Yuhei Shimoyama

Dynamics and local ordering of spin-labeled prion protein: an ESR simulation study of a highly PH-sensitive site.

Abstract Valine 160 on β-sheet-2 (S2) of mouse prion (moPrPC) has been previously identified as the most highly pH-sensitive site on moPrPC by ESR spectroscopy using site-directed spin labeling (SDSL) technique. However, no further theoretical analysis to reveal the molecular dynamics reported on the experimental ESR spectra is available. The X-band ESR spectra of R1 nitroxide spin label at V160 and four other sites are carefully analyzed over large pH and temperature ranges using a spectral simulation method based upon stochastic Liouville equation (SLE). The results clearly reveal the dynamics and ordering of the local environment of V160R1 showing that (i) molecular mobility of V160R1 on S2 gradually increases with a decrease of pH from 7.5 to 4.5; (ii) two distinctly different spectral components are simultaneously present in all spectra of V160R1 studied. The spectral components are, respectively, denoted as immobile (Im), characterized by lower molecular mobility and higher ordering, and mobile (Mb) component of high mobility and low ordering. The population ratio (Im/Mb) increases with increasing pH, while Im remains dominant in all V160R1 spectra. It suggests a more mobile and disordered dynamic molecular structure for mouse PrPC, which is very likely correlated with increased β-sheet content at low pH, as the environment changes from neutral to acidic pH. Together with the results of the SLE-based analyses on the spectra of other sites that appear pH-insensitive, we suggest that the simultaneous presence of the spectral components for V160R1 is strongly correlated with the coexistence of multiple protein conformations in local structure of PrPC over the varied pH range. It demonstrates that the combined approach of the SDSL technique and the SLE-based analysis leads to a powerful method for unraveling the complexity of protein dynamics.

ESR study of free radicals in mango

An electron spin resonance (ESR) spectroscopic study of radicals induced in irradiated fresh mangoes was performed. Mangoes in the fresh state were irradiated with gamma-rays, lyophilized and then crushed into a powder. The ESR spectrum of the powder showed a strong main peak at g=2.004 and a pair of peaks centered at the main peak. The main peak was detected from both flesh and skin specimens. This peak height gradually decreased during storage following irradiation. On the other hand, the side peaks showed a well-defined dose-response relationship even at 9 days post-irradiation. The side peaks therefore provide a useful means to define the irradiation of fresh mangoes.

Free radicals in irradiated wheat flour detected by electron spin resonance

By electron spin resonance (ESR) spectroscopy, we revealed free radicals in wheat flour before and after γ-ray inrradiation and their thermal behavior during heat treatment. The ESR spectrum of wheat flour before irradiation consists of a sextet centered atg=2.0 and a singlet signal at the sameg-value position. The first one is attributable to a signal with hyperfine (hf) interactions of Mn2+ ion (hf constant, 7.4 mT). The second signal originates from the carbon-centered radical. Upon γ-ray irradiation, however, a new signal with two triplet lines at the low- and high-field ends was detected on the Mn2+ sextet lines. We analyzed the triplet ESR lines as due to powder spectra (rhombicg-tensor symmetry) with nitrogen (14N) hf interactions. This indicates that a new organic radical was induced in the conjugated protein portion of wheat flour by γ-ray irradiation. The intensity of the organic free radical atg=2.0 detected in irradiated wheat flour increased monotonically under thermal treatment. The analysis of the time-dependent evolution process on the basis of the theory of transient phenomena as well as the nonlinear least-squares numerical method provided a unique time constant for the radical evolution in wheat flour during thermal treatment.

Optical and Paramagnetic Properties of Size-Controlled Ink Particles Isolated from Sepia officinalis

The optical and paramagnetic properties of size-controlled ink particles isolated from ink sacs of Sepia officinalis were investigated. Topographic images of atomic force microscopy (AFM) revealed that the average heights of the large and small ink particles were 156 nm and 5.3 nm respectively. The ultraviolet-visible (UV-VIS) spectral features of aqueous solutions of ink particles were dependent on particle size. Electron spin resonance (ESR) spectra suggested that the ink particles are highly pure for paramagnetic species and are of reliable quality. These size-controlled ink particles are suitable for a basic study of melanin-related materials.

A novel copper(II) coordination at His186 in full-length murine prion protein

To explore Cu(II) ion coordination by His(186) in the C-terminal domain of full-length prion protein (moPrP), we utilized the magnetic dipolar interaction between a paramagnetic metal, Cu(II) ion, and a spin probe introduced in the neighborhood of the postulated binding site by the spin labeling technique (SDSL technique). Six moPrP mutants, moPrP(D143C), moPrP(Y148C), moPrP(E151C), moPrP(Y156C), moPrP(T189C), and moPrP(Y156C,H186A), were reacted with a methane thiosulfonate spin probe and a nitroxide residue (R1) was created in the binding site of each one. Line broadening of the ESR spectra was induced in the presence of Cu(II) ions in moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) but not moPrP(D143R1). This line broadening indicated the presence of electron-electron dipolar interaction between Cu(II) and the nitroxide spin probe, suggesting that each interspin distance was within 20 A. The interspin distance ranges between Cu(II) and the spin probes of moPrP(Y148R1), moPrP(Y151R1), moPrP(Y156R1), and moPrP(T189R1) were estimated to be 12.1 A, 18.1 A, 10.7 A, and 8.4 A, respectively. In moPrP(Y156R1,H186A), line broadening between Cu(II) and the spin probe was not observed. These results suggest that a novel Cu(II) binding site is involved in His186 in the Helix2 region of the C-terminal domain of moPrP(C).

Development of a control system for pulsed-electron spin resonance spectrometers

A pulse control and data acquisition system with high time resolution of 300 ps and data-averaging rate of 100 kHz for a pulsed-ESR spectrometer was constructed. The system consists of two sets of 3.34 GHz data timing generator and a dual-channel analog-to-digital converter with 1 GHz samples, both of which are commercially available. We developed a scheme and software to control these equipments with high efficiency in pulsing design, data acquisition, and accurate synchronization of the devices. The system was developed at Ku band (17.5 GHz) and demonstrated some examples of electron spin echo and double quantum measurements.

Molecular Orientation and Electromagnetic Properties of Perhydrogenated and Perfluorinated Copper Phthalocyanine Thin Films

X-ray diffraction (XRD) data shows lattice planes with a spacing of 12.8 A for copper phthalocyanine (CuPc) thin films. Comparison between the XRD patterns of CuPc powder and thin films suggests that the molecules are oriented along the (100) lattice plane nearly perpendicular to the substrate. The XRD data of the perfluorinated phthalocyanine (F16CuPc) thin film indicate a similar structure to that of CuPc, but with a wider lattice spacing of 14.6 A. Angular variations of the line position (g-value) of ESR spectra reveal tilt angles of 39 and 34° for the CuPc and F16CuPc thin films, respectively, and the same deviation angle of 24°. This indicates a cone-shaped orientation of CuPc and F16CuPc with similar tilt and deviation angles. The ESR linewidths of both films show angular variation, indicating one-dimensional spin-chain interactions in both the CuPc and F16CuPc thin films. Organic thin-film transistors (OTFTs) with CuPc and F16CuPc films are tested for their suitability as channel layers. The OTFTs with a CuPc film exhibit conduction with holes as carriers, and have a field-effect mobility of 2.6 ×10-5 cm2 V-1 s-1 and an on/off ratio of 10 in the accumulation mode. The OTFTs with F16CuPc films exhibit conduction with electrons as carriers (n-type), and have a field-effect mobility of 2.0 ×10-4 cm2 V-1 s-1 and an on/off ratio of 2.4 ×104 in the accumulation mode.

Electron Spin Resonance Spectroscopic Study of Size-Controlled Ink Particles Isolated from Sepia officinalis

The paramagnetic properties of size-controlled ink particles isolated from the ink sacs of Sepia officinalis were studied by electron spin resonance (ESR) spectroscopy. Both the size-controlled ink particles and synthetic melanins seemingly yielded similar ESR spectra consisting of a singlet with a slightly asymmetrical signal. However, the progressive microwave power saturation revealed a clear difference between their paramagnetic behaviors. In comparison with synthetic melanins, the ESR spectra of the ink particles readily reached saturation, indicating a long spin–lattice relaxation time. On the other hand, the ESR linewidth depended on particle size. This implies that the particle size is related to the distance between paramagnetic species in the particles. Hence, it is reasonable that the large ink particle has the weakest spin–spin interaction among these samples. The employment of the size-controlled ink particles enabled us to determine precisely the paramagnetic parameters of Sepia inks.

Paramagnetic Properties of Size-Controlled Squid Ink Particles Dispersed in Water

The paramagnetic properties of size-controlled ink particles isolated from the ink sacs of squid were studied by electron spin resonance (ESR). ESR spectra of the large and small ink particles dispersed in water were successfully observed at room temperature. Both the ink particles in aqueous suspensions seemingly indicated similar ESR spectra consisting of a singlet with a slightly asymmetrical signal. The linewidth below saturation was almost the same in both the ink particles, but the linewidth of the small ink particle was obviously broadened with an increase in microwave power. On the other hand, the progressive microwave power saturation revealed a clear difference between the paramagnetic behaviors of the ink particles in aqueous suspensions and in solid states. In comparison with dehydrated samples, the ESR signals of the ink particles dispersed in water showed the inhomogeneous broadening and faster spin–lattice relaxation processes. The fundamental characteristics of size-controlled ink particles would serve as basic information for various applications.

A Ferromagnetic Resonance Study of Iron Complexes as Biologically Synthesized in Magnetic Bacteria

In order to analyze the magnetic behaviors of iron complexes biologically synthesized in magnetic bacteria MS-1, we performed FMR (Ferromagnetic Resonance) measurements for each fraction of the cell. We observed FMR spectra from the ferric iron (Fe3+) compounds distributed in each fraction of the MS-1 cell. In particular, the MS fraction yielded an anisotropic FMR signal, whereas other fractions were simple FMR spectra of Gaussian type. Upon counting the numbers of spins in various cell fractions, we compared them with the iron population as determined by the 1.10-phenanthroline method. We found a good correlation between the number of spins and the iron population in several cell fractions. We concluded that the cell fractions other than those fractions containing magnetite, consist mostly of ferric irons rather than ferrous irons.