Solid-state electron transport across azurin: from a temperature-independent to a temperature-activated mechanism

The temperature dependence of current-voltage values of electron transport through proteins integrated into a solid-state junction has been investigated. These measurements were performed from 80 up to 400 K [above the denaturation temperature of azurin (Az)] using Si/Az/Au junctions that we have described previously. The current across the ～3.5 nm thick Az junction was temperature-independent over the complete range. In marked contrast, for both Zn-substituted and apo-Az (i.e., Cu-depleted Az), thermally activated behavior was observed. These striking temperature-dependence differences are ascribed to the pivotal function of the Cu ion as a redox center in the solid-state electron transport process. Thus, while Cu enabled temperature-independent electron transport, upon its removal the polypeptide was capable only of supporting thermally activated transport.     

Zero-point fluctuations in naphthalene and their effect on charge transport parameters

We calculate the effect of vibronic coupling on the charge transport parameters in crystalline naphthalene, between 0 and 400 K. We find that nuclear fluctuations can cause large changes in both the energy of a charge on a molecule and on the electronic coupling between molecules. As a result, nuclear fluctuations cause wide distributions of both energies and couplings. We show that these distributions have a small temperature dependence and that, even at high temperatures, vibronic coupling is dominated by the effect of zero-point fluctuations. Because of the importance of zero-point fluctuations, we find that the distributions of energies and couplings have substantial width, even at 0 K. Furthermore, vibronic coupling with high energy modes may be significant, even though these modes are never thermally activated. Our results have implications for the temperature dependence of charge mobilities in organic semiconductors.     

Participation of the BC Loop in the Correct Folding of Bacteriorhodopsin as Revealed by Solid‐state NMR†

Structural changes in bacteriorhodopsin (bR) in two different processes of retinal reconstitutions were investigated by observing the ¹³C and ¹⁵N solid‐state NMR spectra of [1‐¹³C]Val‐ and [¹⁵N]Pro‐labeled bR. We found that NMR signals of the BC loop were sensitive to changes in protein structure and dynamics, from wild‐type (WT) bR to bacterio‐opsin (bO), regenerated bR and E1001 bR. Regenerated bR was prepared following the addition of retinal into bO obtained from photobleached WT‐bR. E1001 bR was cultured from a retinal‐deficient strain termed E1001 following the addition of retinal to growing cells. ¹⁵N NMR signal at Pro70 in the BC loop in WT‐bR was observed at 122.4 p.p.m., whereas signals were not apparent or partly suppressed in bO and regenerated bR, respectively. Similarly, the ¹³C NMR signal at Val69 in the BC loop at 172.0 p.p.m. that was observed in WT‐bR was significantly decreased in both regenerated bR and bO. These results suggest that the dynamic structure of the BC loop in bO was substantially altered following the removal of retinal. As a consequence, the correct protein structure failed to be recovered via the regenerating process of retinal to bO. On the other hand, ¹³C and ¹⁵N NMR signals at the BC loop in E1001 bR appeared at positions identical to those of WT‐bR. The results of the current study indicate that the BC loop may not always fold correctly in the regenerated bR, which leads to different properties in the regenerated bR compared to that of WT‐bR.     

Contribution of convection,diffusion and migration to electrolyte transport through nanofiltration membranes

Transport mechanisms through nanofiltration membranes are investigated in terms of contribution of convection, diffusion and migration to electrolyte transport. A Donnan steric pore model, based on the application of the extended Nernst-Planck equation and the assumption of a Donnan equilibrium at both membrane-solution interfaces, is used. The study is focused on the transport of symmetrical electrolytes (with symmetric or asymmetric diffusion coefficients). The influence of effective membrane charge density, permeate volume flux, pore radius and effective membrane thickness to porosity ratio on the contribution of the different transport mechanisms is investigated. Convection appears to be the dominant mechanism involved in electrolyte transport at low membrane charge and/or high permeate volume flux and effective membrane thickness to porosity ratio. Transport is mainly governed by diffusion when the membrane is strongly charged, particularly at low permeate volume flux and effective membrane thickness to porosity ratio. Electromigration is likely to be the dominant mechanism involved in electrolyte transport only if the diffusion coefficient of coions is greater than that of counterions.     

Heat flow in proteins: computation of thermal transport coefficients

The rate of vibrational energy transfer and thermal transport coefficients are computed for two structurally distinct proteins, green fluorescent protein (GFP) and myoglobin. The computation of thermal transport coefficients exploits the scaling of the energy diffusion coefficient with the vibrational mode frequency of a protein. Near 300 K we find that vibrational energy transfer due to anharmonicity contributes substantially to thermal transport because of the localization of many thermally accessible normal modes. The thermal diffusivity for the beta-barrel GFP is larger than that for myoglobin, particularly at low temperature due to a mean free path for vibrational energy propagation that is twice as large at low frequency. Vibrational energy transfer is also faster in GFP than in myoglobin for most vibrational modes.     

Thermally stimulated carrier transport due to stepwise sample heating

The article concerns non-isothermal dispersive carrier transport in an insulating solid with traps. The approximate solutions of transport equations derived previously are extended to the case of stepwise sample heating. The specific features of thermally stimulated currents (TSCs) can be attributed to non-linear dependence of the demarcation level on temperature. In particular, the initial TSC rise has a thermally activated character where activation energy equals to the demarcation energy at the end of previous heating cycle. The accuracy of the formulae describing TSCs is verified by Monte Carlo calculations for Gaussian trap distribution.     

Characterization and photochemistry of 13-desmethyl bacteriorhodopsin

The photochemistry of the 13-desmethyl (DM) analogue of bacteriorhodopsin (BR) is examined by using spectroscopy, molecular orbital theory, and chromophore extraction followed by conformational analysis. The removal of the 13-methyl group permits the direct photochemical formation of a thermally stable, photochemically reversible state, P1(DM) (lambda(max) = 525 nm), which can be generated efficiently by exciting the resting state, bR(DM) with yellow or red light (lambda > 590 nm). Chromophore extraction analysis reveals that the retinal configuration in P1(DM) is 9-cis, identical to that of the retinal configuration in the native BR P1 state. Fourier transform infrared and Raman experiments on P1(DM) indicate an anti configuration around the C15=N bond, as would be expected of an O-state photoproduct. However, low-temperature spectroscopy and ambient, time-resolved studies indicate that the P1(DM) state forms primarily via thermal relaxation from the L(D)(DM) state. Theoretical studies on the BR binding site show that 13-dm retinal is capable of isomerizing into a 9-cis configuration with minimal steric hindrance from surrounding residues, in contrast to the native chromophore in which surrounding residues significantly obstruct the corresponding motion. Analysis of the photokinetic experiments indicates that the Arrhenius activation energy of the bR(DM) --> P1(DM) transition in 13-dm-BR is less than 0.6 kcal/mol (vs 22 +/-5 kcal/mol measured for the bR --> P (P1 and P2) reaction in 85:15 glycerol:water suspensions of wild type). Consequently, the P1(DM) state in 13-dm-BR can form directly from all-trans, 15-anti intermediates (bR(DM) and O(DM)) or all-trans, 15-syn (K(D)(DM)/L(D)(DM)) intermediates. This study demonstrates that the 13-methyl group, and its interactions with nearby binding site residues, is primarily responsible for channeling one-photon photochemical and thermal reactions and is limited to the all-trans and 13-cis species interconversions in the native protein.     

Partial dehydration of the retinal binding pocket and proof for photochemical deprotonation of the retinal Schiff base in bicelle bacteriorhodopsin crystals

In bicelle bacteriorhodopsin (bcbR) crystals, the protein has a different structure from both native bacteriorhodopsin (bR) and in-cubo bR (cbR) crystals. Recently, we studied the ability of bcbR crystals to undergo the photocycle upon laser excitation, characterized by the appearance of the M intermediate by single crystal resonance Raman spectroscopy. Calculation of the M lifetime by flash photolysis experiments demonstrated that in our bcbR crystals, the M rise time is much faster than in the native or cbR crystals, with a decay time that is much slower than these other two forms. Although it is now known that the bcbR crystals are capable of photochemical deprotonation, it is not known whether photochemical deprotonation is the only way to create the deprotonated Schiff base in the bcbR crystals. We measured both the visible and Raman spectra of crystals dried under ambient lighting and dried in the dark in order to determine whether the retinal Schiff base is able to thermally deprotonate in the dark. In addition, changes in the visible spectrum of single bcbR crystals under varying degrees of hydration and light exposure were examined to better understand the retinal binding environment.     

A non-equilibrium thermodynamics approach to model mass and heat transport for water pervaporation through a zeolite membrane

Pervaporation through zeolite membranes involves local heat effects and combined heat and mass transport. The current state-of-the-art Maxwell–Stefan (M–S) models do not take these effects into account. In this study, transport equations for the coupled heat and mass transport through a zeolite membrane are derived from the framework of non-equilibrium thermodynamics (NET). Moreover, the assumption of equilibrium between the adjacent bulk phases at the feed and permeate sides of the zeolite layer is abandoned in favor of local equilibrium. The equations have been used to model pervaporation of water through a 2 m thick NaA type zeolite membrane, deposited on an asymmetric -alumina support, at a feed temperature of 348 K. Assuming a flux of 10 kg m⁻² h⁻¹(0.15 mol m⁻² s⁻¹), the transport through the zeolite layer, as well as the liquid feed side boundary layer and the support layers is modeled. The activity, fugacity, and temperature profiles are calculated with and without taking coupling effects and surfaces into account. The profiles show distinct differences between the two cases. Including the surface effects leads to discontinuities in the activity and temperature at the membrane interfaces. A significantly higher temperature drop of 1.3 K is calculated across the zeolite, compared to 0.4 K when surface and coupling effects are not accounted for. The calculated decrease in temperature over the zeolite layer is dominated by the surfaces. This could indicate that temperature polarization is, to a large extent, a surface effect. The heat flux induces an extra driving force for mass transport, reducing the activity difference over the membrane. A positive jump in activity is observed at the interfaces, revealing the mass transport across the interfaces is governed by the coupling with the heat flux. The support layers contribute significantly to the total mass transport resistance.     

Pressure-induced isomerization of retinal on bacteriorhodopsin as disclosed by fast magic angle spinning NMR

Bacteriorhodopsin (bR) is a retinal protein in purple membrane of Halobacterium salinarum, which functions as a light-driven proton pump. We have detected pressure-induced isomerization of retinal in bR by analyzing 15N cross polarization-magic angle spinning (CP-MAS) NMR spectra of [zeta-15N]Lys-labeled bR. In the 15N-NMR spectra, both all-trans and 13-cis retinal configurations have been observed in the Lys N(zeta) in protonated Schiff base at 148.0 and 155.0 ppm, respectively, at the MAS frequency of 4 kHz in the dark. When the MAS frequency was increased up to 12 kHz corresponding to the sample pressure of 63 bar, the 15N-NMR signals of [zeta-15N]Lys in Schiff base of retinal were broadened. On the other hand, other [zeta-15N]Lys did not show broadening. Subsequently, the increased signal intensity of [zeta-15N]Lys in Schiff base of 13-cis retinal at 155.0 ppm was observed when the MAS frequency was decreased from 12 to 4 kHz. These results showed that the equilibrium constant of [all-trans-bR]/[13-cis-bR] in retinal decreased by the pressure of 63 bar. It was also revealed that the structural changes induced by the pressure occurred in the vicinity of retinal. Therefore, microscopically, hydrogen-bond network around retinal would be disrupted or distorted by a constantly applied pressure. It is, therefore, clearly demonstrated that increased pressure induced by fast MAS frequencies generated isomerization of retinal from all-trans to 13-cis state in the membrane protein bR.     

Electron transport and recombination in dye-sensitized mesoporous TiO2 probed by photoinduced charge-conductivity modulation spectroscopy with Monte Carlo modeling

We present a combined experimental and theoretical investigation into the charge transport and recombination in dye-sensitized mesoporous TiO2. We electronically probe the photoinduced change in conductivity through in-plane devices while simultaneously optically probing signatures of the charge species. Our quasi-continuous wave technique allows us to build data sets of electron mobility and recombination versus charge density over a wide temperature range. We observe that the charge density dependence of mobility in TiO2 is strong at high temperatures and gradually reduces with reducing temperature, to an extent where at temperatures below 260 K the mobility is almost independent of charge density. The mobility first increases and then decreases with reducing temperature at any given charge density. These observed trends are surprising and consistent with the multiple-trapping model for charge transport only if the trap density-of-states (DoS) is allowed to become less deep and narrower as the temperature reduces. Our recombination measurements and simulations over a broad range of charge density and temperature are also consistent with the above-mentioned varying DoS function when the recombination rate constant is allowed to increase with temperature, itself consistent with a thermally activated charge-transfer process. Further to using the Monte Carlo simulations to model the experimental data, we use the simulations to aid our understanding of the limiting factors to charge transport and recombination. According to our model, we find that the charge recombination is mainly governed by the recombination reaction rate constant and the charge density dependence is mainly a result of the bimolecular nature of the recombination process. The implication to future material design is that if the mobility can be enhanced without increasing the charge density in the film, for instance by reducing the average trap depth, then this will not be at the sacrifice of comparably enhanced recombination and it will greatly increase the charge carrier diffusion lengths in dye-sensitized or mesoscopic solar cells.     

Dynamics of Bacteriorhodopsin in the Dark-Adapted State from Solution Nuclear Magnetic Resonance Spectroscopy

To achieve efficient proton pumping in the light-driven proton pump bacteriorhodopsin (bR), the protein must be tightly coupled to the retinal to rapidly convert retinal isomerization into protein structural rearrangements. Methyl group dynamics of bR embedded in lipid nanodiscs were determined in the dark-adapted state, and were found to be mostly well ordered at the cytosolic side. Methyl groups in the M145A mutant of bR, which displays only 10 % residual proton pumping activity, are less well ordered, suggesting a link between side-chain dynamics on the cytosolic side of the bR cavity and proton pumping activity. In addition, slow conformational exchange, attributed to low frequency motions of aromatic rings, was indirectly observed for residues on the extracellular side of the bR cavity. This may be related to reorganization of the water network. These observations provide a detailed picture of previously undescribed equilibrium dynamics on different time scales for ground-state bR.     

Dissection of Environmental Changes at the Cytoplasmic Surface of Light‐activated Bacteriorhodopsin and Visual Rhodopsin: Sequence of Spectrally Silent Steps†

The physico‐chemical properties as well as the conformation of the cytoplasmic surface of the 7‐helix retinal proteins bacteriorhodopsin (bR) and visual rhodopsin change upon light activation. A recent study found evidence for a transient softening of bR in its key intermediate M [Pieper et al. (2008) Phys. Rev. Lett. 100 , 228103] as a direct proof for the functional significance of protein flexibility. In this report we compare environmental and flexibility changes at the cytoplasmic surface of light‐activated bR and rhodopsin detected by time‐resolved fluorescence spectroscopy. The changes in fluorescence of covalently bound fluorescent probes and protein real‐time dynamics were investigated. We found that in fluorescently labeled bR and rhodopsin the intensity of fluorescein and Atto647 increased upon formation of the key intermediates M and metarhodopsin‐II, respectively, suggesting different surface properties compared to the dark state. Furthermore, time‐resolved fluorescence anisotropy experiments reveal an increase in steric restriction of loop flexibility because of changes in the surrounding protein environment in both the M‐intermediate as well as the active metarhodopsin‐II state. The kinetics of the fluorescence changes at the rhodopsin surface uncover multiple transitions, suggesting metarhodopsin‐II substates with different surface properties. Proton uptake from the aqueous bulk phase correlates with the first transition, while late proton release seems to parallel the second transition. The last transition between states of different surface properties correlates with metarhodopsin‐II decay.     

Direct Measurements for Isomer Ratio of Retinal in Bacteriorhodopsin by an Electrochemical Method

Abstract— The composition of retinal isomers in bacteriorhodopsin (bR) in purple membrane (PM) was determined by photoelectric response measurements using a sandwich-type electrochemical cell. The measured amplitude of the photocurrent obtained from a dark-adapted sample was 55% lower than that from a light-adapted sample. This ratio, 55:45, would correspond to the 13- cis /aU- trans isomer ratio of retinal in the dark if the 13- cis form of the pigment did not give a response. This amplitude change correlated with the visible spectral shift of bR. The isomer ratio in the dark depended only weakly on the temperature of the electrolyte, whereas the retinal isomerization rate strongly depended on the temperature and the pH of the electrolyte in the cell. Our results indicate that photoelectric response is elicited only by a species originating from bR containing all- trans retinal and that the behavior of the response in the dark is associated with the pKa of the proton release kinetics of Asp-85.     

Ion diffusion coefficients through polyelectrolyte multilayers: temperature and charge dependence

The diffusion coefficient is a fundamental parameter for devices exploiting the ion transport properties of polyelectrolyte multilayers (PEMUs) and complexes. Here, the transport of ferricyanide through a multilayer made from poly(diallyldimethylammonium chloride) (PDADMA) and polystyrene sulfonate (PSS) was studied as a function of temperature or salt concentration. Accurate and precise measurements of ion diffusion coefficients were obtained using steady-state electrochemistry to determine the flux and Fourier transform infrared (FTIR) spectroscopy to measure the PEMU concentration. It was found that the concentration of ferricyanide inside the film decreased with temperature. Membrane transport is strongly thermally activated with activation energy 98 kJ mol(-1). A potential shift with decreasing salt concentration in cyclic voltammograms was translated into a differential flux caused by significantly higher diffusion coefficients for ferricyanide as compared to ferrocyanide.     

Computational model of hole transport in DNA

A computational model based on the molecular dynamics (MD) simulation for the hole transport in DNA has been developed and applied to study hole current in DNA strands consisting of different numbers of GC pairs. The approach is based on the hopping mechanism which is thermally activated. The calculations show that the hole hopping intensifies with the temperature and the transport rate increases in agreement with the experimental evidence. It is also determined that the degree of structural ordering in the DNA strand enhances the hole conductivity and reasons are provided why this may occur.     

IR spectroscopic observation of molecular transport through Pt@CoO yolk-shell nanostructures

FTIR spectroscopy has been used to monitor the transport of CO to the Pt cores of Pt@CoO nanoparticles forming CO/Pt species. It was found that external Pt sites are not present on the outer surfaces of the approximately 10 nm diameter nanostructures and that CO transports to Pt adsorption sites by an activated surface diffusion process through the CoO shells surrounding approximately 2 nm diameter Pt cores. The CO transport process is not due to gas-phase transport below 300 K. The weakly bound adsorbed CO/CoO species responsible for transport was directly observed at approximately 2147 cm(-1) during transport through the CoO shells.     

INTERACTION OF DIBUCAINEHCl LOCAL ANESTHETICS WITH BACTERIORHODOPSIN IN PURPLE MEMBRANE: A SPECTROSCOPIC STUDY

Several spectroscopic techniques (absorption, emission, transient absorption and differential scanning calorimetry--DSC) were used to investigate the deprotonation of dibucaine.HCl in a hydrophobic environment, and the interaction sites and mechanisms of the local anesthetic dibucaine.HCl on bacteriorhodopsin (bR) in purple membrane. The important results are summarized as follows: (1) the visible absorption features of native (lambda max = 568 nm) and deionized (lambda max = 608 nm) bR are sensitive to the amount of dibucaine.HCl added; (2) the emission spectrum of dibucaine.HCl embedded in the retinal-free mutant bR is similar to that of dibucaine free base in Triton X-100 micellar solutions; (3) the phosphorescence emission of dibucaine at 77 K is completely quenched by bR and the fluorescence quenching rate for the incorporated dibucaine.HCl in bR was determined as kq = 4.09 x 10(13) M-1 s-1; (4) the incorporation of dibucaine.HCl in bR inhibits the slow component rate of formation of M412 and decreases the amount of M412 formation in the photochemical cycle of bR; and (5) the thermal stability of native bR was measured by DSC in the presence and absence of dibucaine and yielded an endothermic transition at 95.9 +/- 1.0 degrees C with 13.6 J/g (3.25 +/- 0.12 cal/g) of enthalpy changes. All observations suggest that the action site of the local anesthetic, dibucaine.HCl, is near or at the chromophore, i.e. the retinal Schiff base of bR. The anesthetic action on bR purple membrane is probably via a specific site binding, but not a conformational mechanism.     

氯化血红素分子对牛血清白蛋白电子传输能级的调控

蛋白质分子的电子传输(ETp)性能,即导带(CB)和价带(VB)的能量差(带隙)是影响蛋白质电子器件性能的主要因素之一。因此,调控蛋白质ETp带隙是提高这些电子器件性能并扩展其应用领域的重要途径。本文报道一种通过外部分子结合调控蛋白质ETp带隙的方法。以氯化血红素(hemin)与牛血清白蛋白(BSA)结合为例,首先运用分子对接方法从理论上确定hemin分子能结合到BSA分子IIA域的疏水口袋中,位于Tpr213附近;然后实验(荧光光谱和吸收光谱)证实hemin与BSA结合后,能形成hemin-BSA复合物,并且没有改变BSA的原有结构;最后将hemin-BSA通过BSA分子表面Cys34的―SH固定在金电极表面,形成有序的分子层,研究其ETp性能;I–V结果表明,BSA表现出半导体的ETp特征,并且hemin的结合能使BSA的带隙由原来的~1.50±0.05e V降低到~0.93±0.05e V。本文的结果为调控蛋白质分子的ETp带隙提供了一种简单有效的方法,通过选择不同的结合分子能使蛋白质分子的带隙调控至所需要的范围,并且形成的蛋白质复合物还能用于各种电子器件的制作。     

Thermally activated electron transport in single redox molecules

We have studied electron transport through single redox molecules, perylene tetracarboxylic diimides, covalently bound to two gold electrodes via different linker groups, as a function of electrochemical gate voltage and temperature in different solvents. The conductance of these molecules is sensitive to the linker groups because of different electronic coupling strengths between the molecules and electrodes. The current through each of the molecules can be controlled reversibly over 2-3 orders of magnitude with the gate and reaches a peak near the redox potential of the molecules. The similarity in the gate effect of these molecules indicates that they share the same transport mechanism. The temperature dependence measurement indicates that the electron transport is a thermally activated process. Both the gate effect and temperature dependence can be qualitatively described by a two-step sequential electron-transfer process.