymers. Oligo(Phe) and TREN(Phe) peptides show similar cytotoxicity levels as silk β-
12 sheet peptides, which also form fibril scaffolds.37 Collectively, the above findings indicate that
13 bioconjugates between oligo(Phe) and TREN are not significantly cytotoxic and that they are
14 sufficiently biocompatible to be used in biomedical applications, for example in the development
15 of tissue-engineering scaffolds.
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Conclusions
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This work evaluated the suitability of pro K as an enzyme for KCS of hydrophobic peptides.
Pro K is one of the most widely used proteases because of its high proteolytic activity, but the
high processivity of pro K can be converted to synthesis by using a high substrate/enzyme ratio.
Given the affinity of pro K for aromatic amino acids, the synthesis of phenylalanine oligomers
by pro K was examined and the effects of various conditions on yield and product length were
measured. Polymer length could be controlled by using distinct buffers (DPavg 4.7 to 12), and the
hydrolysis of ester ends could be promoted by substrate engineering (changing ethyl to methyl
ester increased hydrolysis by 70%) or by modifying pH and temperature. The product obtained
formed amyloid-like fibers that self-assembled into a fibrous network depending on
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10 concentration, pH, and temperature; self-assembly was promoted by unprotected carboxylic ends.
11 Conversely, we synthetized branched TREN polymers by KCS and were able to influence the
12 average length and yield of the polymer by modifying the terminator:monomer ratio. TREN(Phe)
13 could self-assemble into fluorescent fibers in 60% methanol or organic solvents. These star
14 peptides showed the propensity to develop interconnections robustly during fibril formation.
15 Despite forming amyloid-like fibers, the phenylalanine oligomers were not found to be more
16 cytotoxic than their hydrolysis product phenylalanine. Pro K is a suitable enzyme for peptide
17 synthesis because it responds to reaction modifications, which makes it possible to engineer the
18 reaction process to generate diverse products. The high cost of pro K compared with that of other
19 proteases is compensated for by the low amounts of pro K required for reactions and its high
20 enzymatic activity. The combination of high affinity for certain amino acids and low overall
21 specificity makes pro K an ideal candidate for further developing precise peptide synthesis
22 methods.
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Supporting Information.
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Figure S1. 2D NMR study of oligo(Phe); Figure S2. 2D NMR study of TREN(Phe) 1:6;
Figure S3. Fourier transform infrared spectra of oligo(Phe) and TREN(Phe); Figure S4: Self-
assembling pattern of oligo(Phe). This material is available free of charge via the Internet at
http://pubs.acs.org.
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AUTHOR INFORMATION
Corresponding Author
* Tel: +81-48-467-9525. Fax: +81-48-462-4664. E-mail: keiji. numata@riken.jp.
9
Author Contributions
10 The manuscript was written through the contributions of all authors. All authors have given
11 approval to the final version of the manuscript.
12 Funding Sources
13
This study was financially supported by the RIKEN Biomass Engineering Program.
14 ACKNOWLEDGMENT
15 We thank Dr. Kazuyuki Ishikawa for his help with SEM imaging and Dr. Jo-Ann Chuah for her
16 support in cytotoxicity assays.
17 REFERENCES
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20 (3) Hojo, K.; Ichikawa, H.; Maeda, M.; Kida, S.; Fukumori, Y.; Kawasaki, K. J. Pept. Sci. 2007,
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