Infrared spectroscopy analysis determining secondary structure change in albumin by cerium oxide nanoparticles.

Cerium oxide (CeO2) nanoparticles are expected to have applications in the biomedical field because of their antioxidative properties. Inorganic nanoparticles interact with proteins at the nanoparticle surface and change their conformation when administered; however, the principle underlying this interaction is still unclear. This study aimed to investigate the secondary structural changes occurring in bovine serum albumin (BSA) mixed with CeO2 nanoparticles having different surface modifications using Fourier transform infrared spectroscopy. CeO2 nanoparticles (diameter: 240 nm) were synthesized from an aqueous cerium (III) nitrate solution using a homogeneous precipitation method. The surfaces of the nanoparticles were modified by the catechol compounds dopamine and 3,4-dihydroxyhydrocinnamic acid (DHCA). In the presence of these CeO2 nanoparticles (0.11-0.43 mg/mL), ß-sheet formation of BSA (30 mg/mL) was promoted especially on the amine-modified (positively charged) nanoparticles. The local concentration of BSA on the surface of the positively charged nanoparticles may have resulted in structural changes due to electrostatic and other interactions with BSA. Further investigations of the interaction mechanism between nanoparticles and proteins are expected to lead to the safe biomedical applications of inorganic nanoparticles.

Disassembly of Amyloid Fibril with Infrared Free Electron Laser.

Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid ß-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated through a linear accelerator, and the oscillation wavelengths are tunable from 3 µm to 100 µm. Many biological and organic compounds can be structurally altered by the mode-selective vibrational excitations due to the wavelength variability and the high-power oscillation energy (10-50 mJ/cm2). We have found that several different kinds of amyloid fibrils in amino acid sequences were commonly disassembled by the irradiation tuned to amide I (6.1-6.2 µm) where the abundance of ß-sheet decreased while that of α-helix increased by the vibrational excitation of amide bonds. In this review, we would like to introduce the IR-FEL oscillation system briefly and describe combination studies of experiments and molecular dynamics simulations on disassembling amyloid fibrils of a short peptide (GNNQQNY) from yeast prion and 11-residue peptide (NFLNCYVSGFH) from ß2-microglobulin as representative models. Finally, possible applications of IR-FEL for amyloid research can be proposed as a future outlook.

Probing protein misfolding and dissociation with an infrared free-electron laser.

Misfolding is observed in the mutant proteins that are causative for neurodegenerative disorders such as polyglutamine diseases. These proteins are prone to aggregate in the cytoplasm and nucleus of cells. To reproduce cells with the aggregated proteins, gene expression system is usually applied, in which the expression construct having the mutated DNA sequence of the interest is transfected into cells. The transfected DNA is finally converted into the mutant protein, which is gradually aggregated in the cells. In addition, a simple method to prepare the cells having aggregates inside has been recently applied. Peptides were first aggregated by incubating them in water. The aggregates are spontaneously taken up by cells because aggregated proteins generally transfer between cells. Peptides with different degrees of aggregation can be made by changing the incubation times and temperatures, which enables to examine contribution of aggregation to the toxicity to the recipient cells. Moreover, such cells can be used for therapeutic researches of diseases in which aggregates are involved. In this chapter, we show methods to induce aggregation of peptides. The functional analyses of the cells with aggregates are also described. Then, experimental dissociation of the aggregates produced using this method by mid infrared free electron laser irradiation and its theoretical support by molecular dynamics simulation are introduced as the therapeutic research for neurodegenerative disorders.

Application study of infrared free-electron lasers towards the development of amyloidosis therapy.

Amyloidosis is known to be caused by the deposition of amyloid fibrils into various biological tissues; effective treatments for the disease are little established today. An infrared free-electron laser (IR-FEL) is an accelerator-based picosecond-pulse laser having tunable infrared wavelengths. In the current study, the irradiation effect of an IR-FEL was tested on an 11-residue peptide (NFLNCYVSGFH) fibril from ß2-microglobulin (ß2M) with the aim of applying IR-FELs to amyloidosis therapy. Infrared microspectroscopy (IRM) and scanning electron microscopy showed that a fibril of ß2M peptide was clearly dissociated by IR-FEL at 6.1 µm (amide I) accompanied by a decrease of the ß-sheet and an increase of the α-helix. No dissociative process was recognized at 6.5 µm (amide II) as well as at 5.0 µm (non-specific wavelength). Equilibrium molecular dynamics simulations indicated that the α-helix can exist stably and the probability of forming interchain hydrogen bonds associated with the internal asparagine residue (N4) is notably reduced compared with other amino acids after the ß-sheet is dissociated by amide I specific irradiation. This result implies that N4 plays a key role for recombination of hydrogen bonds in the dissociation of the ß2M fibril. In addition, the ß-sheet was disrupted at temperatures higher than 340 K while the α-helix did not appear even though the fibril was heated up to 363 K as revealed by IRM. The current study gives solid evidence for the laser-mediated conversion from ß-sheet to α-helix in amyloid fibrils at the molecular level.

Exploring Biomolecular Self-Assembly with Far-Infrared Radiation.

Physical engineering technology using far-infrared radiation has been gathering attention in chemical, biological, and material research fields. In particular, the high-power radiation at the terahertz region can give remarkable effects on biological materials distinct from a simple thermal treatment. Self-assembly of biological molecules such as amyloid proteins and cellulose fiber plays various roles in medical and biomaterials fields. A common characteristic of those biomolecular aggregates is a sheet-like fibrous structure that is rigid and insoluble in water, and it is often hard to manipulate the stacking conformation without heating, organic solvents, or chemical reagents. We discovered that those fibrous formats can be conformationally regulated by means of intense far-infrared radiations from a free-electron laser and gyrotron. In this review, we would like to show the latest and the past studies on the effects of far-infrared radiation on the fibrous biomaterials and to suggest the potential use of the far-infrared radiation for regulation of the biomolecular self-assembly.

Degradation of Lignin by Infrared Free Electron Laser.

Lignin monomers have attracted attention as functional materials for various industrial uses. However, it is challenging to obtain these monomers by degrading polymerized lignin due to the rigid ether linkage between the aromatic rings. Here, we propose a novel approach based on molecular vibrational excitation using infrared free electron laser (IR-FEL) for the degradation of lignin. The IR-FEL is an accelerator-based pico-second pulse laser, and commercially available powdered lignin was irradiated by the IR-FEL under atmospheric conditions. Synchrotron-radiation infrared microspectroscopy analysis showed that the absorption intensities at 1050 cm-1, 1140 cm-1, and 3400 cm-1 were largely decreased alongside decolorization. Electrospray ionization mass chromatography analysis showed that coumaryl alcohol was more abundant and a mass peak corresponding to hydrated coniferyl alcohol was detected after irradiation at 2.9 µm (νO-H) compared to the original lignin. Interestingly, a mass peak corresponding to vanillic acid appeared after irradiation at 7.1 µm (νC=C and νC-C), which was supported by our two-dimensional nuclear magnetic resonance spectroscopy analysis. Therefore, it seems that partial depolymerization of lignin can be induced by IR-FEL irradiation in a wavelength-dependent manner.

Toxicity of internalized polyalanine to cells depends on aggregation.

In polyalanine (PA) diseases, the disease-causing transcription factors contain an expansion of alanine repeats. While aggregated proteins that are responsible for the pathogenesis of neurodegenerative disorders show cell-to-cell propagation and thereby exert toxic effects on the recipient cells, whether this is also the case with expanded PA has not been studied. It is also not known whether the internalized PA is toxic to recipient cells based on the degree of aggregation. In this study, we therefore prepared different degrees of aggregation of a peptide having 13 alanine repeats without flanking sequences of PA disease-causative proteins (13A). The aggregated 13A was spontaneously taken up by neuron-like cultured cells. Functionally, strong aggregates but not weak aggregates displayed a deficit in neuron-like differentiation in vitro. Moreover, the injection of strong but not weak 13A aggregates into the ventricle of mice during the neonatal stage led to enhanced spontaneous motor activity later in life. Thus, PA in the extracellular space has the potential to enter adjacent cells, and may exert toxicity depending on the degree of aggregation.

Role of Water Molecules and Helix Structure Stabilization in the Laser-Induced Disruption of Amyloid Fibrils Observed by Nonequilibrium Molecular Dynamics Simulations.

Water plays a crucial role in the formation and destruction of biomolecular structures. The mechanism for destroying biomolecular structures was thought to be an active breaking of hydrogen bonds by water molecules. However, using nonequilibrium molecular dynamics simulations, in which an amyloid-ß amyloid fibril was destroyed via infrared free-electron laser (IR-FEL) irradiation, we discovered a new mechanism, in which water molecules disrupt protein aggregates. The intermolecular hydrogen bonds formed by C═O and N-H in the fibril are broken at each pulse of laser irradiation. These bonds spontaneously re-form after the irradiation in many cases. However, when a water molecule happens to enter the gap between C═O and N-H, it inhibits the re-formation of the hydrogen bonds. Such sites become defects in the regularly aligned hydrogen bonds, from which all hydrogen bonds in the intermolecular ß-sheet are broken as the fraying spreads. This role of water molecules is entirely different from other known mechanisms. This new mechanism can explain the recent experiments showing that the amyloid fibrils are not destroyed by laser irradiation under dry conditions. Additionally, we found that helix structures form more after the amyloid disruption; this is because the resonance frequency is different in a helix structure. Our findings provide a theoretical basis for the application of IR-FEL to the future treatment of amyloidosis.

Application of mid-infrared free-electron laser for structural analysis of biological materials.

A mid-infrared free-electron laser (MIR-FEL) is a synchrotron-radiation-based femto- to pico-second pulse laser. It has unique characteristics such as variable wavelengths in the infrared region and an intense pulse energy. So far, MIR-FELs have been utilized to perform multi-photon absorption reactions against various gas molecules and protein aggregates in physical chemistry and biomedical fields. However, the applicability of MIR-FELs for the structural analysis of solid materials is not well recognized in the analytical field. In the current study, an MIR-FEL is applied for the first time to analyse the internal structure of biological materials by using fossilized inks from cephalopods as the model sample. Two kinds of fossilized inks that were collected from different strata were irradiated at the dry state by tuning the oscillation wavelengths of the MIR-FEL to the phosphoryl stretching mode of hydroxyapatite (9.6 µm) and to the carbonyl stretching mode of melanin (5.8 µm), and the subsequent structural changes in those materials were observed by using infrared microscopy and far-infrared spectroscopy. The structural variation of these biological fossils is discussed based on the infrared-absorption spectral changes that were enhanced by the MIR-FEL irradiation, and the potential use of MIR-FELs for the structural evaluation of biomaterials is suggested.

Irradiation effect of a submillimeter wave from 420†GHz gyrotron on amyloid peptides in vitro.

On using the far-infrared radiation system, whether the irradiation effect is thermal or non-thermal is controversial. We irradiated amyloid peptides that are causal factors for amyloidosis by using a submillimeter wave from 420 GHz gyrotron. Fluorescence reagent assay, optical and electron microscopies, and synchrotron-radiation infrared microscopy showed that the irradiation increased the fibrous conformation of peptides at room temperature for 30 min. The temperature increase on the sample was only below 5 K, and a simple heating up to 318 K hardly induced the fibril formation. Therefore, the amyloid aggregation was driven by the far-infrared radiation with little thermal effect.

Infrared Laser-Induced Amyloid Fibril Dissociation: A Joint Experimental/Theoretical Study on the GNNQQNY Peptide.

Neurodegenerative diseases are usually characterized by plaques made of well-ordered aggregates of distinct amyloid proteins. Dissociating these very stable amyloid plaques is a critical clinical issue. In this study, we present a joint mid-infrared free electron laser experiment/nonequilibrium molecular dynamics simulation to understand the dissociation process of a representative example GNNQQNY fibril. By tuning the laser frequency to the amide I band of the fibril, the resonance takes place and dissociation is occurred. With the calculated and observed wide-angle X-ray scattering profiles and secondary structures before and after laser irradiation being identical, we can propose a dissociation mechanism with high confidence from our simulations. We find that dissociation starts in the core of the fibrils by fragmenting the intermolecular hydrogen bonds and separating the peptides and then propagates to the fibril extremities leading to the formation of unstructured expanded oligomers. We suggest that this should be a generic mechanism of the laser-induced dissociation of amyloid fibrils.

Carbon nanoparticles induce endoplasmic reticulum stress around blood vessels with accumulation of misfolded proteins in the developing brain of offspring.

Nano-particulate air pollution threatens developing brains and is epidemiologically related to neurodegenerative diseases involving deposition of misfolded proteins. However, the mechanism underlying developmental neurotoxicity by nanoparticles remains unknown. Here, we report that maternal exposure to low doses of carbon black nanoparticle (CB-NP) induces endoplasmic reticulum (ER) stress associated with accumulation of misfolded proteins. Notably, offspring specifically showed high induction of ER stress in perivascular macrophages and reactive astrocytes only around brain blood vessels, along with accumulation of ß-sheet-rich proteins regarded as misfolded proteins. Our results suggest that maternal CB-NP exposure induced ER stress in PVMs and reactive astrocytes around blood vessels in the brain of offspring in mice. The induction of ER stress accompanied by the perivascular accumulation of misfolded proteins is likely to be associated with perivascular abnormalities and neurodegeneration, and development of neurodegenerative diseases related to particulate air pollution.

Degradation of Human Serum Albumin by Infrared Free Electron Laser Enhanced by Inclusion of a Salen-Type Schiff Base Zn (II) Complex.

A salen-type Schiff base Zn(II) complex included in human serum albumin (HSA) protein was examined by UV-Vis, circular dichroism (CD), and fluorescence (PL) spectra. The formation of the composite material was also estimated by a GOLD program of ligand-protein docking simulation. A composite cast film of HSA and Zn(II) complex was prepared, and the effects of the docking of the metal complex on the degradation of protein molecules by mid-infrared free electron laser (IR-FEL) were investigated. The optimum wavelengths of IR-FEL irradiation to be used were based on experimental FT-IR spectra and vibrational analysis. Using TD-DFT results with 6-31G(d,p) and B3LYP, the IR spectrum of Zn(II) complex could be reasonably assigned. The respective wavelengths were 1652 cm-1 (HSA amide I), 1537 cm-1 (HSA amide II), and 1622 cm-1 (Zn(II) complex C=N). Degradation of HSA based on FT-IR microscope (IRM) analysis and protein secondary structure analysis program (IR-SSE) revealed that the composite material was degraded more than pure HSA or Zn(II) complex; the inclusion of Zn(II) complex enhanced destabilization of folding of HSA.

Dissolution of a fibrous peptide by terahertz free electron laser.

Fibrous peptides such as amyloid fibrils have various roles in biological system, e.g., as causal factor of serious amyloidosis in human and as functional regulator of cell formation in bacteria and eukaryotes. In addition, the fiber-type format is promising as biocompatible scaffold. Therefore, the dissolution method of peptide fibril is potentially useful at many scenes in medical and material fields: as reductive way of pathogenic amyloid, as modification technique of cell structure, and as fabrication tool of biomaterials. However, the fibril structure is generally difficult to be dissociated due to its rigid stacked conformation. Here, we propose a physical engineering technology using terahertz free electron laser (FEL) at far-infrared wavelengths from 70 to 80 µm. Infrared microscopy analysis of the irradiated fibril of calcitonin peptide as a model showed that ß-sheet was decreased, and α-helix, turn, and others were increased, compared to those of the fibril before the FEL irradiation. Interestingly, the dissociative effect by the far-infrared laser was remarkable than that by the mid-infrared laser tuned to 6.1 µm that corresponds to amide I. In addition, simple heating at 363 K deformed the fibril state but increased the amount of ß-sheet, which was contrast with the action by the FEL, and scanning-electron microscopy and Congo-red staining revealed that the fibril was collapsed power-dependently within a range from 25 to 900 mJ energies supplied with the FEL at 74 µm. It can be considered that irradiation of intense terahertz wave can dissociate fibrous conformation of peptide with little influence of thermal effect.

Investigation by DFT Methods of the Damage of Human Serum Albumin Including Amino Acid Derivative Schiff Base Zn(II) Complexes by IR-FEL Irradiation.

An infrared free electron laser (IR-FEL) can decompose aggregated proteins by excitation of vibrational bands. In this study, we prepared hybrid materials of protein (human serum albumin; HSA) including several new Schiff base Zn(II) complexes incorporating amino acid (alanine and valine) or dipeptide (gly-gly) derivative moieties, which were synthesized and characterized with UV-vis, circular dichroism (CD), and IR spectra. Density functional theory (DFT) and time dependent DFT (TD-DFT) calculations were also performed to investigate vibrational modes of the Zn(II) complexes. An IR-FEL was used to irradiate HSA as well as hybrid materials of HSA-Zn(II) complexes at wavelengths corresponding to imine C=N, amide I, and amide II bands. Analysis of secondary structures suggested that including a Zn(II) complex into HSA led to the structural change of HSA, resulting in a more fragile structure than the original HSA. The result was one of the characteristic features of vibrational excitation of IR-FEL in contrast to electronic excitation by UV or visible light.

Photo-Modification of Melanin by a Mid-infrared Free-electron Laser.

Melanin is rigidly constructed by several nitrogen-containing aromatic rings, and its excess accumulation in skin tissue is closely associated with melanosis. Although visible lasers (wavelength: 600-1000 nm) are conventionally used for the photo-thermolysis of melanocyte, several pigmented nevi are difficult to be treated. Here, we propose an alternate method for targeting the molecular structure of melanin using an infrared free-electron laser (FEL) tuned to 5.8 µm that corresponds to the stretching vibrational mode of carboxylate group. A drastic morphological change on the black-colored surface of melanin powder was observed after the pulse irradiation with power energy of 500 mJ cm-2 , and the minimum irradiation time for damage to the morphology was 1.4 s. Analyses by mass spectroscopy, infrared spectroscopy, and 13 C-nuclear magnetic resonance implied that a pyrrole group was removed by the FEL irradiation. In addition, the FEL irradiation dispersed almost all of the melanoma cells from a culture solution without any influence on other ingredients in the medium, and one-cell analysis by infrared microscopy showed that the structure of melanoma could be substantially damaged by the irradiation. This study proposes the potency of intense mid-infrared laser as novel alternative way to reduce melanin.

Restoration from polyglutamine toxicity after free electron laser irradiation of neuron-like cells.

Proteins containing an expanded polyglutamine tract tend to aggregate, leading to the neuronal damage observed in polyglutamine diseases. We recently reported that free electron laser (FEL) irradiation markedly dissociates naked polyglutamine aggregates as well as the aggregate in the 293 T cells. In the present study, we investigated whether FEL irradiation of neuron-like cells with polyglutamine aggregates would restore the cellular damage and dysfunction. The aggregated polyglutamine peptides induced neurite retraction of differentiated SH-SY5Y cells. Upon FEL irradiation, the polyglutamine aggregates in the SH-SY5Y cells were dissociated, and the shorter length of individual neurite, fewer number of neurites per cell and shorter total length of neurite by polyglutamine were inhibited. Same results were essentially obtained in PC12 cells. Moreover, when FEL irradiation was applied to undifferentiated SH-SY5Y cells, the deficits in neuron-like differentiation seen in expanded polyglutamine peptide-containing cells were also rescued. Thus, FEL irradiation restored both the damage and differentiation caused by polyglutamine in neuron-like cells.

Dissociation of ß-Sheet Stacking of Amyloid ß Fibrils by Irradiation of Intense, Short-Pulsed Mid-infrared Laser.

Structure of amyloid ß (Aß) fibrils is rigidly stacked by ß-sheet conformation, and the fibril state of Aß is profoundly related to pathogenesis of Alzheimer's disease (AD). Although mid-infrared light has been used for various biological researches, it has not yet been known whether the infrared light changes the fibril structure of Aß. In this study, we tested the effect of irradiation of intense mid-infrared light from a free-electron laser (FEL) targeting the amide bond on the reduction of ß-sheet content in Aß fibrils. The FEL reduced entire contents of proteins exhibiting ß-sheet structure in brain sections from AD model mice, as shown by synchrotron-radiation infrared microscopy analysis. Since Aß1-42 fibril absorbed a considerable FEL energy at amide I band (6.17 µm), we irradiated the FEL at 6.17 µm and found that ß-sheet content of naked Aß1-42 fibril was decreased using infrared microscopic analysis. Consistent with the decrease in the ß-sheet content, Congo-red signal is decreased after the irradiation to Aß1-42 fibril. Furthermore, electron microscopy analysis revealed that morphologies of the fibril and proto-fibril were largely changed after the irradiation. Thus, mid-infrared light dissociates ß-sheet structure of Aß fibrils, which justifies exploration of possible laser-based therapy for AD.

Perivascular Accumulation of ß-Sheet-Rich Proteins in Offspring Brain following Maternal Exposure to Carbon Black Nanoparticles.

Environmental stimulation during brain development is an important risk factor for the development of neurodegenerative disease. Clinical evidence indicates that prenatal exposure to particulate air pollutants leads to diffuse damage to the neurovascular unit in the developing brain and accelerates neurodegeneration. Maternal exposure to carbon black nanoparticles (CB-NPs), used as a model for particulate air pollution, induces long-lasting diffuse perivascular abnormalities. We aimed to comprehensively characterize the perivascular abnormalities related to maternal NPs exposure using Fourier transform infrared microspectroscopy (in situ FT-IR) and classical staining analysis. Pregnant ICR mice were intranasally treated with a CB-NPs suspension (95 µg/kg at a time) on gestational days 5 and 9. Brains were collected 6 weeks after birth and sliced to prepare 10-µm-thick serial sections. Reflective spectra of in situ FT-IR were acquired using lattice measurements (x-axis: 7, y-axis: 7, 30-µm apertures) around a centered blood vessel. We also performed mapping analysis of protein secondary structures. Serial sections were stained with using periodic acid-Schiff or immunofluorescence to examine the phenotypes of the perivascular areas. Peaks of amide I bands in spectra from perivascular areas were shifted by maternal NPs exposure. However, there were two types of peak-shift in one mouse in the exposure group. Some vessels had a large peak-shift and others had a small peak-shift. In situ FT-IR combined with traditional staining revealed that the large peak-shift was induced around blood vessel adjacent to astrocytes with glial fibrillary acidic protein and aquaporin-4 over-expression and perivascular macrophages (PVMs) with enlarged lysosome granules. Furthermore, protein secondary structural analysis indicated that maternal NPs exposure led to increases in ß-sheet content and decreases in α-helix content in areas that are mostly close to the centered blood vessel displaying histopathological changes. These results suggest that ß-sheet-rich waste proteins, which are denatured by maternal NPs exposure, likely accumulate in the perivascular space as they are processed by the clearance systems in the brain. This may in turn lead the denaturation of PVMs and astrocyte activation. The risk of neurodegeneration may be enhanced by exposure to particulate air pollutants during brain development following the perivascular accumulation of ß-sheet-rich waste proteins.