Possible mechanism for the influence of weak magnetic fields on biological systems

A physical mechanism is suggested for a resonant interaction of weak magnetic fields with biological systems. An ion inside a Ca(2+)-binding protein is approximated by a charged oscillator. A shift in the probability of ion transition between different vibrational energy levels occurs when a combination of static and alternating magnetic fields is applied. This in turn affects the interaction of the ion with the surrounding ligands. The effect reaches its maximum when the frequency of the alternating field is equal to the cyclotron frequency of this ion or to some of its harmonics or sub-harmonics. A resonant response of the biosystem to the magnetic field results. The proposed theory permits a quantitative explanation for the main characteristics of experimentally observed effects.     

Isotope effects on electron tunneling reactions in biological systems conformational mobility of proteins

Effects of D2O substitution on electron transport reactions in proteins were analysed on the basis of generally adopted ideas of electronic vibration interactions and conformational mobility of macromolecules. At the molecular level, a mechanism for cytochrome c oxidation was established. On the basis of general viscosity and elasticity properties of proteins, the effects of temperature and chemical composition of the medium on conformational relaxation were analysed. For chromatophores of photosynthetising bacteria, a mechanism is discussed by which abnormal effects of temperature and abnormal isotope effects may be exercised on charge recombination.     

Cell cycle-dependent mobility of Cdc45 determined in vivo by fluorescence correlation spectroscopy

Eukaryotic DNA replication is a dynamic process requiring the co-operation of specific replication proteins. We measured the mobility of eGFP-Cdc45 by Fluorescence Correlation Spectroscopy (FCS) in vivo in asynchronous cells and in cells synchronized at the G1/S transition and during S phase. Our data show that eGFP-Cdc45 mobility is faster in G1/S transition compared to S phase suggesting that Cdc45 is part of larger protein complex formed in S phase. Furthermore, the size of complexes containing Cdc45 was estimated in asynchronous, G1/S and S phase-synchronized cells using gel filtration chromatography; these findings complemented the in vivo FCS data. Analysis of the mobility of eGFP-Cdc45 and the size of complexes containing Cdc45 and eGFP-Cdc45 after UVC-mediated DNA damage revealed no significant changes in diffusion rates and complex sizes using FCS and gel filtration chromatography analyses. This suggests that after UV-damage, Cdc45 is still present in a large multi-protein complex and that its mobility within living cells is consistently similar following UVC-mediated DNA damage.     

Aggregation characteristics of ovalbumin in beta-sheet conformation determined by spectroscopy

Protein misfolding and aggregation are involved in a number of the so-called "conformational" diseases (e.g., transmissible spongiform encephalopathies and Alzheimer disease). The development of rational strategies to interfere with aggregation is a potential therapeutic approach that requires complete knowledge of the aggregation process. We studied the aggregation of ovalbumin in beta-sheet conformation using mainly the spectral changes in the spectra of two dyes (Congo Red and pinacyanol) caused by the aggregates. We assumed a linear model of polymerization that fit to the experimental data. The critical aggregation constant, concentration of half-aggregation, nucleation parameter, growth parameter, and number of aggregation and free energy changes (total and per residue) were determined as aggregation-related parameters. Beta-Ovalbumin aggregates in a cooperative way. Moreover, the differences between such parameters obtained with Congo Red and pinacyanol suggest that each dye interacts with the protein in its own way.     

Solvent effects on the secondary structure of the membrane-active zervamicin determined by PELDOR spectroscopy

Zervamicin is a voltage-gated ion-channel-forming peptide. Channels are generally considered to be formed by first insertion of amphipathic molecules into the phospholipid bilayer, followed by self-assembly of a variable number of transmembrane helices. We have studied the length of the peptide structure to address the question whether this peptide is long enough to span the phospholipid bilayer. The pulsed electron-electron double resonance (PELDOR) spectroscopic technique was used to determine the length of the helical molecule in membrane-mimicking solvents. This was achieved from the distance-related dipole-dipole interaction between spin labels, which were located at both ends of the linear peptide chain. The data were obtained by using samples of frozen glassy solutions of MeOH, MeOH/toluene, and MeOH/CHCl(3). Contributions of inter- and intramolecular interactions of spin labels were separated to analyze the intramolecular interaction and the distance distribution function between the labels. It is shown that the main maximum of the distribution functions is located at a distance of ca. 3.3 nm, and this distance appears to be only slightly dependent on the solvent composition. The distribution function was observed to narrow after addition of either CHCl(3) or toluene to MeOH. This effect is rationalized in terms of a decreased mobility of the terminal amino acid residues. By molecular-dynamics simulations, it was shown that the conformation, corresponding with the predominant distance found by PELDOR, agrees well with the mixed alpha/3(10)-helical that was previously determined by NMR. However, in the case toluene was added to the MeOH solution to further increase the hydrophobicity of the environment of the membrane-active peptide, the distribution function gives rise to a minor fraction (7-8%) with a distance of 4.2 nm. This distance corresponds most likely to the more extended 2(7)-helix structure.     

Ultrasensitive investigations of biological systems by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) extracts information about molecular dynamics from the tiny fluctuations that can be observed in the emission of small ensembles of fluorescent molecules in thermodynamic equilibrium. Employing a confocal setup in conjunction with highly dilute samples, the average number of fluorescent particles simultaneously within the measurement volume (approximately 1 fl) is minimized. Among the multitude of chemical and physical parameters accessible by FCS are local concentrations, mobility coefficients, rate constants for association and dissociation processes, and even enzyme kinetics. As any reaction causing an alteration of the primary measurement parameters such as fluorescence brightness or mobility can be monitored, the application of this noninvasive method to unravel processes in living cells is straightforward. Due to the high spatial resolution of less than 0.5 microm, selective measurements in cellular compartments, e.g., to probe receptor-ligand interactions on cell membranes, are feasible. Moreover, the observation of local molecular dynamics provides access to environmental parameters such as local oxygen concentrations, pH, or viscosity. Thus, this versatile technique is of particular attractiveness for researchers striving for quantitative assessment of interactions and dynamics of small molecular quantities in biologically relevant systems.     

Study of molecular mobility in biological membranes by 2-mm band ESR spectroscopy

Temperature relationship was measured of ESR spectra of spin probes--derivatives of fatty acids whose nitroxyl fragments are incorporated into surface and inner layers of phosphatidylcholine liposomes (T = 180-260 K), as well as of the probe in model ethanol solution (T = 110-220 K). Data on the nature and rotation frequency of probe nitroxyl fragments were obtained from the analysis of the spectra. It was shown that the frequency of the probes movement in the systems under study corresponds to the slow movement region, i.e. it is not above 10(7) s-1.     

Modelling the dynamic structure of biological state-based systems

The paper discusses the modelling aspects of systems with dynamic processes and dynamic structure. A combination of models bringing together the benefits of two paradigms, Population P Systems and Communicating X-machines, is introduced. A simple case study is used in order to illustrate the potential of the combined use of the two methods.     

Possible effects of counterions on biological activities of anionic surfactants

The aggressiveness in terms of apogenic and necrotic activities of lysine-derived anionic surfactants towards a mammalian cell line (U937) were studied. We used N(alpha)N(epsilon)-dioctanoyl lysine as the model surfactant with lysine, tris, Na(+) or Li(+) as counterions. The aggressiveness of the different surfactants was assessed as the concentrations leading to apoptosis or necrosis after the cells were incubated in the presence of surfactants and then cultivated in their absence. Used in the same conditions, acetates associated with the same cations, had no effects on the cells. Our results show that the aggressiveness of the surfactants depended on the nature of the counterions: it was high when surfactants were associated with small counterions, and low with large counterions.     

Comparison of the effects of selected chalcones, dihydrochalcones and some cyclic flavonoids on mitochondrial outer membrane determined by fluorescence spectroscopy

The effect on mitochondrial outer membrane of 4-hydroxychalcone (1), the cyclic chalcone analogues E-2-(4'-hydroxybenzylidene)-1-indanone (2a) and E-2-(4'-hydroxybenzylidene)-1-tetralone (2b), the dihydrochalcones phloretin (3a) and phloridzin (3b), the flavanones naringenin (4a) and naringin (4b), and the flavonol quercetin (5) was investigated by fluorescence spectroscopy. Excitation and emission fluorescence spectra of each flavonoid and synthetic analogue were recorded in respiration medium containing 1 mM succinate. Initial interaction of the compounds with the outer mitochondrial membrane was investigated by recording their fluorescence polarization in the presence of rat liver mitochondria. Most of the compounds displayed an elevated fluorescence polarization on mixing with mitochondria at the zero time point. During the investigated 20 min period the initial fluorescence polarization values remained constant (1, 2a), or a gradual depression of the measured polarization values could be observed (2b, 3a, 4b, 5). In the case of naringenin (4a), however, similar to the previously investigated seven-membered cyclic chalcone analogue E-2-(4 -methoxybenzylidene)-1-benzosuberone, a slight, continuous increase of fluorescence polarization could be detected during the 20 min experiment. Phloridzin (3b) showed an increased fluorescence polarization in first 10 min, which was slightly depressed by the 20 min time point.     

Probing the sequence effects on NarI-induced -2 frameshift mutagenesis by dynamic 19F NMR, UV, and CD spectroscopy

The NarI recognition sequence (5'-G1G2CG3CN-3') is the most vulnerable hot spot for frameshift mutagenesis induced by the carcinogen 2-aminofluorene and its analogues in Escherichia coli. Lesioning of the guanine in the G3 position induces an especially high frequency of -2 deletion mutations; vulnerability to these mutations is modulated by the nature of the nucleotide in the N position (C approximately A > G > T). The objective of the present study was to probe the structural basis of this N-mediated influence on the propensity of the G3 lesion to form a slipped mutagenic intermediate (SMI) during translesion synthesis. We studied NarI-based fully paired [(5'-CTCG1G2CG3*CNATC-3')(5'-GATNCGGCCGAG-3'), N = dC or dT] and -2 deletion [(5'-CTCG1G2CG3*CNATC-3')(5'-GATNGCCGAG-3'), N = dC or dT] duplexes, in which G* was either AF [N-(2'-deoxyguanosin-8-yl)-2-aminofluorene] or the 19F probe FAF [N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene]. The latter sequences mimic the bulged SMI for -2 deletion mutations. Dynamic 19F NMR, circular dichroism, and UV melting results indicated that the NarI-dC/-2 deletion duplex adopts exclusively an intercalated conformer, whereas the NarI-dT/-2 deletion duplex exists as multiple conformers. The data support the presence of a putative equilibrium between a carcinogen-intercalated and a carcinogen-exposed SMI for the dT/-2 duplex. A similar dT-induced conformational heterogeneity was observed for the fully paired duplexes in which all three guanines were individually modified by AF or FAF. The frequency of the carcinogen stacked S-conformation was found to be highest (69-75%) at the G3 hot spot in NarI-dC duplexes. Taken together, our results support the hypothesis that the conformational stability of the SMI is a critical determinant for the efficacy of -2 frameshift mutagenesis in the NarI sequence. We also provide evidence for AF/FAF conformational compatibility in the NarI sequences.     

A systems biological study on the comorbidity of autism spectrum disorders and bipolar disorder

Autism Spectrum Disorder (ASD) is a "spectrum" of disorders, characterized by varying degrees of symptoms ranging from mild to severe. Among Psychiatric disorders, Autism Spectrum Disorders have the strongest evidence for a genetic basis, yet the search for specific genes contributing to these often devastating developmental syndromes has proven extraordinarily difficult. Bipolar Disorder (BP) is a manic-depressive disorder whose symptoms are characterized by extremities in moods. It is also called as the "Mood disorder". BP, like, ASD also has a strong genetic basis and identification of the candidate genes still remains an ongoing effort. Literature studies point to the hypothesis that ASD and BP have good chances of comorbidity and that they may share common pathways for their manifestation. But this hypothesis has not been worked on in depth. Thus, the study focuses on identifying the chances of their comorbidity by identifying their common pathways and the genes involved in the pathways and also discuss the degree of chances of their comorbidity based on the genes involved in the common pathways. Networks for the genes are also constructed to represent their commonness or uniqueness for the disorders.     

Effect of a constant magnetic field on biological systems]

The effect of magnetic field on biological systems is discussed. A number of existing theories are evaluated, and a conclusion is made that it is difficult to explain from the standpoint of physics, neglecting the specifies of the living cell, the effect of the constant magnetic field on biological systems at the microscopic level.     

On Fr?hlich's coherent effects in biological systems: influence of carriers and high order dissipative effects.

Following Fr?hlich we consider a system that models a biological one, for example, a long chain of proteins possessing polar modes of vibration and where energy is pumped through metabolic processes. We consider the effect produced by free electrons that are usually present as hole carriers in proteins with electron-donor molecules. A theory of relaxation based on the non-equilibrium statistical operator method is used in the derivation of the kinetic equations to introduce non-linearities due to interactions of the polar vibrations with the carriers and with a thermal bath. These non-linearities arising from high order relaxation processes lead to the emergence of the Fr?hlich effect in the polar modes, i.e. the occurrence of a (non-equilibrium) Bose-Einstein-like condensation. It points to an instability of the system that seems to be followed by a morphological transformation in the form of a spatially ordered dissipative structure.