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Biomolecular Electronics and Optical Computing
Published in Günter Mahler, Volkhard May, Michael Schreiber, Molecular Electronics, 2020
Robert R. Birge, Richard B. Gross, Albert F. Lawrence
Bacteriorhodopsin (MW = 26,000) is the light harvesting protein in the purple membrane of a microorganism called Halobacterium salinarium (Halobacterium halobium) (35, 36). This bacterium thrives in salt marshes where the concentration of salt is roughly six times higher than that of sea water. The purple membrane, which constitutes a specific functional site in the plasma membrane of the bacterial cell, houses semicrystalline protein trimers in a phospholipid matrix (3:1 protein to lipid). The bacterium synthesizes the purple membrane when the concentration of dissolved oxygen in its surroundings becomes too low to sustain ATP production through aerobic respiration. The light absorbing chromophore of bacteriorhodopsin is all-trans retinal (Vitamin A aldehyde (Fig. 1). It is bound to the protein through a protonated Schiff base linkage to a lysine residue attached to one of the seven α-helices that make up the protein’s secondary structure. The absorption of light energy by the chromophore initiates a complex photochemical cycle characterized by a series of spectrally distinct thermal intermediates and a total cycle time of approximately 10 milliseconds (see Fig. 2). As a result of this process, the protein expels a proton from the intracellular to the extracellular side of the membrane. This light induced proton pumping generates an electrochemical gradient that the bacterium uses to synthesize ATP. Accordingly, Halobacterium salinarium can switch from aerobic respiration to photosynthesis in response to changing environmental conditions. The functioning of the
Protein-Based Optical Memories
Published in Sergey Edward Lyshevski, Nano and Molecular Electronics Handbook, 2018
Jeffrey A. Stuart, Robert R. Birge, Mark P. Krebs, Xi Bangwei, William Tetley, Duane L. Marcy, Jeremy F. Koscielecki, Jason R. Hillebrecht
Bacteriorhodopsin (Figure 16.1) is the primary integral membrane protein produced by the halophilic archaea, Halobacterium salinarum (syn. Halobacterium halobium, salinarium). This organism thrives in salt marshes where the temperature can exceed 60°C, and the concentration of sodium chloride can reach 4 M, roughly six times that of seawater. BR has 248 amino acids with a molecular weight of 26 kD, and shares a common structural motif with G-protein coupled receptors (GPCRs), consisting of a seven transmembrane alpha helical bundle. The similarities may be serendipitous, however, as BR functions as a photosynthetic protein, and GPCRs play an important role in intercellular communication. An all-trans retinal cof actor is coupled with the BR apoprotein, bound to Lys-216 via a protonated Schiff base bond. The retinal prosthetic group mediates visible light absorption and is responsible for the protein’s characteristic deep purple color. Furthermore, the retinal chromophore enables light to chemical energy transduction by the protein.
Color-Sensitive Biosensors for Imaging Applications
Published in George K. Knopf, Amarjeet S. Bassi, Smart Biosensor Technology, 2018
Lasse Lensu, Michael Frydrych, Jussi Parkkinen, Sinikka Parkkinen, Timo Jaaskelainen
The objective of this chapter was to discuss the nature of color and design factors for the application of biomolecules, in particular bacteriorhodopsin to color imaging systems. Since color has an important role in visual perception, it should be properly considered in every design of color-sensitive or color-reproduction systems in which humans have some role. The practical goal of our research has been to develop photosensors and imaging devices based on bacteriorhodopsin as a case study of a biomaterial proposed even for molecular electronics and nanoscale applications. Experiments with the imaging arrays based on different types of bacteriorhodopsin showed reliable photoelectric responsivity and usability of the arrays to color-sensitive and even video applications.
Bio-interactive nanoarchitectonics with two-dimensional materials and environments
Published in Science and Technology of Advanced Materials, 2022
Xuechen Shen, Jingwen Song, Cansu Sevencan, David Tai Leong, Katsuhiko Ariga
Fullerene nanosheets are two-dimensional crystalline assemblies of C60 fullerene shaped like thin hexagonal prisms. Fullerene nanosheets are prepared using LLIP at the interface between carbon tetrachloride (CCl4) and an alcohol. The size of nanosheets depends on the alcohol used; the hexagonal face of nanosheets produced with methanol, ethanol, and isopropyl alcohol (IPA) has diameters between 500–700 nm, 2–3 µm, and 7–9 µm, respectively, [188]. Luo et al. reprogrammed human fibroblasts to neural lineages through optogenetic modulation on a fullerene nanosheet platform [189] (Figure 8). Human fibroblasts were transfected with highly expressible bacteriorhodopsin (HEBR) genes, which produce photo-responsive proton pumps with the potential to trigger neural activity. C60 nanosheets prepared through LLIP (CCl4/benzene and IPA) were formed into Langmuir-Blodgett (LB) films on glass and polyurethane substrates. Transfected fibroblasts cultured on C60 nanosheet substrates and stimulated with light significantly upregulated neural lineage-related genes GFAP, β-tubulin, MAP2 and corresponding marker proteins; transfected fibroblasts differentiated toward neural lineages without induction medium. Optogenetic modulation is synergistically enhanced by photoelectric properties of C60. Fullerene nanosheet substrates are promising for neural therapies based on optogenetics.
Structural and spectroscopic features of proton hydrates in the crystalline state. Solid-state DFT study on HCl and triflic acid hydrates
Published in Molecular Physics, 2018
M. V. Vener, I. Yu. Chernyshov, A. A. Rykounov, A. Filarowski
The IR-intensive band at around 1730 cm−1 was detected for H5O+2 [30,113], as well as its partially H5O+2(H2O)2 [114] and fully H5O+2(H2O)4 hydrated forms [115,116] in the gas and liquid phases. It has been shown [117] that the interaction with the bulky counter ion in a polar solvent slightly impacts the frequency of the considered band. The band at around 1730 cm−1 was detected in the light-driven proton pump bacteriorhodopsin [118] and during hydration/dehydration cycles of Nafion NRE211 membrane at room temperature [24]. The presence of this band indicates the existence of H5O+2 in the considered systems. In the previous studies [1,25,119,120], the peak at around 1730 cm−1 was also assigned to the asymmetric bending vibration of H3O+. It is located in the 1800–1600 cm−1 region in the crystalline hydrates of strong monobasic acids [66,67,104]. The unambiguous identification of the H3O+ ion in acidic aqueous solutions requires a combined IR and Raman investigation, because the fundamental vibrations of the cation are Raman-active (Table 3 in [7]). All attempts to detect the hydronium bands in the Raman spectra of the acid solutions were unsuccessful [121]. However, on passing to liquid systems in which the H3O+ ion does exist (with the ratio, acid: water 1:1), the situation changes sharply. Raman polarisation measurements of solutions containing H3O+SbCl6− in CH2Cl2 exhibit four bands: 3560, 3510, 1600 and 1095 cm−1 [122] that correspond to the frequencies of the fundamental transitions of the ion in the gas phase and molecular crystals (Tables 1 and 2 in [7]).