scholarly journals Exploring the Retinal Binding Cavity of Archaerhodopsin-3 by Replacing the Retinal Chromophore With a Dimethyl Phenylated Derivative

2021 ◽  
Vol 8 ◽  
Author(s):  
Taichi Tsuneishi ◽  
Masataka Takahashi ◽  
Masaki Tsujimura ◽  
Keiichi Kojima ◽  
Hiroshi Ishikita ◽  
...  
Keyword(s):  
Energy Gap ◽  
Blue Shift ◽  
Proton Pumping ◽  
Molecular Properties ◽  
Ph Change ◽  
Time Resolved ◽  
Spectroscopic Measurements ◽  
Binding Cavity ◽  
Retinal Chromophore ◽  
The Difference

Rhodopsins act as photoreceptors with their chromophore retinal (vitamin-A aldehyde) and they regulate light-dependent biological functions. Archaerhodopsin-3 (AR3) is an outward proton pump that has been widely utilized as a tool for optogenetics, a method for controlling cellular activity by light. To characterize the retinal binding cavity of AR3, we synthesized a dimethyl phenylated retinal derivative, (2E,4E,6E,8E)-9-(2,6-Dimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenal (DMP-retinal). QM/MM calculations suggested that DMP-retinal can be incorporated into the opsin of AR3 (archaeopsin-3, AO3). Thus, we introduced DMP-retinal into AO3 to obtain the non-natural holoprotein (AO3-DMP) and compared some molecular properties with those of AO3 with the natural A1-retinal (AO3-A1) or AR3. Light-induced pH change measurements revealed that AO3-DMP maintained slow outward proton pumping. Noteworthy, AO3-DMP had several significant changes in its molecular properties compared with AO3-A1 as follows; 1) spectroscopic measurements revealed that the absorption maximum was shifted from 556 to 508 nm and QM/MM calculations showed that the blue-shift was due to the significant increase in the HOMO-LUMO energy gap of the chromophore with the contribution of some residues around the chromophore, 2) time-resolved spectroscopic measurements revealed the photocycling rate was significantly decreased, and 3) kinetical spectroscopic measurements revealed the sensitivity of the chromophore binding Schiff base to attack by hydroxylamine was significantly increased. The QM/MM calculations show that a cavity space is present at the aromatic ring moiety in the AO3-DMP structure whereas it is absent at the corresponding β-ionone ring moiety in the AO3-A1 structure. We discuss these alterations of the difference in interaction between the natural A1-retinal and the DMP-retinal with binding cavity residues.

scholarly journals Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation

2019 ◽  
Vol 88 (1) ◽  
pp. 59-83 ◽  
Author(s):  
Cecilia Wickstrand ◽  
Przemyslaw Nogly ◽  
Eriko Nango ◽  
So Iwata ◽  
Jörg Standfuss ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Proton Pumping ◽  
Time Resolved ◽  
Structural Mechanism ◽  
X Ray ◽  
Recent Developments ◽  
Retinal Chromophore ◽  
Directional Transport ◽  
Structural Insights ◽  
Serial Femtosecond Crystallography

Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.

Localized Nature of Photoluminescence from Anodically Oxidized Porous Silicon

1994 ◽  
Vol 358 ◽  
Author(s):  
T. Ito ◽  
K. Furuta ◽  
T. Yoneda ◽  
O. Arakaki ◽  
A. Hatta ◽  
...  
Keyword(s):  
Porous Silicon ◽  
Energy Gap ◽  
Blue Shift ◽  
Large Temperature ◽  
Activation Process ◽  
Time Resolved ◽  
Thermally Activated ◽  
Peak Energy ◽  
Thermal Activation Process ◽  
Oxidized Porous Silicon

ABSTRACTPhotoluminescence (PL) properties from anodically oxidized porous silicon (PS) have been investigated. Large temperature coefficients (-0.5 meV/K) of PL peak energy are observed for relatively strongly oxidized PS specimens which show saturation of PL peak blue shift upon further anodic oxidation. Time-resolved PL data show that the PL decay is characteristic of thermal activation process with an energy of 9-27 meV at low temperatures between 80 and 180 K. Those results can be explained using a luminescence model which assumes several PL centers in the energy gap and considers thermally activated and tunneling processes.

scholarly journals Effect of Laser Irradiation on Emissivity of Flame-Generated Nanooxides

Materials ◽  
2021 ◽  
Vol 14 (9) ◽  
pp. 2303
Author(s):  
Silvana De Iuliis ◽  
Roberto Dondè ◽  
Igor Altman
Keyword(s):  
Laser Irradiation ◽  
Light Emission ◽  
Energy Gap ◽  
Particle Temperature ◽  
Electron Excitation ◽  
Flame Spray ◽  
Energy Bands ◽  
Light Emitting ◽  
Spectral Behavior ◽  
The Difference

The application of pyrometry to retrieve particle temperature in particulate-generating flames strictly requires the knowledge of the spectral behavior of emissivity of light-emitting particles. Normally, this spectral behavior is considered time-independent. The current paper challenges this assumption and explains why the emissivity of oxide nanoparticles formed in flame can change with time. The suggested phenomenon is related to transitions of electrons between the valence and conduction energy bands in oxides that are wide-gap dielectrics. The emissivity change is particularly crucial for the interpretation of fast processes occurring during laser-induced experiments. In the present work, we compare the response of titania particles produced by a flame spray to the laser irradiation at two different excitation wavelengths. The difference in the temporal behavior of the corresponding light emission intensities is attributed to the different mechanisms of electron excitation during the laser pulse. Interband transitions that are possible only in the case of the laser photon energy exceeding the titania energy gap led to the increase of the electron density in the conduction band. Relaxation of those electrons back to the valence band is the origin of the observed emissivity drop after the UV laser irradiation.

scholarly journals A diffusion anisotropy descriptor links morphology effects of H-ZSM-5 zeolites to their catalytic cracking performance

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xiaoliang Liu ◽  
Jing Shi ◽  
Guang Yang ◽  
Jian Zhou ◽  
Chuanming Wang ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Catalytic Cracking ◽  
Catalytic Performance ◽  
Zeolite Catalysts ◽  
Time Resolved ◽  
Cracking Performance ◽  
Morphology Effect ◽  
Ft Ir ◽  
The Difference ◽  
Dynamics Simulations

AbstractZeolite morphology is crucial in determining their catalytic activity, selectivity and stability, but quantitative descriptors of such a morphology effect are challenging to define. Here we introduce a descriptor that accounts for the morphology effect in the catalytic performances of H-ZSM-5 zeolite for C4 olefin catalytic cracking. A series of H-ZSM-5 zeolites with similar sheet-like morphology but different c-axis lengths were synthesized. We found that the catalytic activity and stability is improved in samples with longer c-axis. Combining time-resolved in-situ FT-IR spectroscopy with molecular dynamics simulations, we show that the difference in catalytic performance can be attributed to the anisotropy of the intracrystalline diffusive propensity of the olefins in different channels. Our descriptor offers mechanistic insight for the design of highly effective zeolite catalysts for olefin cracking.

scholarly journals Overheating In Silicon During Pulsed-Laser Irradiation?

1985 ◽  
Vol 51 ◽  
Author(s):  
B. C. Larson ◽  
J. Z. Tischler ◽  
D. M. Mills
Keyword(s):  
Laser Irradiation ◽  
Thermal Strain ◽  
Pulsed Laser ◽  
Interface Velocity ◽  
High Energy ◽  
Time Resolved ◽  
Synchrotron Source ◽  
Zero Velocity ◽  
The Difference ◽  
Pulsed Laser Irradiation

ABSTRACTNanosecond resolution time-resolved x-ray diffraction measurements of thermal strain have been used to measure the interface temperatures in silicon during pulsed-laser irradiation. The pulsed-time-structure of the Cornell High Energy Synchrotron Source (CHESS) was used to measure the temperature of the liquid-solid interface of <111> silicon during melting with an interface velocity of 11 m/s, at a time of near zero velocity, and at a regrowth velocity of 6 m/s. The results of these measurements indicate 110 K difference between the temperature of the interface during melting and regrowth, and the measurement at zero velocity shows that most of the difference is associated with undercooling during the regrowth phase.

Time-resolved spectroscopic measurements of high density in Ar-filled microballoon implosions

1989 ◽  
Vol 63 (3) ◽  
pp. 267-270 ◽  
Author(s):  
C. F. Hooper Jr. ◽  
D. P. Kilcrease ◽  
R. C. Mancini ◽  
L. A. Woltz ◽  
D. K. Bradley ◽  
...  
Keyword(s):  
High Density ◽  
Time Resolved ◽  
Spectroscopic Measurements

Time-resolved IR spectroscopy reveals mechanistic details of ion transport in the sodium pump Krokinobacter eikastus rhodopsin 2

2019 ◽  
Vol 21 (8) ◽  
pp. 4461-4471 ◽  
Author(s):  
Marvin Asido ◽  
Peter Eberhardt ◽  
Clara Nassrin Kriebel ◽  
Markus Braun ◽  
Clemens Glaubitz ◽  
...  
Keyword(s):  
Ir Spectroscopy ◽  
Comparative Study ◽  
Ion Transport ◽  
Structural Dynamics ◽  
Sodium Pump ◽  
Proton Pumping ◽  
Wild Type ◽  
Time Resolved

We report a comparative study on the structural dynamics of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 wild type under sodium and proton pumping conditions by means of time-resolved IR spectroscopy.

Quantum Dot Solar Cells Based on CdSe-Assembled Titania Semiconductors

2008 ◽  
Vol 1102 ◽  
Author(s):  
Chien-Tsung Wang ◽  
Chung-Hsiao Yeh
Keyword(s):  
Particle Size ◽  
Solar Cells ◽  
Energy Gap ◽  
Blue Shift ◽  
Cdse Nanocrystals ◽  
Cdse Qds ◽  
One Pot ◽  
Optical Absorbance ◽  
Quantum Size ◽  
The One

AbstractIn the study, semiconductor quantum dots (QDs) of CdSe nanocrystals have been demonstrated effective as the light energy harvesting assemblies in solar cells. Colloidal CdSe QDs were synthesized by the one-pot approach and linked through a surface modifier onto titania (TiO2) nanoparticles. The TiO2-CdSe composite, while employed as the photoanode in a photoelectrochemical apparatus, exhibited a higher photon-to-electron conversion efficiency (3-fold) than the TiO2 alone, and also a higher stability for photocurrent generation, according to photocurrent transient responses. The optical absorbance and photoluminescence of the CdSe colloid showed a blue shift in the absorption edge with decreasing the particle size (band energy gap shifts from 2.0 to 2.19 eV), suggesting a quantum size effect. The CdSe particle size was determined up to 5 nm by a transmission electron microscopy. A scheme describing the charge carrier rectification for the coupled semiconductor system is proposed.

scholarly journals Structure of bovine cytochromecoxidase in the ligand-free reduced state at neutral pH

2018 ◽  
Vol 74 (2) ◽  
pp. 92-98 ◽  
Author(s):  
Fangjia Luo ◽  
Kyoko Shinzawa-Itoh ◽  
Kaede Hagimoto ◽  
Atsuhiro Shimada ◽  
Satoru Shimada ◽  
...  
Keyword(s):  
Ph Value ◽  
Proton Pumping ◽  
Molecular Surface ◽  
Cellular Respiration ◽  
Inner Mitochondrial Membrane ◽  
Ph Change ◽  
Structural Alterations ◽  
Ligand Free ◽  
Wide Ph Range ◽  
Ph Range

Cytochromecoxidase (CcO), the terminal oxidase in cellular respiration, couples proton pumping to O2reduction. Mammalian CcO resides in the inner mitochondrial membrane. Previously, a model of H-pathway proton pumping was proposed based on various CcO crystal structures. However, all previously determined structures were solved using crystals obtained at pH 5.7, which differs from the environmental pH of CcO in the inner membrane. The structures of fully oxidized and ligand-free reduced CcO at pH 7.3 have now been determined. Structural comparison between the oxidized and reduced states revealed that the structural alterations that occurred upon redox change at pH 5.7 in Asp51, the magnesium-containing cluster, haem groups and helix X, which provide important structural evidence for the H-pathway proton-pumping proposal, also occur at pH 7.3. These structural alterations were restricted to a local region of CcO; no domain movement was detected, nor were significant structural alterations detected in peripheral regions at either pH value. These observations indicate that the small and precise structural alterations that occur over the course of the reaction cycle are not affected by pH change, and that isolated CcO precisely performs proton pumpingviathe H-pathway over a wide pH range. Because the pH is not uniform across the molecular surface of CcO, the fact that the overall structure of CcO is not affected by pH changes ensures the high enzymatic efficiency of this protein in the mitochondria.

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