Biomedical subjects

Masahide Terazima

Publications and source records attributed to Masahide Terazima.

At least 19 recordsLinked to original sources

PubMed2006

Laser-induced transient grating analysis of dynamics of interaction between sensory rhodopsin II D75N and the HtrII transducer.

The interaction between sensory rhodopsin II (SRII) and its transducer HtrII was studied by the time-resolved laser-induced transient grating method using the D75N mutant of SRII, which exhibits minimal visible light absorption changes during its photocycle, but mediates normal phototaxis responses. Flash-induced transient absorption spectra of transducer-free D75N and D75N joined to 120 amino-acid residues of the N-terminal part of the SRII transducer protein HtrII (DeltaHtrII) showed only one spectrally distinct K-like intermediate in their photocycles, but the transient grating method resolved four intermediates (K(1)-K(4)) distinct in their volumes. D75N bound to HtrII exhibited one additional slower kinetic species, which persists after complete recovery of the initial state as assessed by absorption changes in the UV-visible region. The kinetics indicate a conformationally changed form of the transducer portion (designated Tr*), which persists after the photoreceptor returns to the unphotolyzed state. The largest conformational change in the DeltaHtrII portion was found to cause a DeltaHtrII-dependent increase in volume rising in 8 micros in the K(4) state and a drastic decrease in the diffusion coefficient (D) of K(4) relatively to those of the unphotolyzed state and Tr*. The magnitude of the decrease in D indicates a large structural change, presumably in the solvent-exposed HAMP domain of DeltaHtrII, where rearrangement of interacting molecules in the solvent would substantially change friction between the protein and the solvent.

Archaeal Proteins↗

PubMed2006

Diffusion of platinum ions and platinum nanoparticles during photoreduction processes using the transient grating method.

The photoreduction process of PtCl(6)2- to Pt nanoparticles in poly(N-vinyl-2-pyrrolidone) solutions upon UV light irradiation was investigated by monitoring the change in the diffusion coefficient (D). The D values of chemical species during UV irradiation was measured by the laser-induced transient grating (TG) method. The TG signal of the PtCl(6)2- solution before UV irradiation was composed of three kinds of contributions, the thermal grating, the species grating due to the creation of PtCl4(2-), and the species grating due to the depletions of PtCl6(2-). Upon UV irradiation of the solution, the species grating signal due to PtCl6(2-) diminished and then the TG signal of Pt nanoparticles gradually appeared. This result indicates that the gradual clustering of Pt0 atoms into Pt nanoparticles occurs after all PtCl(6)2- ions are photochemically reduced to PtCl(4)2- and subsequently transformed to Pt0 atoms with a short delay. With increasing time of the UV irradiation, the TG signal intensity increased, while D of the Pt nanoparticles did not change. This suggests that the number of Pt nanoparticles increases, but the size of the Pt nanoparticles with the polymer layer is unchanged, in the course of the UV irradiation.

Chlorine↗

PubMed2006

Time-resolved detection of conformational changes in oat phytochrome A: time-dependent diffusion.

Conformational changes in oat phytochrome A (phy) in solution after photoexcitation of the red-absorbing form (Pr) were studied in time-domain by the pulsed laser-induced transient grating technique. It was found that the diffusion coefficient (D) of far-red-absorbing form (Pfr) of large phy (1.3 x 10(-11) m(2) s(-1)) is markedly reduced compared with that of Pr (5.8 x 10(-11) m(2) s(-1)). This large reduction indicates that the conformation of Pfr is significantly changed from that of Pr, so that the intermolecular interaction with water molecules increases. This change completes within 1 ms after the photoexcitation. On the other hand, D of Pr of intact phy (4.1 x 10(-11) m(2) s(-1)) first decreases upon photoexcitation to 0.89 x 10(-11) m(2) s(-1) within 1 ms and then gradually increases with a time constant of 100 ms to the value of Pfr, 1.7 x 10(-11) m(2) s(-1). This slower phase suggests that the conformation of the N-terminal region changes with 100 ms to decrease the intermolecular interaction with water after a global change in the large phy region. The increase of D was interpreted in terms of alpha-helix formation in the Pfr form from the random coil structure in the Pr form.

Avena↗

PubMed2006

Intermolecular interaction of myoglobin with water molecules along the pH denaturation curve.

A method of diffusion coefficient (D) measurement for proteins based on the pulsed laser-induced transient grating method using a photosensitive cross-linker was applied to the characterization of the pH denaturation process of holo- and apo-myoglobin (Mb) from the viewpoint of protein-water interaction. It was found that the pH denaturation curve monitored by D agrees quite well with that determined by the circular dichroism intensity for holo-Mb. This fact indicates that the changes in intermolecular interaction and the alpha-helix content occur simultaneously during the unfolding process. However, the pH dependence of D for apo-Mb was different from that of alpha-helix content. This different behavior can be explained in terms of the different denaturation steps for the secondary structure and the hydrogen bonding network of the intermediate species around pH 4; i.e., this intermediate is partially unfolded, but the hydrogen bonding network is dominantly an intramolecular one. Taking previously reported properties of this species into account, we conclude that water molecules are trapped in the hydrophobic core of the apo-Mb pH 4 intermediate. This fact suggests that the kinetic intermediate state of the protein folding process is a swollen state without water molecular exchange with the bulk phase.

Azides↗

PubMed2006

Conformational changes during apoplastocyanin folding observed by photocleavable modification and transient grating.

A new method to investigate the initial protein folding dynamics is developed based on a pulsed laser light triggering method and a unique transient grating method. The side chain of the cysteine residue of apoplastocyanin (apoPC) was site-specifically modified with a 4,5-dimethoxy-2-nitrobenzyl derivative, where the CD and 2D NMR spectra showed that the modified apoPC was unfolded. The substituent was cleaved with a rate of about 400 ns by photoirradiation, which was monitored by the disappearance of the absorption band at 355 nm and the increase in the transient grating signal. After a sufficient time from the photocleavage reaction, the CD and NMR spectra showed that the native beta-sheet structure was recovered. Protein folding dynamics was monitored in the time domain with the transient grating method from a viewpoint of the molecular volume change and the diffusion coefficient, both of which reflect the global structural change, including the protein-water interaction. The observed volume decrease of apoPC with a time scale of 270 micros is ascribed to the initial hydrophobic collapse. The increase in the diffusion coefficient (23 ms) is considered to indicate a change from an intermolecular to an intramolecular hydrogen bonding network. The initial folding process of apoPC is discussed based on these observations.

Apoproteins↗

PubMed2006

Raman spectroscopic study on solvation of diphenylcyclopropenone and phenol blue in room temperature ionic liquids.

We investigated the solvation of several room temperature ionic liquids by Raman spectroscopy using diphenylcyclopropenone (DPCP) and phenol blue (PB) as probe molecules. We estimated acceptor numbers (AN) of room temperature ionic liquids by an empirical equation associated with the Raman band of DPCP assigned as a C=C stretching mode involving a significant C=O stretching character. According to the dependence of AN on cation and anion species, the Lewis acidity of ionic liquids is considered to come mainly from the cation charge. The frequencies and bandwidths of the C=O and C=N stretching modes of phenol blue are found to be close to those in conventional polar solvents such as methanol and dimethyl sulfoxide. The frequencies of these vibrational modes show similar dependence upon the electronic absorption band center as is observed in conventional liquid solvents. However, peculiar behavior was found in the Raman bandwidths and the excitation wavelength dependence of the C=N stretching mode in room temperature ionic liquids. Both the bandwidth of the C=N stretching mode and the extent of the excitation wavelength dependence of the Raman shift of the C=N stretching mode tend to decrease as the absorption band center decreases, in contrast to the case of conventional solvents. This anomaly is discussed in terms of the properties of room temperature ionic liquids.

Journal Article↗

PubMed2006

Kinetic measurement of transient dimerization and dissociation reactions of Arabidopsis phototropin 1 LOV2 domain.

Photochemical reaction of a plant blue-light photoreceptor, Arabidopsis phototropin 1-LOV (light-oxygen-voltage sensing) domain 2, was studied with a view to the diffusion coefficients (D) using the pulsed-laser-induced transient grating method. Although the reaction dynamics completes at a rate of several microseconds as long as it is monitored by the absorption change, the diffusion coefficient was found to be time-dependent in a time range of submilliseconds to seconds. The observed signal can be analyzed by the two-state model, which includes the D-value decrease from D of the reactant (9.8 +/- 0.4) x 10(-11) m2/s to D of the product (8.0 +/- 0.4) x 10(-11) m2/s. The D-value of the reactant implies that the dominant form in the ground state of phototropin 1 LOV2 is the monomeric form in a concentration range of 50-200 microM. According to the Stokes-Einstein relationship, the D-change can be explained by a volume increase of 1.8 times. Furthermore, the rate of the D-change was roughly proportional to the concentration of the sample. These two observations indicate that the LOV2 domain transiently forms a dimer upon photoexcitation. When the sample concentration is increased (>180 microM), a new signal component appears within a few milliseconds. This signal represents a D increase from 8.0 x 10(-11) m2/s to 9.8 x 10(-11) m2/s with a time constant of 300 micros. The completely opposite D-change from that observed in a lower concentration, as well as the concentration dependence, implies that a dimer is formed in the ground state in a higher concentration range, even though the fraction of the dimer is still minor in this range. This dimer is photodissociated, with a time constant of 300 micros. This research clearly shows that the time-resolved diffusion measurement is a very powerful tool for detecting spectrally silent association/dissociation processes during chemical reactions. The photoreaction of the LOV2 domain is discussed.

Arabidopsis Proteins↗

PubMed2006

Tetramer formation kinetics in the signaling state of AppA monitored by time-resolved diffusion.

The photoreaction kinetics of the BLUF domain of AppA(5-125) was studied by monitoring time-dependence of an apparent diffusion coefficient (D) using the pulsed laser-induced transient grating technique. It was found that D of the photoproduct is time-dependent. From the concentration dependence of the reaction rate, it was concluded that the BLUF domain of AppA forms a dimer upon the photoexcitation. Since AppA exists as a dimeric form in the ground state, this dimerization reaction indicates the tetramer formation in the signaling state. From the slope of the plot of observed rate constants (k(obs)) against the AppA concentration, the second order rate constant is determined to be approximately 2.5 x 10(5) M(-1) s(-1), which is approximately 4 orders in magnitude lower than the diffusion controlled reaction. It indicates that a relative orientation of the protein molecules during the dimerization process causes additional constraints, which slow down the reaction rate.

Dimerization↗

PubMed2006

Conformational changes of PYP monitored by diffusion coefficient: effect of N-terminal alpha-helices.

Conformational changes in the light illuminated intermediate (pB) of photoactive yellow protein (PYP) were studied from a viewpoint of the diffusion coefficient (D) change of several N-truncated PYPs, which lacked the N-terminal 6, 15, or 23 amino acid residues (T6, T15, and T23, respectively). For intact PYP (i-PYP), D of pB (D(pB)) was approximately 11% lower than that (D(pG)) of the ground state (pG) species. The difference in D (D(pG) - D(pB)) decreased upon cleavage of the N-terminal region in the order of i-PYP>T6>T15>T23. This trend clearly showed that conformational change in the N-terminal group is the main reason for the slower diffusion of pB. This slower diffusion was interpreted in terms of the unfolding of the two alpha-helices in the N-terminal region, increasing the intermolecular interactions due to hydrogen bonding with water molecules. The increase in friction per one residue by the unfolding of the alpha-helix was estimated to be 0.3 x 10(-12) kg/s. The conformational change in the N-terminal group upon photoillumination is discussed.

Bacterial Proteins↗

PubMed2006

Time-resolved thermodynamics: heat capacity change of transient species during photoreaction of PYP.

Heat capacity changes of short-lived transient species in different time ranges were measured for the first time by using the thermal component of the transient grating and transient lens signals at various temperatures. This method was applied to the transient intermediates of Photoactive Yellow Protein (PYP). The temperature dependence of the enthalpy change shows that the heat capacity of the short-lived intermediate pR2 (also called I1 or PYP(L)) species is the same as that of the ground state (pG) species within our experimental accuracy, whereas that of the long-lived intermediate pB (I2 or PYP(M)) is much larger (2.7 +/- 0.4 kJ/mol K) than that of pG. The larger heat capacity is interpreted in terms of the conformational change of the pB species such as melted conformation and/or exposure of the nonpolar residues to the aqueous phase. This technique can be used for photochemical reactions in general to investigate the conformational change and the hydrophobic interaction in a time domain.

Bacterial Proteins↗

PubMed2005

Diffusion coefficient and the secondary structure of poly-L-glutamic acid in aqueous solution.

The diffusion coefficients (D) of poly-L-glutamic acid (PLG) at various pHs are investigated by the laser-induced transient-grating method with a new photoreactive probe molecule. The pH dependence of D is compared with that of the helical content of PLG measured by circular dichroism. It is found that the pH dependences of both quantities are very similar. Since the frictions of the translational diffusion of charged and protonated carboxyl groups are found to be similar each other, it is concluded that the conformation of the main polymer chain is the main factor in determining the diffusion process; in other words, the alpha-helix conformation makes the molecular diffusion faster. This result indicates that the conformational change of a protein can be detected by monitoring the diffusion coefficient.

Diffusion↗

PubMed2005

Diffusion coefficients as a monitor of reaction kinetics of biological molecules.

For revealing spectrally silent dynamics in chemical reactions, a new method, the time-dependent diffusion coefficient, is presented. Principles and typical examples of this method, in particular applications to biologically related reactions, are reviewed. The pulsed laser induced transient grating signal of the photo-decomposition reaction of caged ATP showed that the diffusion coefficient increases gradually with time reflecting the molecular size decrease by the dissociation. Hence, this rate should be a direct measurement of the photo-dissociation rate of ATP from the caged state. In an application to a protein folding reaction, the time-development of the diffusion coefficient was observed during the folding reaction. This time dependence was interpreted in terms of the intermolecular interaction change; i.e., conversion from the intermolecular hydrogen bonding to intramolecular one. It was found that the change of the hydrogen bonding network occurred by the two state manner in entire refolding process of cytochrome c. The unique feature of this time-dependent diffusion coefficient method is discussed.

Adenosine Triphosphate↗

PubMed2005

A biosensor in the time domain based on the diffusion coefficient measurement: intermolecular interaction of an intermediate of photoactive yellow protein.

A new type of biosensor is presented for the first time. This method is based on the diffusion measurement in the time domain by the transient grating method. As the first demonstration of this new method, various intermolecular interactions with a reaction intermediate of photoactive yellow protein, such as the protein-protein interaction, protein-DNA interaction, and protein-small molecule binding are detected. The characteristic advantages and limitations are summarized.

Bacterial Proteins↗

PubMed2005

Conformational dynamics of phototropin 2 LOV2 domain with the linker upon photoexcitation.

Conformational dynamics of LOV2 domain of phototropin, a plant blue light photoreceptor, is studied by the pulsed laser induced transient grating (TG) technique. The TG signal of LOV2 without the linker part to the kinase domain exhibits the thermal grating signal due to the heat releasing from the excited state and a weak population grating by the adduct formation. The diffusion coefficients of the adduct product after forming the chemical bond between the chromophore and Cys residue are found to be slightly smaller than that of the reactant, which implies that the core shrinks slightly on the adduct formation. After that change, no significant conformational change was observed. On the other hand, the signal of LOV2 with the linker part to the kinase domain clearly shows very different diffusion coefficients between the original and the adduct species. The large difference indicates significant global conformational change of the protein moiety upon the adduct formation. More interestingly, the diffusion coefficient is found to be time-dependent in the observation time range. The dynamics representing the global conformational change is a clear indication of a spectral silent intermediate between the excited triplet state and the signaling product. From the temporal profile analysis of the signal, the rate of the conformational change is determined to be 2 ms.

Cryptochromes↗

PubMed2005

Hydrogen bonding dynamics during protein folding of reduced cytochrome c: temperature and denaturant concentration dependence.

Folding dynamics of reduced cytochrome c triggered by the laser-induced reduction method is investigated from a viewpoint of the intermolecular interaction change. Change of the diffusion coefficient of cytochrome c during the refolding process is traced in the time domain from the unfolded value to the native value continuously at various denaturant (guanidine hydrochloride (GdnHCl)) concentrations and temperatures. In the temperature range of 288 K-308 K and GdnHCl concentration range of 2.5 M-4.25 M, the diffusion change can be analyzed well by the two-state model consistently. It was found that the m(double dagger)-value and the activation energy of the transition state from the unfolded state for the hydrogen bonding network change are surprisingly similar to that for the local structural change around the heme group monitored by the fluorescence quenching experiment. This agreement suggests the existence of common or similar fundamental dynamics including water molecular movement to control the refolding dynamics. The nature of the transition state is discussed.

Animals↗

PubMed2004

The escape process of carbon monoxide from myoglobin to solution at physiological temperature.

The carbon monoxide (CO) docking sites involved in the ligand escape process from the iron atom in hem of myoglobin (Mb) to solution at physiological temperature were studied on the basis of the effect of xenon (Xe) on the ligand escape rate by the transient grating (TG) technique. The TG method provides a direct measurement of the changes in molecular volume. The apparent CO escaping rate and the volume contraction increase with increasing Xe pressure. The pressure dependence of the rate is consistent with that of the Xe population at the Xe(1) site. This result clearly shows that CO is trapped at the Xe(1) site before escaping to solvent in a Xe-free solution at room temperature. It is shown that only CO but not the trapped Xe is released by the photoexcitation of the Xe-trapped MbCO. A dissociation scheme is proposed to explain the enhancement of the escaping rate by the presence of Xe(1). There are two branches for the CO escaping pathway. The dominant part of the dissociated CO escapes to the solvent through the Xe(1) trapping site under the Xe-free condition, and there are at least three intermediate states along this pathway. When a Xe atom blocks the Xe(1) site, the CO escapes through another route.

Animals↗

PubMed2004

Oscillation of the refractive index at the focal region of a femtosecond laser pulse inside a glass.

The temporal evolution of refractive-index change produced by a tightly focused femtosecond (fs) laser pulse inside a soda-lime glass plate was investigated by use of a transient lens method with subpicosecond time resolution. An oscillating behavior of the light intensity in the central region of the probe beam was observed 0-1500 ps after irradiation of the plate. The oscillation was interpreted in terms of a rapid temperature increase and the ensuing propagation of the pressure wave. This study is to our knowledge the first real-time observation of refractive-index change inside a glass induced by a fs laser pulse.

Journal Article↗

PubMed2004

Experimental verification of the Smoluchowski theory for a bimolecular diffusion-controlled reaction in liquid phase.

We report experimental verification of the Smoluchowski theory for diffusion-controlled reactions in solution at the steady-state limit. We have determined both the diffusion coefficients and the self-termination reaction rates of the diphenylmethyl radical simultaneously. Smoluchowski theory is insufficient to discuss the reaction rate for the self-termination reaction of the diphenylmethyl radical, so the reaction rate of an encounter complex based on the Collins-Kimball treatment is estimated.

Binding Sites↗