Том 61, № 2 (2016)

The effect of isothermal and adiabatic evaporation on the state of a water–protein droplet is discussed. The considered problem relates to the design of various approaches for structural and dynamic experiments with single molecules involving X-ray lasers. The delivery of the sample into the X-ray beam is performed by a microdroplet injector in these experiments; and the approach time is in the microsecond range. A version of molecular-dynamics simulation for all-atom modeling of an irreversible isothermal evaporation process is developed. The parameters of the isothermal evaporation of a water–protein droplet that contains sodium and chloride ions at concentrations of approximately 0.3 M have been determined in computational experiments for different temperatures. The in silico experiments showed that the energy of irreversible evaporation at the initial stages of the process was virtually the same as the specific heat of evaporation for water. An exact analytical solution of the problem for the kinetics of irreversible adiabatic evaporation has been obtained in the limit of the high heat conductivity of the droplet (or a droplet size not exceeding ~100 Å). This solution contains parameters that were derived from simulation of the isothermal evaporation of the droplets. The kinetics of the evaporation and adiabatic cooling of the droplet were shown to be scalable according to the size of the droplet. Estimation of the rate of freezing of the water–protein droplet upon adiabatic evaporation in a vacuum chamber revealed the necessity of using additional procedures for stabilizing the temperature in the droplet nucleus that contains the protein molecule. Isothermal or quasi-isothermal conditions are more favorable for the investigation of macro-molecular structural rearrangements that are related to the functioning of the object. However, the effects of dehydration and a sharp increase in the ionic strength of the aqueous microenvironment of the protein must be taken into account in this case.

Tryptophan fluorescence lifetimes were analyzed for three proteins: human serum albumin, bovine serum albumin, and bacterial luciferase, which contain one, two, and seven tryptophan residues, respectively. For all of the proteins, the fluorescence decays were fitted by three lifetimes: τ₁ = 6–7 ns, τ₂ = 2.0–2.3 ns, and τ₃ ≤ 0.1 ns (the native state), and τ₁ = 4.4–4.6 ns, τ₂ = 1.7–1.8 ns, and τ₃ ≤ 0.1 ns (the denatured state). Corresponding decay-associated spectra had similar peak wavelengths and spectrum half-widths both in the native state (\(\lambda _{\max }^{{\tau _1}} = 324nm\), \(\lambda _{\max }^{{\tau _2}} = 328nm\), and \(\lambda _{\max }^{{\tau _3}} = 315nm\)), and in the denatured state (\(\lambda _{\max }^{{\tau _1}} = 350nm\), \(\lambda _{\max }^{{\tau _2}} = 343nm\), and \(\lambda _{\max }^{{\tau _3}} = 317nm\)). The differences in the steady-state spectra of the studied proteins were accounted for the individual ratio of the lifetime component contributions. The lifetime components were compared with a classification of tryptophan residues in the structure of these proteins within the discrete states model.

The changes in the structure and catalytic properties of fungal lipases (Candida rugosa, Rhizomucor miehei, Mucor javanicus) were investigated in micellar solutions of bile salts that differ in their hydrophilic–lypophilic balance and reaction medium properties. The methods of circular dichroism and tryptophan fluorescence were applied to estimate the changes in peptide structure within complexes with bile-salt micelles. Bile salts do not exert a significant influence on the structure of the enzymes under study: in the Rh. miehei and M. javanicus lipases the α-helix content was slightly decreased; an influence of the bile salts on the C. rugosa structure was not revealed. Despite negligible structural modifications in the enzymes, a considerable change in their catalytic properties, namely an abrupt decrease in catalytic effectiveness was observed in bile-salt solutions. Substrate–bile salt micelle complex formation was demonstrated by the NMR self-diffusion method. A model of the regulation of fungal lipase activity was proposed.

It is generally accepted that important features of the Watson–Crick duplex (WCD) originate from the molecular structure of its subunits. However, it is still unclear what properties of each subunit are responsible for significant features of the WCD structure. Computations of deoxydinucleoside monophosphate (dDMP) complexes with Na ions on the basis of the density functional theory (DFT) have shown that conformational properties of minimal single-stranded fragments of DNA play a pivotal role in the origin of the unique features of the WCD. The directionality of the sugar-phosphate backbone (SPB) and preferable ranges of its torsion angles combined with the difference in geometry between purines and pyrimidines have been found to define the nucleotide sequence dependence of the WCD three-dimensional structure. In this work, density functional theory computations were extended to minimal duplex fragments, that is, complementary dDMP (cdDMP) complexes with Na ions. Using several computational methods and various functionals, energy minima were searched for the BI conformation of cdDMP complexes with different nucleotide sequences. Two sequences were optimized using an ab initio method at the MP2/6-31++G** level of theory. An analysis of the SPB torsion angles, sugar-ring puckering, and mutual base positions in the optimized structures showed that the conformational features of cdDMP complexes with Na ions remained within the BI ranges and become more similar to the corresponding features that WCDs display in a crystal. Qualitatively, the main features of each cdDMP complex were invariant with different computational methods, although the values of certain conformational parameters could vary, but still within the limits that are typical of the corresponding family. Common functionals that are employed in DFT calculations were observed to overestimate the distance between base pairs, while MP2 computations and new complex functionals yielded structures with atom–atom contacts that are too close. Several energy minima that correspond to the BI conformation have been proven to exist for certain cdDMP complexes with Na ions, indicating that the topography of the potential energy surface is complex. This circumstance accounts for the variation of conformational parameters among duplex fragments with the same nucleotide sequence. The common AMBER and CHARMM molecular mechanics force fields reproduce many conformational characteristics of dDMPs and their complementary complexes with Na ions, but fail to reproduce certain details of the nucleotide sequence dependence of the WCD conformation.

Aminoacyl-tRNA synthetases are an ancient enzyme family that specifically charge a tRNA molecule with a cognate amino acid that is required for protein synthesis. Glycyl-tRNA synthetase is one of the most interesting aminoacyl-tRNA synthetases due to its structural variability and functional features in different organisms. Recently, it has been shown that human glycyl-tRNA synthetase is a regulator of translational initiation of poliovirus mRNA. The details and mechanisms of this process are still unknown. While exploring the stage of poliovirus functioning, we studied the interactions of the cytoplasmic form of human glycyl-tRNA synthetase and its domains with fragments of the poliovirus IRES element. As a result, we identified the minimal fragment of the viral mRNA that glycyl-tRNA synthetase adequately interacts with and we estimated the contribution of some of the domains to the interaction between glycyl-tRNA synthetase and RNA.

The conformational behavior of biologically important chiral molecules of cholesterol and ergosterol was studied via the method of molecular dynamics. The formation of strings and their absence was experimentally observed in methanol solutions of cholesterol and ergosterol, respectively. It was shown that the intermolecular dynamics of the molecule significantly affects the possibility of structure formation. We proposed an alternative explanation of the functional significance of cholesterol, which is apparently associated with the formation of commutation structures outside the membrane, and the biological feasibility of the presence of ergosterol in the non-commuting cells of fungi and cholesterol in the commuting cells of macroorganisms.

A nonlinear dependence of E. coli cell inhibition was found during the simultaneous irradiation by the blue and red spectral regions at a power density of 100 mW/cm². This dependence can be explained by the cascade two-photon light absorption by DNA molecules with intermediate resonance at the cellular chromophores, which leads to excitation and subsequent DNA damage similar to the damage that is caused by exposure to UV quanta.

Hypoxia (5% O₂) and the basic fibroblast growth factor (bFGF) were shown to reduce the doubling time of bone marrow mesenchymal stem cells (MSCs) in vitro, indicating an increase in cell proliferation. In addition, abcg2 expression at both the mRNA and protein levels increased in MSCs that were exposed to hypoxia and bFGF. The two factors acting together potentiated the effects of hypoxia in MSCs. Blocking the functional activity of ABCG2 led to a higher production of reactive oxygen species (ROS) in MSCs. Hypoxia and bFGF were tested for effects on the MSC protein profile. These findings, combined with the published data, implicate ABCG2 expression and function in maintaining the viability and proliferative activity of MSCs that are cultured in hypoxia, with ABCG2 playing a protective role.

Oxidative stress acts as a pathogenetic factor in many diseases; estimating its level is important for early diagnosis and therapy adjustment. The antioxidant status was evaluated for the blood plasma. A set of chemiluminescence (CL) kinetic-curve parameters (latent period τ_lat and analytical signal increment ΔI_CL) in a 2,2’-azo-bis(2-amidinopropane)dihydrochloride–luminol system were proposed for estimating the oxidative stress level. Uric acid and albumin were identified as major components that are responsible for the changes in the plasma CL kinetic curve. UV light caused oxidative modification of serum albumin in a dose-dependent manner, thus enhancing its antioxidant properties. Changes in plasma CL kinetics were proposed as a means to measure oxidative stress in the human body.

The two mechanisms of cardiac arrhythmia that are currently known involve transition of some of the cells into a self-oscillating mode and the emergence of circulating waves. A mechanism for the emergence of circulating waves due to a unidirectional blockage is considered in the present study. A narrow gap between two non-conductive areas may provide the conditions for such a mechanism. However, this mechanism cannot occur in the human heart, since the minimal path length for circulation at the action potential duration of 0.3 s and the wave propagation velocity of 33 cm/s is approximately 10 cm, whereas the average distance from the top of the ventricles to the atrioventricular septum is 8 cm. Therefore, the inhomogeneity that is described above cannot exist on the scale of the human heart. Low-conductivity areas that lead to slow propagation of a wave have been introduced in order to adapt this mechanism to the size of the heart. The conductivity values were calculated using the dependence between the conductivity and the velocity of the wave front that is determined using computational methods. Analysis of wave propagation through the boundary between two areas with different conductivities revealed the dependence of the refractory period on the ratio of the conductivities. A transition zone in which the conductivity value changes linearly from the normal value to a lower value has been introduced to attenuate this dependence. As a result, an inhomogeneity that is 12 mm in size that triggers the formation of a circulating wave was modeled.

In this review, three essentially important processes in the development of cognitive behavior are considered, viz., knowledge of a spatial environment by means of physical activity, coding, and the calling of the existential context of episodic memory and imitation learning based on the mirror neural mechanism. The data show that the parietal and frontal systems, which are involved in learning by imitation, allow a developing animal to obtain skills of management and motive synergies in perisomatic space, as well as to understand the intentions and the purposes of the observed actions of other individuals. At the same time the widely distributed parietal and frontal and entorhinal–hippocampal system mediates spatial knowledge and the solution of the navigation tasks that are important for the creation of the existential context of episodic memory.

A model scenario of a drastic increase in the number of a phytophagous species (jumping plant lice) at the expense of primary and secondary Encyrtidae parasites (a large family of parasitic microwasps) has been developed based on the case study of changes in the local density of a Psyllidae species in Australia. A phenomenological model differentially describes the reproduction efficiency in several ranges of the population state. A continuous-event structure is proposed where the rate of decrease in the abundance of generations is uneven at different developmental stages of the insect with an incomplete metamorphosis and the points where it changes are determined by the state of internal variables in the auxiliary equation for the continuous system. A spontaneous time-limited local outbreak occurs after overcoming the threshold equilibrium in the iterative dynamic system, which reduces the effect of normal regulatory mechanisms of psyllid reproduction and changes the rate of the decrease in the abundance of generations. The method of supplementing the right-hand part of the first equation by special functional with a limited range of values simulates a drastic decrease in survival with depletion of resources. This modification causes a backward tangent bifurcation. Several generations after the bifurcation, the population switches to the mode of fluctuations without any pronounced cyclic component, which is common for small insects with a low abundance.

It is known that in quantum mechanics the observation of an experiment may in some cases change the results of this experiment. In particular, this occurs for the so-called Zeno effect. It is shown that, unlike the standard Zeno effect for which observation reduces its probability, for a particle that penetrates a potential barrier the opposite situation (called the barrier anti-Zeno effect) can occur, i.e., observation can considerably increase the probability of barrier penetration. The possibility of utilizing the barrier anti-Zeno effect for explaining the paradoxical results of experiments on “cold nuclear fusion” that have been observed in various, including biological, systems is discussed. (According to the experimentalists who performed such studies, in these systems energy release that cannot be explained by any chemical processes, as well as changes of the isotope and even elemental composition of the studied substance, occur).