Presently we report that enzymatic oxidation of ethanol (EtOH) by ADH1A alcohol dehydrogenase is strongly accelerated in presence of adenosine triphosphate (ATP), by up to the factor of 20 in vitro. ...This result provides a different look on the role of ATP in functioning of alcohol dehydrogenases (ADH), which until presently were a textbook example of enzymes not requiring ATP and successfully operating without it. However, ATP is available in every living cell and will activate reactions conducted by ADH enzymes in vivo. Therefore, the body of published literature describing properties of numerous ADH enzymes requires a thorough revision.
Process (A) is the textbook spontaneous enzymatic oxidation of ethanol, producing acetaldehyde, while process (B) is ATP-activated enzymatic oxidation of ethanol. The rate of process (B) is much faster than that of process (A) and will dominate in vivo. Display omitted
•It was found that ATP accelerates enzyme oxidation rate of ethanol.•ATP-sensitized ethanol oxidation by ADH1A was faster by up to the factor of 20 than spontaneous oxidation.•These results contradict the consensus nation that ADH enzymes do not need ATP.
Photo-activation of mitochondrial ATP synthesis Khmelinskii, Igor; Makarov, Vladimir I.
Journal of photochemistry and photobiology. B, Biology,
March 2022, 2022-Mar, 2022-03-00, 20220301, Letnik:
228
Journal Article
Recenzirano
ATP production by mitochondria isolated from Saccharomyces cerevisiae cells was accelerated upon both direct and indirect mitochondrial photo-activation (MPA). The extent of direct MPA was dependent ...on the wavelength of excitation light. Direct MPA was created by light in cytochrome c spectral absorption bands (440, 520 and 550 nm), this light was absorbed producing electronically excited cytochrome c, and the excitation energy of the latter was used in the ATP production chain. The activity of cytochrome c was tested with 600 nm light, where cytochrome c does not absorb, and thus ATP production rate remained the same as in darkness. Note that ATP production rates were significantly larger under light at 550, 520 and 440 nm. Therefore, photo-activation of cytochrome c was the first step of MPA synthesis of ATP. Indirect MPA of ATP production also proceeded via electronically excited cytochrome c, by energy transfer from electronically excited Co/BN film to cytochrome c located in the inner mitochondrial membrane (IMM). Co/BN excitons were generated by photons absorbed by the Co/BN film, which was not in contact with the mitochondrial sample. Next, these excitons propagated along the Co/BN film to the part of the film that was in contact with the mitochondrial sample. There the exciton energy was transferred to cytochrome c located in the IMM, producing electronically excited cytochrome c. Thus, excited cytochrome c was generated in a way different from that of direct MPA. Next, the energy of excited cytochrome c was used in activated ATP synthesis, with virtually the same effect for 519 and 427 nm excitation. Thus, the first step of ATP synthesis in indirect MPA was the exciton energy transfer from Co/BN film to cytochrome c located in the IMM, producing an electronically excited cytochrome c molecule. A phenomenological mechanism of direct and indirect MPA was proposed, and the model parameters were obtained by fitting the model to the experimental data. However, more information is needed before the detailed mechanism of ATP synthesis activation by electronically excited cytochrome c could be understood. The present results support the earlier proposed hypothesis of indirect MPA of ATP production in vertebrate retina in daylight.
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•ATP synthesis by yeast mitochondria was photo-activated by light at 440, 520 and 550 nm.•The same reaction was activated by exciton energy transfer from Co/BN nanofilm to mitochondrial cytochrome c.•Detailed theoretical model of mitochondrial photo-activation developed and discussed.
Spectrum of transmitted IR radiation energy by exciton propagation along the MC IFs filling capillary matrix. Spectrum was recorded in the step-scan mode with 30 s of accumulation time per one ...spectral step. Spectrum was recorded at 5°C. Deconvoluted bands are as well shown in figure.
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•IR emission of porcine retinal Müller cell (MC) intermediate filaments (IFs) recorded.•ATP hydrolysis energy transfer efficiency via MC IFs measured.•Excitons produced by simultaneous hydrolysis of two ATPs by dimeric ADH1A enzyme.•ATP hydrolysis energy was transferred via MC IFs over distances exceeding 100 μm.
IR exciton propagation was explored in Müller cell (MC) intermediate filaments (IFs) filling a capillary matrix. These IFs have been isolated from porcine retina using different methods, while their properties were almost identical. Therefore, IFs isolated from the whole retinas were used presently. IR excitons were generated by IR radiation at 2 μm wavelength, or by enzymatic ATP hydrolysis, with the energy transferred to IFs. Excitons produced by ATP hydrolysis required simultaneous energy contribution of two ATP molecules, indicating simultaneous hydrolysis of two ATP molecules in the naturally dimeric human alcohol dehydrogenase enzyme (ADH1A). ATP hydrolysis was thus catalyzed by ADH1A…NAD+ enzymatic complexes absorbed at the IF extremities protruding out of the capillary matrix. The IR emission spectra of excitons were dependent on the exciton generation method. We believe this resulted from the exciton energy distribution varying in function of the generation method used. The latter seems reasonable, given the very long excited-state lifetimes, implying low nonradiative relaxation rates. The energy liberated by ATP hydrolysis has been measured directly in these experiments, for the first time. The results demonstrate that contrary to the predictions of equilibrium thermodynamics, the liberated energy is independent on the ATP/ADP concentration ratio, indicating that non-equilibrium reactions take place. Time-resolved experiments with excitons produced by pulsed IR radiation evaluated characteristic exciton propagation and emission times. For the first time, biexcitonic processes were observed in biological objects, whereby simultaneous hydrolysis of two ATP molecules bound to the same dimeric ADH1A molecule generated excitons carrying twice the energy liberated by hydrolysis of a single ATP molecule. The results reported indicate that ATP-liberated energy may be transmitted along natural polypeptide nanofibers in vivo, within and between live cells. These ideas could promote new understanding of the biophysics of life.
Temperature dependences of IR exciton properties in Müller cell (MC) intermediate filaments (IFs) isolated from porcine retina were studied. It was found that the widths of the spectral emission ...bands in the 2500 cm−1 and 5000 cm−1 energy ranges grow with temperature. It was found that temperature effects on the bandwidth may be described by thermal activation of the low-frequency vibrational modes of the IFs. The average activation energies for the two IR bands were estimated. Considering the dynamics of IR emission, its buildup time was independent on the sample temperature, while its decay time decreased with temperature. Thus, the emission decay rate increased exponentially with the sample temperature. The mechanisms explaining the observed temperature effects were proposed and discussed. Taking into account that MC IFs are capable of transmitting ATP hydrolysis energy within and between cells, with these properties being apparently common for all IFs, these IFs may be used by cells for physical energy transport and communications. As presently reported, temperature effects upon IR exciton spectra should not affect these proposed physiological functions to any significant extent. Therefore, the currently reported data are important for improving our understanding of the physical communication mechanisms operating within and between cells.
•Temperature dependence of IR exciton spectra in MC IFs was studied.•Temperature dependences of exciton emission dynamics was studied.•Mechanisms explaining temperature dependences were proposed.
•Zone structure of α-helix polypeptides (PP) studied ab initio at different chain lengths.•The lowest bandgap of ca. 0.43 to 0.63 eV, weakly dependent on PP composition.•The energy propagation ...mechanism along PP considered in detail.
We report new theoretical and experimental results that may significantly change our ideas on the workings of life. We performed ab initio analysis of the band structure of periodic α-helix polypeptides (PP) in function of the chain length. Three different calculation approaches were tested: (a) PP described semiempirically as a one-dimensional object, with the amino acids substituted by effective atoms; (b) density functional theory (DFT) as implemented in WIEN2k approach, and (c) CRYSTAL-17 software package. The approach (c) was used for the detailed ab initio analysis, as it provided better accuracy in less computation time. We found that the bandgap was weakly dependent on the PP composition, with the asymptotic values in the 0.43 – 0.63 eV range. We estimated the effective electron and hole masses, their mean free path and mobility for the glycine-PP. The electron mobility in the PP conductive band was about half of that in polycrystalline silicon. The PP zone structure was used to study the mechanism of energy transfer along the PP. The current-voltage (I/V) characteristics of Müller cell (MC) intermediate filaments (IFs) from porcine retina were experimentally measured. The measured I/V characteristics show that the IFs behave as semiconductors. These results were discussed in light of the presently reported PP zone structure theory. The results obtained may open new areas in biomedical research and applications.
The influence of motivation and alertness on brain activity associated with visual perception was studied experimentally using the Necker cube, which ambiguity was controlled by the contrast of its ...ribs. The wavelet analysis of recorded multichannel electroencephalograms (EEG) allowed us to distinguish two different scenarios while the brain processed the ambiguous stimulus. The first scenario is characterized by a particular destruction of alpha rhythm (8-12 Hz) with a simultaneous increase in beta-wave activity (20-30 Hz), whereas in the second scenario, the beta rhythm is not well pronounced while the alpha-wave energy remains unchanged. The experiments were carried out with a group of financially motivated subjects and another group of unpaid volunteers. It was found that the first scenario occurred mainly in the motivated group. This can be explained by the increased alertness of the motivated subjects. The prevalence of the first scenario was also observed in a group of subjects to whom images with higher ambiguity were presented. We believe that the revealed scenarios can occur not only during the perception of bistable images, but also in other perceptual tasks requiring decision making. The obtained results may have important applications for monitoring and controlling human alertness in situations which need substantial attention. On the base of the obtained results we built a brain-computer interface to estimate and control the degree of alertness in real time.
We highlight mechanical stretching and bending of membranes and the importance of membrane deformations in the analysis of swelling dynamics of biological systems, including cells and subcellular ...organelles. Membrane deformation upon swelling generates tensile stress and internal pressure, contributing to volume changes in biological systems. Therefore, in addition to physical (internal/external) and chemical factors, mechanical properties of the membranes should be considered in modeling analysis of cellular swelling. Here we describe an approach that considers mechanical properties of the membranes in the analysis of swelling dynamics of biological systems. This approach includes membrane bending and stretching deformations into the model, producing a more realistic description of swelling. We also discuss the effects of membrane stretching on swelling dynamics. We report that additional pressure generated by membrane bending is negligible, compared to pressures generated by membrane stretching, when both membrane surface area and volume are variable parameters. Note that bending deformations are reversible, while stretching deformation may be irreversible, leading to membrane disruption when they exceed a certain threshold level. Therefore, bending deformations need only be considered in reversible physiological swelling, whereas stretching deformations should also be considered in pathological irreversible swelling. Thus, the currently proposed approach may be used to develop a detailed biophysical model describing the transition from physiological to pathological swelling mode.
First-order interactions between quantum states; the matrix element V describes the strength of the interaction between the state |s> and the set of states {|j>} with the state density ρj. The state ...energies are characterized by complex values, with the imaginary part describing the respective state width.
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•Theoretical methods for quantum coherence dynamics in biology reviewed.•Namely, effective Hamiltonian (EH), Green’s function and density matrix methods.•Quantum coherence dynamics in photosynthesis, brain and vision discussed.•The EH method recommended for interpreting quantum coherence effects in biology.
We reviewed the tools of quantum physics used in modeling of quantum coherence (QC) effects in different systems, including biological systems, which behave as quantum objects in some of their degrees of freedom. In particular, we considered the usage of the effective Hamiltonian (EH), Green’s function (GF) and density matrix (DM) methods in the analysis of QC, focusing on QC in biological systems. We discussed the two main mechanisms of loss of quantum state coherence: (i) dephasing of the originally prepared coherent wave package and (ii) population relaxation in the same wave package. Dephasing does not affect the quantum state population, e.g. as in spin-spin relaxation, where dephasing is described by the τ2 relaxation time. On the other hand, the state population relaxation of the spin wavepackage is attributed to spin-lattice relaxation and is described by the τ1 relaxation time. Presently we discussed EH and GF formalisms in terms of the complex energy, dependent on intra- and intersystem interactions that induce state population relaxation. We provided a detailed analysis of these approaches for the exciton relaxation dynamics in a glycine polypeptide chain. The same phenomena were described in the DM formalism using the relaxation matrix. We discussed QC in different biological systems, showing that QC is conserved when the interactions of the coherent wavepackage with other degrees of freedom are weak, as otherwise population relaxation causes loss of QC. We believe that our results will be useful for the researchers in the area of quantum biology.
In the current study, we tested a possible mechanism of low- and high-contrast image component discrimination by the vertebrate eye-brain system. Apparently the eye-brain system has to discriminate ...between the low-contrast image component formed by light scattered within the retina, due to interaction of photons with cells and their parts, and the high-contrast image component transmitted by excitons via the quantum mechanism. Presently, effects of pulsed electric fields applied to Müller cell (MC) intermediate filaments (IFs) on the efficiency of exciton propagation were explored. The effects of both pulse duration and amplitude were recorded. These experimental results show that the eye-brain system may be using signal modulation to discriminate between high- and low-contrast image components, improving our understanding of high-contrast vision in vertebrates.
Exciton propagation along MC IFs filling capillary matrix. Only one IF is shown of the total 2.5 × 105. MC IFs are 10 nm in diameter, and capillaries 15 nm in diameter. Excitons generated on the left extremities of the IFs decayed on their right extremities, emitting photons. Electric field was created in the 30 μm gap between gold electrodes within the capillary matrix. Display omitted
•Exciton propagation along MC IFs explored under external electric fields.•Both field amplitude and pulse duration effects were explored.•Mechanism of high- and low contrast image component separation by the eye-brain system was discussed.
Recently we have reported properties of ZnO semiconductor films attached to CaF2 substrate. Presently we characterized absorption, emission and superluminescence of freestanding ZnO films, comparing ...these to the attached films with the same thickness values. The absorption spectra of the freestanding films had resolved bands, with the band density increasing with the nanofilm thickness. Additionally, the spectral transitions in these films were blue-shifted as compared to attached films. The absorption and emission spectra of freestanding films were resolved better than those of attached films, with the difference traceable to the surface roughness of the substrate used for deposition. We also explored exciton dynamics and propagation over macroscopic distances in freestanding films. The excitons lived longer and propagated further in freestanding films as compared to attached films. The superluminescence yield in freestanding 9.3 nm film of 0.43 ± 0.05 was significantly larger than 0.17 ± 0.03 in an equivalent attached film. We provided a detailed analysis of the results obtained. The reported data are unique, demonstrating significant difference in the optical properties of attached and freestanding ZnO thin films. Freestanding ZnO films are promising for optoelectronic applications.
(a) Absorption spectra and (d) emission spectra of ZnO freestanding thin films: (1) 4.1 nm thick (emission excited at 223 nm); (2) 9.3 nm thick (emission excited at 219–225 nm); (3) 13.1 nm thick (emission excited at 235 nm); and (4) 17.3 nm thick (emission excited at 230 nm). Both absorption and emission spectra have discrete structures. The emission spectra of the thicker films lose some of the spectral resolution. Display omitted
•Optical properties of freestanding (FS) ZnO nanofilms studied at different thicknesses.•Macroscopic exciton propagation explored in FS ZnO films.•Superemission studied for both substrate-attached and FS ZnO nanofilms.
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