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Nishi-Tokyo-shi, Japan

Ishikita H.,Kyoto University | Ishikita H.,Japan Science and Technology Agency | Hasegawa K.,AdvanceSoft Corporation | Noguchi T.,Nagoya University

The redox potential of the primary quinone Q A [E m(Q A)] in photosystem II (PSII) is lowered by replacement of the native plastoquinone (PQ) with bromoxynil (BR) at the secondary quinone Q B binding site. Using the BR-bound PSII structure presented in the previous Fourier transform infrared and docking calculation studies, we calculated E m(Q A) considering both the protein environment in atomic detail and the protonation pattern of the titratable residues. The calculated E m(Q A) shift in response to the replacement of PQ with deprotonated BR at the Q B binding site [ΔE m(Q A) PQ→BR] was -55 mV when the three regions, Q A, the non-heme iron complex, and Q B (Q B = PQ or BR), were treated as a conjugated supramolecule (Q A-Fe-Q B). The negative charge of BR apparently contributes to the downshift in ΔE m(Q A) PQ→BR. This downshift, however, is mostly offset by the influence of the residues near Q B. The charge delocalization over the Q A-Fe-Q B complex and the resulting H-bond strength change between Q A and D2-His214 are crucial factors that yield a ΔE m(Q A) PQ→BR of -55 mV by (i) altering the electrostatic influence of the H-bond donor D2-His214 on E m(Q A) and (ii) suppressing the proton uptake events of the titratable residues that could otherwise upshift ΔE m(Q A) PQ→BR during replacement of PQ with BR at the Q B site. © 2011 American Chemical Society. Source

Hasegawa K.,AdvanceSoft Corporation | Mohri S.,Japanese National Institute of Animal Health | Yokoyama T.,Japanese National Institute of Animal Health

The e200K mutation of the human prion protein (PrP) is known to cause familial creutzfeldt-Jakob disease. In order to elucidate the effects of the mutation on the local structural stability of PrP, we performed ab initio fragment molecular orbital calculations for the wild-type human PrP and the e200K variant modeled under neutral and mild acidic conditions. The calculations revealed that this substitution markedly altered the intramolecular interactions in the PrP, suggesting that the local structural instabilities induced by the e200K mutation might cause initial denaturation of the PrP and its subsequent conversion to a pathogenic form. This work presents a new approach for quantitatively elucidating structural instabilities in proteins that cause misfolding diseases. Source

Takahashi R.,University of Tsukuba | Hasegawa K.,AdvanceSoft Corporation | Takano A.,University of Tsukuba | Noguchi T.,Nagoya University | Noguchi T.,University of Tsukuba

Herbicides targeting photosystem II (PSII) block the electron transfer beyond QA by binding to the QB site. Upon binding, the redox potential of QA shifts differently depending on the types of herbicides. In this study, we have investigated the structures, interactions, and locations of phenolic herbicides in the QB site to clarify the molecular mechanism of the QA potential shifts by herbicides. Fourier transform infrared (FTIR) difference spectra upon photoreduction of the preoxidized non-heme iron (Fe2+/Fe3+ difference) were measured with PSII membranes in the presence of bromoxynil or ioxynil. The CN and CO stretching vibrations of these phenolic herbicides were identified at 2215-2200 and 1516-1505 cm-1, respectively, in the Fe 2+/Fe3+ difference spectra. Comparison with the spectra of bromoxynil in ethanol solutions along with density functional theory analysis strongly suggests that the phenolic herbicides take a deprotonated form in the binding pocket. In addition, the CN stretching, NH bending, and NH stretching vibrations of a His side chain, which were found at 1109-1101, 1187-1185, and 3000-2500 cm-1, respectively, in the Fe2+/Fe3+ difference spectra, showed characteristic features in the presence of phenolic herbicides. These signals are probably attributed to D1-His215, one of the ligands to the non-heme iron. Docking calculations for herbicides to the Q B pocket confirmed the binding of deprotonated bromoxynil to D1-His215 at the CO group, whereas the protonated form of bromoxynil and DCMU were found to bind to the opposite side of the pocket without an interaction with D1-His215. From these results, it is proposed that a strong hydrogen bond of the phenolate CO group with D1-His215 induces the change in the hydrogen bond strength of the QA CO group through the QA-His-Fe-His- phenolate bridge causing the downshift of the QA redox potential. © 2010 American Chemical Society. Source

Ida Y.,AdvanceSoft Corporation
Journal of Volcanology and Geothermal Research

Time-dependent magma ascent processes were analyzed using a computer simulation of bubbly and gassy (gas-particle dispersion) magma flows in a vertical conduit connected at its bottom to a magma chamber having finite capacity. Volatile elements in the bubbly flow were assumed to escape from the magma through lateral permeable gas flow driven by the pressure gradient originating from viscous resistance to the ascent velocity-dependent expansion of bubbles. The bubbly flow was assumed to fragment and to transform into a gassy flow when its gas volume fraction exceeded a critical value. Based on the simulation, an eruption is predicted to be explosive or effusive when a dimensionless degassing factor, which is proportional to the permeability and viscosity of the magma, is smaller or greater than a critical value, respectively. The state of gassy flow was calculated from the mass and momentum conservations that are met quasi-statically with continuities of mass flux and pressure at the interface with the underlying bubbly flow. The inertia force and an effective wall friction were considered as resistive forces working on the gassy flow. Some of the results of the simulation are shown to be consistent with observations of some recent eruptions. An effusive or explosive eruption is predicted to have relatively high activity with large exit velocities at its initial stage. The initial high activity is particularly significant for explosive eruptions that involve the rapid growth of a gassy flow zone. Explosive eruptions are shown to involve more efficient magma transport with higher mass flow rates than effusive eruptions, as has been predicted by some previous analyses of stationary magma flow. The efficient magma transport of explosive eruptions is associated with a peculiar pressure distribution consisting of gentler and steeper pressure gradients in the gassy and bubbly flow zones, respectively. At the interface between bubbly and gassy flows, the pressure scaled by that at the conduit bottom was found to be nearly constant through time. This peculiar pressure distribution allows explosive eruptions to be fed with more magma than has been stored in excess of the lithostatic balance. This mechanism can produce such anomalously low pressure in the chamber that significant surface subsidence and caldera formation may result. © 2010 Elsevier B.V. Source

Ren S.,Tokyo Institute of Technology | Hasegawa K.,AdvanceSoft Corporation | Hyodo M.,Hokkaido University | Hayakawa Y.,Aichi Institute of Technology | And 3 more authors.

Organisms adapt their physiologies in response to the quality and quantity of environmental light. Members of a recently identified photoreceptor protein family, BLUF domain proteins, use a flavin chromophore to sense blue light. Herein, we report that PapB, which contains a BLUF domain, controls the biofilm formation of the purple photosynthetic bacterium Rhodopseudomonas palustris. Purified PapB undergoes a typical BLUF-type photocycle, and light-excited PapB enhances the phosphodiesterase activity of the EAL domain protein, PapA, which degrades the second messenger, cyclic dimeric GMP (c-di-GMP). PapB directly interacts with PapA in vitro in a light-independent manner and induces a conformational change in the preformed PapA-PapB complex. A PapA-PapB docking simulation, as well as a site-directed mutagenesis study, identified amino acids partially responsible for the interaction between the PapA EAL domain and the two C-terminal α-helices of the PapB BLUF domain. Thus, the conformational change, which involves the C-terminal β-helices, transfers the flavin-sensed blue light signal to PapA. Deletion of papB in R. palustris enhances biofilm formation under high-intensity blue light conditions, indicating that PapB functions as a blue light sensor, which negatively regulates biofilm formation. These results demonstrate that R. palustris can control biofilm formation via a blue light-dependent modulation of its c-di-GMP level by the BLUF domain protein, PapB. © 2010 American Chemical Society. Source

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