Effect of Mid-infrared Free-Electron Laser Irradiation on Refolding of Amyloid-Like Fibrils of Lysozyme into Native Form
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Aggregation of lysozyme in an acidic solution generates inactive amyloid-like fibrils, with a broad infrared peak appearing at 1,610–1,630 cm−1, characteristic of a β-sheet rich structure. We report here that spontaneous refolding of these fibrils in water could be promoted by mid-infrared free-electron laser (mid-IR FEL) irradiation targeting the amide bands. The Fourier transform infrared spectrum of the fibrils reflected a β-sheet content that was as low as that of the native structure, following FEL irradiation at 1,620 cm−1 (amide I band); both transmission-electron microscopy imaging and Congo Red assay results also demonstrated a reduced fibril structure, and the enzymatic activity of lysozyme fibrils recovered to 70–90 % of the native form. Both irradiations at 1,535 cm−1(amide II band) and 1,240 cm−1 (amide III band) were also more effective for the refolding of the fibrils than mere heating in the absence of FEL. On the contrary, either irradiation at 1,100 or 2,000 cm−1 afforded only about 60 % recovery of lysozyme activity. These results indicate that the specific FEL irradiation tuned to amide bands is efficient in refolding of lysozyme fibrils into native form.
KeywordsAggregation Amide bands Amyloid fibril Free electron laser Refolding
Fourier transform infrared spectroscopy
- Mid-IR FEL
Mid-infrared free-electron laser
Sodium dodecyl sulfate polyacrylamide gel electrophoresis
In many instances, protein aggregation processes accompanied by decrease of solubility lead to suppression of protein functions such as enzymatic activities, a putative cause of several diseases in humans. For example, amyloid fibrils are formed by amyloid beta Aβ (40–43) [7, 21], tau protein , polyglutamine , transthyretin , α-synuclein , prion protein , and β2-microgulobulin . In addition, it has been recently reported that sequentially non-homologous proteins, insulin , proinsulin c-peptide , lysozyme , calcitonin , and myoglobin  may form amyloid-like fibrils under certain conditions. These observations imply that amyloid structures are common to the intrinsic structures of various proteins, although the mechanism of their formation is not completely understood. According to recent studies investigating short peptides (which have a tendency to form amyloid fibrils), the aggregation reaction is purportedly caused by ionic amino acid residues such as lysine and glutamic acid, while hydrophobic interactions between aromatic amino acids have been proposed to be the promotion factors for fibril formation via π–π interactions [20, 26]. The ionic interactions between acidic and basic (i.e., arginine) residues have also been proposed to play an important role in the formation of toxic soluble oligomers of Aβ42 [10, 33]. An inhibition experiment using β-sheet breaker peptides indicates that the aggregation process of amyloid is reversible ; therefore, it is hypothesized that the fibrils are spontaneously refolded into their native form by dissociation of the aforementioned non-covalent bonds of the β-sheet clusters, or incorporation of water molecules into the hydrophobic core of the fibrils .
A mid-infrared free-electron laser (mid-IR FEL) can excite the specific bonds within mid-IR region, including amide bands, accounting for its use in multi-photon dissociation reactions [4, 27] and ablation of biological tissues and various proteins [1, 5, 28, 30, 31]. Investigators in Vanderbilt University have performed mid-IR FEL-induced ablation of cornea tissue, observing secondary structural changes and peptide fragmentation of collagen [29, 36]. In addition, Oomens et al.  observed the detachment of potassium ions from proteins in the gas phase following the irradiation with FEL at 6 μm (1,667 cm−1) by using Fourier transform ion cyclotron resonance mass spectrometry. From these studies, it may be concluded that FEL irradiation can induce major changes in the higher-order structure of proteins. In the present study, we targeted the amyloid fibrils for mid-IR FEL irradiation. During the amyloid-formation process, vibrational modes of amide bonds, including C=O stretch, C–N stretch, and N–H bend, are affected by β-sheet formation and are observed by FTIR spectra [2, 9]. Variables that influence the infrared data include hydrogen bonding, ionic interactions, and hydrophobic interactions formed during the course of β-sheet cluster formation. It has been hypothesized that these non-covalent interactions in the fibrils can be affected by FEL irradiation. In this study, we selected lysozyme as a model protein for mid-IR FEL irradiation, because the enzyme is commercially available in abundance and has been reported to form amyloid-like fibrils under specific acidic conditions in vitro . Here, we report that dissociation of amyloid-like fibrils of lysozyme into the native form of the protein could be promoted by mid-IR FEL irradiation at the amide band.
2 Materials and Methods
Chicken egg white lysozyme, Micrococcus lysodeikticus ATCC 4698, phosphotungstic acid, and Congo Red were purchased from Sigma-Aldrich (Tokyo, Japan). Acetic acid and sodium chloride (NaCl) were purchased from Wako Pure Chemical Industries (Osaka, Japan). The KBr-mini-plate was purchased from Jasco Engineering Co. (Tokyo, Japan).
2.2 Preparation of Lysozyme Fibrils
Lysozyme powder was dissolved to a concentration of 2.5 mg/mL in H2O (1 mL) containing 20 % acetic acid and 0.5 M NaCl, and incubated for 20 h at 37 °C. The resulting aggregates were precipitated by centrifugation at 14,000 rpm for 10 min at room temperature, washed by the addition of 0.5 mL of distilled water, and dried. The fibrils generated were re-suspended in distilled water and were analyzed by a variety of methods described in the subsequent sections.
2.3 Method of Mid-infrared Free-Electron Laser Irradiation at the Tokyo University of Science (FEL-TUS)
2.4 Fourier-Transform Infrared Spectroscopy
Fourier transform infrared spectra were recorded on an FT/IR 615 spectrophotometer (Jasco International Co., Ltd., Tokyo, Japan) by using a solid KBr mini-plate. The protein sample was mixed with KBr pellet and a thin plate was prepared, and the measurements were performed using 16 scans under 4 cm−1 resolutions. Secondary structures of the lysozyme samples were estimated by using the bundled protein analysis software (IR-SSE; JASCO Co., Ltd.), which was developed for evaluation of protein conformational changes in biological tissue .
2.5 Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis (SDS-PAGE)
The lysozyme samples (approximately 1.0 mg/mL) were mixed with sodium dodecyl sulfate (SDS) sample buffer (25 mM of Tris, 192 mM of glycine, and 0.1 % of SDS) and loaded onto a 15 % polyacrylamide gel (ATTO Corporation, Tokyo, Japan). The migrated proteins on the gel were detected by performing Coomassie staining.
2.6 Transmission Electron Microscopy
Specimens for transmission electron microscopic (TEM) observation were prepared as follows: First 2 μL of each lysozyme sample was deposited onto copper grids (200 mesh; Nisshin EM Co., Ltd, Tokyo, Japan) covered with collodion film hydrophilized by an electric glow discharge. After 30 s of deposition, any excess amount of the sample was blotted out using a filter paper, followed by 2 deposition-blotting cycles with 20 μL of water and 2 additional cycles of phosphotungstic acid (25 μL of 1 % w/v). Prior to sample preparation, the staining solution was filtered using a 0.22-μm membrane filter to remove large crystals. The TEM observation was performed using a Hitachi H-7650 (Tokyo, Japan) at 120 kV of accelerating voltage.
2.7 Congo Red Binding Assay
The absorbance peak of Congo Red is known to shift from 490 to 510 nm in the presence of the fibrils . Aliquots of lysozyme solution (30 μL) were added to an equivalent volume of Congo Red solution (0.2 mM in PBS) and incubated for 10 min at room temperature. The resulting absorbance values were obtained from a 400 to 700 nm scan using a multi-label counter (PerkinElmer, Tokyo, Japan).
2.8 Measurements of Lysozyme Activities
Lysozyme activity was defined as follows, based on the product information from Sigma-Aldrich. In brief, the substrate, a cell wall extract of Micrococcus lysodeikticus (Sigma), was dissolved in PBS (100 μL), and the optical density (OD) at 600 nm was adjusted to about 1.0. The lysozyme solution (10 μL) was added to the substrate solution, and the mixture was incubated for 30 min at room temperature. Change in OD per minute was calculated and divided by enzyme concentration to provide a unit number of the enzyme activity. The concentration of lysozyme was determined by measuring the absorbance peak at 595 nm by using Coomassie staining.
3.1 FTIR Analyses of the FEL-Irradiated Lysozyme Fibrils
Fragmentation of the peptide backbone of lysozyme did not occur during FEL irradiation, as shown by SDS-PAGE analysis (Fig. 2C). That is, the band of native lysozyme (MW, 14 kDa) was observed between 8.6 and 17.4 kDa of the marker proteins (lane a). In the case of fibrils, one major band was observed at the same position as that of the native protein, and another minor band was observed in small quantities below 31.3 kDa, the putative dimer of lysozyme (lane b). By contrast, following FEL irradiation at 1,620 cm−1, one band was seen at the same position as that of the native protein (lane c). The above results indicate that FEL irradiation under the above condition does not destroy the primary structure of lysozyme.
3.2 TEM Analysis
3.3 CR Assay
Congo Red binding assay was also performed to clarify the effect of FEL on refolding of lysozyme fibrils into the native form (Fig. 3c). The dye is known to bind to amyloid fibrils, and shift the absorbance peak from 490–500 nm to 500–510 nm upon binding . While one peak was observed at 492 nm in the case of native lysozyme bound to the dye (solid line), the peak was shifted to 510 nm when the fibrils were bound to the dye (dashed line). When the dye was mixed with the fibrils following FEL irradiation, the absorbance peak was shifted to near 492 nm, indicating that non-fibrils were more abundant than fibrils (dotted line). Therefore, the number of lysozyme fibrils decreased following FEL irradiation.
3.4 Specificity of the FEL Irradiation on the Refolding of Lysozyme Fibrils
The FEL system has been used in the field of laser surgery for ablation of pathological tissues [5, 18]. In many instances, protein matrices were destroyed and the higher-order structures of proteins were altered by FEL irradiation. From these studies, it can be inferred that the denatured structure of a protein may also be affected by FEL irradiation. The aggregation processes of proteins into the inactive, denatured forms are, in many instances, associated with the onset of human diseases, such as Alzheimer’s disease. Dissociation of these fibrils into soluble and active forms of the protein is expected to have both mechanistic and clinical applications. In the present study, we applied mid-IR FEL to the process of refolding of amyloid-like fibrils of lysozyme into the native form and observed that FEL irradiation markedly affected the β-sheet content of the protein and promoted the refolding of the fibrils. Although there should be many structural differences between lysozyme fibrils and amyloid β fibrils and it may be difficult to apply the present result using the FEL for reducing the fibrils in vivo, we consider that a possibility indicating that amyloid-like fibrils can be refolded under the FEL-irradiation condition could be found in this study. Oomens et al.  suggested that FEL irradiation at the amide I band of the protein affects the ionic interactions between the amide backbone and various ligands. Therefore, in the instance of fibril refolding, we suggest that non-covalent bonds between the β-sheet structures can be affected by FEL irradiation. The vaporization of water with FEL irradiation is also suggested to be a driving force of tissue ablation . In addition, wavenumber-dependent refolding of fibrils could be observed (Fig. 4). It can be estimated that the FEL irradiation at amide absorption heats the fibrils and surrounding water which leads to higher temperatures which drive dissociation of the fibrils and refolding of lysozyme to its active state. Although it can be suspected that the native structure may be also affected by the FEL irradiation, the structural damage of native protein is probably caused by the higher power of FEL more than the present value (max. 15 mJ per macro-pulse) for a long-term irradiation.
In conclusion, refolding of amyloid-like fibrils of lysozyme can be promoted by mid-IR FEL irradiation under mild condition at 37 °C. Although further studies are required to clarify a detailed mechanism of FEL-induced refolding, mid-IR FEL is expected to be useful for dissolving the insoluble amyloid-like fibrils of additional proteins into their active forms.
We thank Dr. Kanjiro Torigoe (Graduate School of Science and Technology, Tokyo University of Science) for technical supporting of TEM analyses. We also thank Mr. Tetsuo Morotomi and Mr. Keiichi Hisazumi (Mitsubishi Electric System & Service Co., Ltd.) for operating the FEL instrument. This work was partly supported by Open Advanced Research Facilities Initiative by the Ministry of Education, Culture, Sport, Science and Technology, Japan.
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