Computational Modeling Analysis of Generation of Reactive Oxygen Species by Mitochondrial Assembled and Disintegrated Complex II.

Reactive oxygen species (ROS) function as critical mediators in a broad range of cellular signaling processes. The mitochondrial electron transport chain is one of the major contributors to ROS formation in most cells. Increasing evidence indicates that the respiratory Complex II (CII) can be the predominant ROS generator under certain conditions. A computational, mechanistic model of electron transfer and ROS formation in CII was developed in the present study to facilitate quantitative analysis of mitochondrial ROS production. The model was calibrated by fitting the computer simulated results to experimental data obtained on submitochondrial particles (SMP) prepared from bovine and rat heart mitochondria upon inhibition of the ubiquinone (Q)-binding site by atpenin A5 (AA5) and Complex III by myxothiazol, respectively. The model predicts that only reduced flavin adenine dinucleotide (FADH2) in the unoccupied dicarboxylate state and flavin semiquinone radical (FADH•) feature the experimentally observed bell-shaped dependence of the rate of ROS production on the succinate concentration upon inhibition of respiratory Complex III (CIII) or Q-binding site of CII, i.e., suppression of succinate-Q reductase (SQR) activity. The other redox centers of CII such as Fe-S clusters and Q-binding site have a hyperbolic dependence of ROS formation on the succinate concentration with very small maximal rate under any condition and cannot be considered as substantial ROS generators in CII. Computer simulation results show that CII disintegration (which results in dissociation of the hydrophilic SDHA/SDHB subunits from the inner membrane to the mitochondrial matrix) causes crucial changes in the kinetics of ROS production by CII that are qualitatively and quantitatively close to changes in the kinetics of ROS production by assembled CII upon inhibition of CIII or Q-binding site of CII. Thus, the main conclusions from the present computational modeling study are the following: (i) the impairment of the SQR activity of CII resulting from inhibition of CIII or Q-binding site of CII and (ii) CII disintegration causes a transition in the succinate-dependence of ROS production from a small-amplitude sigmoid (hyperbolic) shape, determined by Q-binding site or [3Fe-4S] cluster to a high-amplitude bell-shaped kinetics with a shift to small subsaturated concentrations of succinate, determined by the flavin site. © Copyright © 2020 Markevich, Markevich and Hoek

Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades

Mitogen-activated protein kinase (MAPK) cascades can operate as bistable switches residing in either of two different stable states. MAPK cascades are often embedded in positive feedback loops, which are considered to be a prerequisite for bistable behavior. Here we demonstrate that in the absence of any imposed feedback regulation, bistability and hysteresis can arise solely from a distributive kinetic mechanism of the two-site MAPK phosphorylation and dephosphorylation. Importantly, the reported kinetic properties of the kinase (MEK) and phosphatase (MKP3) of extracellular signal–regulated kinase (ERK) fulfill the essential requirements for generating a bistable switch at a single MAPK cascade level. Likewise, a cycle where multisite phosphorylations are performed by different kinases, but dephosphorylation reactions are catalyzed by the same phosphatase, can also exhibit bistability and hysteresis. Hence, bistability induced by multisite covalent modification may be a widespread mechanism of the control of protein activity

Termination Reaction in the Anionic Polymerization of Methacrylonitrile

The anionic polymerization of methacrylonitrile initiated by triethylphosphine in dimethylformamide was studied. Experimental evidence for two mechanisms of termination reaction was obtained. By addition of water or alcohol in polymerizing system the rate of polymerization and molecular weight of polymethacrylon1itrile decrease, which proves the termination reaction to be bimolecular and proceed by interaction of the active carbanion with water or alcohol. The rate constant for termination of free anions with water was determined, k~,0 = 2.2 x 102 dm3 moP s-1• The termination reaction could not be excluded by purification and prolonged drying of all components of the system, which indicates that the second mechanism of termination is operative as well. Conductivity measurements gave evidence for a monomolecular spontaneous reaction leading to deactivation of the anion

Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades

A hallmark of protein kinase/phosphatase cascades, including mitogen-activated protein kinase (MAPK) pathways, is the spatial separation of their components within cells. The top-level kinase, MAP3K, is phosphorylated at the cell membrane, and cytoplasmic kinases at sequential downstream levels (MAP2K and MAPK) spread the signal to distant targets. Given measured protein diffusivity and phosphatase activities, signal propagation by diffusion would result in a steep decline of MAP2K activity and low bisphosphorylated MAPK (ppMAPK) levels near the nucleus, especially in large cells, such as oocytes. Here, we show that bistability in a two-site MAPK (de)phosphorylation cycle generates a novel type of phosphoprotein wave that propagates from the surface deep into the cell interior. Positive feedback from ppMAPK to cytoplasmic MAP2K enhances the propagation span of the ppMAPK wave, making it possible to convey phosphorylation signals over exceedingly long distances. The finding of phosphorylation waves traveling with constant amplitude and high velocity may solve a long-standing enigma of survival signaling in developing neurons

Multiphoton Transitions in a Spin System Driven by Strong Bichromatic Field

EPR transient nutation spectroscopy is used to measure the effective field (Rabi frequency) for multiphoton transitions in a two-level spin system bichromatically driven by a transverse microwave (MW) field and a longitudinal radio-frequency (RF) field. The behavior of the effective field amplitude is examined in the case of a relatively strong MW field, when the derivation of the effective Hamiltonian cannot be reduced to first-order perturbation theory in w_{1} / w_{rf} (w_{1} is the microwave Rabi frequency, w_{rf} is the RF frequency). Experimental results are consistently interpreted by taking into account the contributions of second and third order in w_{1} / w_{rf} evaluated by Krylov-Bogolyubov-Mitropolsky averaging. In the case of inhomogeneously broadened EPR line, the third-order correction modifies the nutation frequency, while the second-order correction gives rise to a change in the nutation amplitude due to a Bloch-Siegert shift.Comment: 7 pages, 6 figure

The Dynamics of Zeroth-Order Ultrasensitivity: A Critical Phenomenon in Cell Biology

It is well known since the pioneering work of Goldbeter and Koshland [Proc. Natl. Acad. Sci. USA, vol. 78, pp. 6840-6844 (1981)] that cellular phosphorylation- dephosphorylation cycle (PdPC), catalyzed by kinase and phosphatase under saturated condition with zeroth order enzyme kinetics, exhibits ultrasensitivity, sharp transition. We analyse the dynamics aspects of the zeroth order PdPC kinetics and show a critical slowdown akin to the phase transition in condensed matter physics. We demonstrate that an extremely simple, though somewhat mathematically "singular" model is a faithful representation of the ultrasentivity phenomenon. The simplified mathematical model will be valuable, as a component, in developing complex cellular signaling network theory as well as having a pedagogic value.Comment: 8 pages, 3 figure

Infrared activity of hydrogen molecules trapped in Si

The rovibrational-translational states of a hydrogen molecule moving in a cage site in Si, when subjected to an electrical field arising from its surroundings, are investigated. The wave functions are expressed in terms of basis functions consisting of the eigenfunctions of the molecule confined to move in the cavity and rovibrational states of the free molecule. The energy levels, intensities of infrared and Raman transitions, effects of uniaxial stress, and a neighboring oxygen defect are found and compared with existing experimental data

Electron-enhanced reactions responsible for photoluminescence spectrum change in II-VI compounds

Electron-enhanced reactions in II-VI compounds are shown to be caused by the presence of some mobile defects which diffusion is not enhanced under excitation. At the same time, electron-enhanced diffusion can be imitated in these reactions due to carrier trapping by deep centers that do or even do not take part in the reaction. To elucidate the real defect reaction mechanism a detailed study is required in every case. For this purpose, a method of mobile defect detection and their diffusion characteristic direct investigation has been elaborated

Effective Field and the Bloch-Siegert Shift at Bihromatic Excitation of Multiphoton EPR

The dynamics of multiphoton transitions in a two-level spin system excited by transverse microwave and longitudinal RF fields with the frequencies w_{mw} and w_{rf}, respectively, is analyzed. The effective time-independent Hamiltonian describing the "dressed" spin states of the "spin + bichromatic field" system is obtained by using the Krylov-Bogoliubov-Mitropolsky averaging method. The direct detection of the time behavior of the spin system by the method of nonstationary nutations makes it possible to identify the multiphoton transitions for resonances w_{0} = w_{mw} + rw_{rf} (w_{0} is the central frequency of the EPR line, r = 1, 2), to measure the amplitudes of the effective fields of these transitions, and to determine the features generated by the inhomogeneous broadening of the EPR line. It is shown that the Bloch-Siegert shifts for multiphoton resonances at the inhomogeneous broadening of spectral lines reduce only the nutation amplitude but do not change their frequencies.Comment: 6 pages, 5 figure

ВЛИЯНИЕ ИМПУЛЬСНОГО ФОТОННОГО ОТЖИГА НА СТРУКТУРУ И ФАЗОВЫЙ СОСТАВ ТОНКОПЛЕНОЧНЫХ СИСТЕМ НА ОСНОВЕ КРЕМНИЯ И ПЕРЕХОДНЫХ МЕТАЛЛОВ

The present paper investigates element composition,  regularities of structural and phase transformations in Si–Fe–Si and TiN–Ti–Si thin film systems in the process of impulse photon annealing depending on radiation energy density while applying such methods as transmission  electron microscopy, electron  diffraction analysis and energy dispersive x-ray microanalysis. Optimum characteristics of impulse photon annealing for formation FeSi2 thin films of β-modification on silicon and TiSi2 films in C54 modification have been determined in the paper.Методами просвечивающей электронной микроскопии, электронографии и энергодисперсионного рентгеновского микроанализа проведены исследования элементного состава, закономерностей структурных и фазовых превращений, происходящих в тонкопленочных системах Si–Fe–Si и TiN–Ti–Si при импульсном фотонном отжиге в зависимости от плотности энергии облучения. Определены оптимальные параметры импульсного фотонного отжига для формирования на кремнии тонких пленок FeSi2 β-модификации и TiSi2 в модификации C54