Structure and properties of liquid water are investigated by means of molecular dynamics at temperature of 298 K. As a model of water molecule the SP3-model - flexible three-dot model with force centers on atoms is used. From the analysis of "life maps" of hydrogen bonds it is established, that lifetimes change from subpicoseconds up to tens picoseconds. The break of hydrogen bonds is not necessarily accompanied by change of the molecule-partner, and can be caused by switching. Statistical characteristics of hydrogen bonds and value of self-diffusion coefficient of water are obtained. The results agree with experimental data and the conclusions drawn in the works employing alternative models of the water molecule.
This work is devoted to the study of the energy characteristics of the F1ATPase-substrate complex. The results of calculations of the electrostatic energy in the enzyme-substrate complex are presented in the first part. In calculations, we take into account the electrostatic interactions between the charged groups of the substrate (MgATP) and reaction products (MgADP and Pi) and charged amino acid residues of the α3β3γ complex that correspond to various conformations of the enzyme. The hydrolysis of ATP in the catalytic site leads to coordinated conformational changes in α, β subunits and to ordered rotation of γ subunit located in the center of F1ATPase complex. The calculations show that the energetically favorable process involving MgATP binding at the catalytic site in the "open" conformation initiates γ subunit rotation followed by the hydrolysis in the other (tight) catalytic site. In the second part, we propose the simplest stochastic model describing the ordered rotation of γ subunit (the rotor of F1-ATPase molecular motor). In the model we take into account the electrostatic interaction using the results of the previous calculations. We employ experimentally obtained dynamic parameters. The model takes into account the thermal fluctuations of the bath and the random processes of the substrate binding and the escape of the reaction products.
F1-ATPase is one of the most important enzymes of membrane bioenergetics. F1-ATPase is the constituent complex that provides the ATP formation from ADP and inorganic phosphate (Pi) at the expense of energy of electrochemical gradient of hydrogen ions generated across the energy transducing mitochondrial, chloroplast or bacterial membrane. F1-ATPase is a reversible molecular machine that can work as a proton pump due to energy released in the course of ATP hydrolysis (ATPase reaction). The unusual feature of this enzyme is that it operates as a rotary molecular motor. Recently, using the fluorescence microscopy method for the real time visualization of molecular mobility of individual molecules, it was demonstrated directly that the ATP hydrolysis by F1-ATPase is accompanied by unidirectional rotations of mobile subunits (rotor) of F1F0-ATP synthase. In this work, we calculated the contribution of electrostatic interactions between charged groups of a substrate (MgATP), products molecules (MgADP and Pi), and charged amino acid residuals of ATPase molecule to the energy changes associated with the substrate binding and their chemical transformations in the catalytic centers located at the interface of α and β subunits of the enzyme (oligomer complex α3β3γ of bovine mitochondria ATPase). A catalytic cycle of ATP hydrolysis considered in our work includes conformational changes of α and β subunits caused by unidirectional rotations of an eccentric γ subunit. The knowledge of energy characteristics and force field in catalytic center of an enzyme in different conformational states may be important for further simulation dynamic properties of ATP synthase complex.
One of important stages of the substrate bond breaking in the active site (AS) of α-chymotrypsin (ACT) is considered. Three tasks are solved by methods of quantum mechanics and stochastic molecular dynamics: the loosening of peptide bond of a substrate attacked by O- ion of Ser195 of catalytic group; the opportunity of increase of a peptide bond (PB) breaking probability; the increase of this probability related to nonlinear interacting modes (or Fermi resonance (FR)) of oscillations of group N-H in PB. It is shown also that the splitting of vibrational levels Amide A and Amide B in a spectrum of an amide group pays off due to FR.
The problems studied here are relevant for an understanding of the functioning of hydrolytic enzyme molecules. These enzymes work like molecular machines breaking off the valence peptid bonds of substrates. In particular the role of Fermi resonance which is evident from a spectral lines of valence oscillations is studied. The influence of this resonance on valence splitting is discussed. It is shown that the breaking of these bonds has a higher probability, if the stochastic oscillations of atoms in catalytic groups at the active site have a large quality coefficient. We show that the corresponding low damping is essential for the Fermi resonance modes of these oscillations.
KEYWORDS: Signal processing, Light wave propagation, Ions, Mathematical modeling, Extremely high frequency, Electrodes, Radio propagation, Systems modeling, Wave propagation, Physics
Propagation of bioelectric potentials generated in green plants by light and millimeter wavelength range irradiation was experimentally investigated. The standard technique of multi-electrode superficial potentials measuring was used. The carried out experiments continue the previous investigations of light and millimeter waves influence on green plants. Theoretical part includes the development of numerical models of bioelectric potentials propagation and measurement.
Raman spectra of crystalline subglobular proteins exhibit peaks in the low-frequency spectral range. These peaks can be related to resonance oscillations of subglobules and possibly play an important role in the catalytic act. The low-frequency spectral features were not observed in aqueous solutions. According to the hydrodynamics, the corresponding oscillations must be overdamped. The results obtained by the methods of molecular dynamics how that the Q-factor of subglobular oscillations can be larger than 10, which stimulated further experimental studies of solutions of proteins.
The efficiency of the molecular machines can be determined by the Q-factor of oscillations in the selected degrees of freedom. In particular, the quasi-harmonic oscillations of chymotrypsin decrease the threshold for the diffusion limitation of its functioning as molecular scissors. It was demonstrated by the methods of molecular dynamics that the Q-factor of the subglobular oscillations of proteins in water at the frequencies (omega) about 1012 Hz can reach 10, although the Raman bands in the corresponding spectral range were found only in crystal samples. Q quadratically increases with (omega) . The earlier hypothesis regarding the catalytic importance of the Fermi resonance for the oscillations of ligands and atomic groups in the enzyme- substrate complexes was not proved in experiments with simple models. The Fermi resonance can be observed if the Q- factor of the selected degree of freedom exceeds 100.
Bioelectric plant reactions induced by local low-intensity electromagnetic millimeter wavelength excitation were studied; the results are presented in this article. Plant reaction was obtained in this range where the absorption is determined by collective resonant properties of water. As a result, the previous investigations were continued and we can present the action spectrum in the range 300 nm-6mm.
We studied the enzyme acetylcholinesterase (AChE) that catalyses the hydrolysis of acetylcholine (ACh) -- cell neuromediator. After transfer of excitation ACh must be removed from the synaptic cleft in hundreds of microseconds. This is accomplished by removing of acetate (A) and choline (Ch) that are the products of 'cutting' of ACh by AChE. High activity of the enzyme is related with the large dipole moment of AChE that attracts positively charged molecules of ACh into active site (AS) and also with the fast removing of the reaction products from AS. One of the hypothesis accounting for the fast removing of A and Ch from the AS pocket presumes the existence of a 'back door' that allows them to leave the pocket without interference with the molecules of ACh that penetrate inside the AS. We made an attempt of verification of the 'back door' hypothesis by means of computational experiment for 2D and 3D spaces. We considered the problem of penetration of ACh and exit of the negatively charged A and positively charged Ch under the conditions of fluctuating potential relief of the AChE AS. For the laser spectroscopy we pose two problems: (a) determination of the dipole moment of AChE in the case this molecule is surrounded by ACh molecules by means of the electro-optical method and (b) detection of AS conformations related with functioning of the 'back door' (the ring-system of Trp84). We report on Raman spectroscopy study of the influence of crown-esters on amino groups.
In our previous works we presented our results of experimental investigations of plant bioelectrical reactions to low- intensity local irradiation at certain ranges of wavelengths. It was demonstrated that the qualitative and quantitative estimation of the reaction of plants can be performed with the help of bioelectric potential (BEP) gradients generated by plants. We consider BEP as the difference of electric potentials at the surface of a plant resulting from the difference of the functional activity of cells in tissue and organs. In particular we presented typical plant responses to light stimuli, the action spectrum (AS) of light on the conductive system of a plant in the wavelength range 330 - 1300 nm as well as a transmission spectrum of intact green leaf in the same spectral range. The aim of this paper is the investigation of plant responses to light stimuli in wide spectral range (330 - 3390 nm) including far IR, to obtain new data (transitional characteristics on different wavelengths) and to specify our previous ones (AS, transmission spectrum).
The choice of the qualitative method of estimation of the reaction of a living system to the light irradiation is the main problem in the measurements of spectra of action. It was demonstrated earlier that the bioelectric reaction (BER) on a low-level local laser irradiation can be used for these measurements. We determined the dependence of the BER of a plant on the wavelength (lambda) of the coherent and incoherent irradiation. In the visible spectral range the dependence of BER on (lambda) coincides with chlorophyll absorption spectrum and the peak at 1015 - 1300 nm is related probably with water absorption. The dependence of BER on I is of the threshold type. The wavelength dependence of the transmittance of an intact green leaf nearly coincides with its photoacoustic spectrum. Thus, the proposed nondisturbing methods make it possible to determine the optical parameters of a living plant.
The intracellular motility of the huge amoeboid cell, Physarum plasmodium, is defined by autowave processes, which are caused by interaction of actomyosin-based contractile apparatus in ectoplasm and intracellular endoplasmic flows. With the use of cell tensiometry and laser Doppler spectroscopy technique the autowave regimes in plasmodial strands (which look like blood-vessels) was investigated under the conditions when endogenous contractile rhythm in a part of the strand was eliminated by respiratory inhibitors. Mathematical model for ectoplasm contraction waves and shuttle endoplasm streaming in the strand is presented. Solutions of the model expanded to simulate the case of non- uniform parameter distribution satisfactorily agree with the experimentally observed effects of the respiratory inhibitors.
The issues about the behavior of variant test particles (TP) in 2D potential field with complex relief are studied. The cases with time-dependent parameters of potential field are considered. In particular the mathematical models that are discussed in this paper can describe either the process of penetration of TP (ligand) in active site of the enzyme or proton's transition from one potential pit to another.
A review of the optical methods designed for the study of intracellular protoplasmic streaming is presented. While in case of low streaming velocities (less than 10 mcm/s) the computer analysis of the images of moving protoplasm is effective, for higher velocities the laser Doppler microscopy has an advantage. With the help of the Doppler technique it is possible to determine the velocity profiles for nonstationary protoplasmic streamings in amoeboid cells. These data and also complex time changes of protoplasmic flow in response to external factors enable to determine and to specify parameters used for designing mathematical models of intracellular dynamics. As an example, results of experiments, modelling and simulations are presented for myxomycete plasmodium Physarum polycephalum which is a huge cell with typical amoeboid properties.
KEYWORDS: Molecules, Energy transfer, Motion models, Chemical species, Life sciences, Laser applications, Complex systems, Modeling, Hydrogen, Molecular energy transfer
Influence of intramolecular dynamic structure on the process of energy transfer from the place of original localization to the active site and processes in the active site of enzyme is under consideration. The possibility of realization of `marked' degrees of freedom when the system motion occurs in a narrow area of phase space was considered within the framework of a simplest cluster model of an enzyme molecule. Under certain conditions the motion of the system becomes complex and perhaps stochastic and the spectrum of oscillations becomes more rich. the role of the interaction potential curve shapes of the system is discussed. Problems of spectral transformation and complexization and characteristic times determination are important for interpretation of the data obtained by the methods of laser spectroscopy and CARS, in particular. We discuss the problem of overcoming the potential energy barrier inside the active site in terms of the location and energy of definite parts of the substrate within the framework of a 2D model. The special role of fluctuations of atom groups and the substrate influence on the process are taken into account.
A mathematical model of contact laser destruction of normal and tumor liver tissues by radiation of YAG:Nd laser is described. We present the results of the simulation of tissue heat destruction, taking into account the influence of blood and lymph circulation on the processes of heat transfer. The problem is adapted to the case of liver tissue with tumor. A liver is considered as a capillary-porous body with internal blood circulation. Heatconductivity and tissue-blood heat transfer are considered. Heat action is assumed to be implemented with contact laser scalpel. The mathematical model consists of two inhomogeneous nonlinear equations of heatconductivity with spherical symmetry. Nonstationary temperature fields of tissue and blood are determined. The power of laser radiation (LR) was taken into account in boundary conditions set for the center of coagulated tissue volume. We also took into account the processes connected with changing of substance phase (vaporization). The original computer programs allow one to solve the problem varying in a wide range of the main parameters. Reasonable agreement was found between the calculation results and the experimental data for operations on macrosamples and on test animals.
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