Frequency and amplitude windows in the combined action of DC and low frequency AC magnetic fields on ion thermal motion in a macromolecule: theoretical analysis

We solved the differential equation describing combined action of DC and AC magnetic fields on thermal motion of ions in a biological macromolecule. The solution showed the occurrence of a new set of resonant peaks for ion oscillations under the influence of magnetic fields. After establishment of steady ion oscillations in the macromolecule interior that is well shielded from the action of small particles of the medium surrounding this molecule, the change in energy of ion thermal motion could be sufficient to alter the conformation state of the macromolecule. On this basis, a diversity of biological phenomena can be explained, including the appearance of the known "frequency" and "amplitude" windows, without any resort to the ideas of participation of cyclotron or parametric resonances in these effects.     

Modeling of slow glutamate diffusion and AMPA receptor activation in the cerebellar glomerulus

Synaptic conductances are influenced markedly by the geometry of the space surrounding the synapse since the transient glutamate concentration in the synaptic cleft is determined by this geometry. Our paper is an attempt to understand the reasons for slow glutamate diffusion in the cerebellar glomerulus, a structure situated around the enlarged mossy fiber terminal in the cerebellum and surrounded by a glial sheath. For this purpose, analytical expressions for glutamate diffusion in the glomerulus were considered in models with two-, three-, and fractional two-three-dimensional (2D-3D) geometry with an absorbing boundary. The time course of average glutamate concentration in the synaptic cleft of the mossy fiber-granule cell connection was calculated for both direct release of glutamate from the same synaptic unit, and for cumulative spillover of glutamate from neighboring release sites. Several kinetic schemes were examined, and the parameters of the diffusion models were estimated by identifying theoretical activation of AMPA receptors with direct release and spillover components of published experimental AMPA receptor-mediated EPSCs. For model selection, the correspondence of simulated paired-pulse ratio and EPSC increase after prevention of desensitization to experimental values were also taken into consideration. Our results suggest at least a 7- to 10-fold lower apparent diffusion coefficient of glutamate in the porous medium of the glomerulus than in water. The modeling of glutamate diffusion in the 2D-3D geometry gives the best fit of experimental EPSCs. We show that it could be only partly explained by normal diffusion of glutamate in the complex geometry of the glomerulus. We assume that anomalous diffusion of glutamate occurs in the glomerulus. A good match of experimental estimations and theoretical parameters, obtained in the simulations that use an approximation of anomalous diffusion by a solution for fractional Brownian motion, confirms our assumption.     

Release of ADP from the catalytic subunit of protein kinase A: a molecular dynamics simulation study

Substrate phosphorylation by cAMP-dependent-protein kinase A (protein kinase A, PKA) has been studied extensively. Phosphoryl transfer was found to be fast, whereas ADP release was found to be the slow, rate-limiting step. There is also evidence that ADP release may be preceded by a partially rate-limiting conformational change. However, the atomic details of the conformational change and the mode of ADP release are difficult to obtain experimentally. In this work, we studied ADP release from PKA by carrying out molecular dynamics simulations with different pulling forces applied to the ligand. The detailed ADP release pathway and the associated conformational changes were analyzed. The ADP release process was found to involve a swinging motion with the phosphate of ADP anchored to the Gly-rich loop, so that the more buried adenine base and ribose ring came out before the phosphate. In contrast to the common belief that a hinge-bending motion was responsible for the opening of the ligand-binding cleft, our simulations showed that the small lobe exhibited a large amplitude "rocking" motion when the ligand came out. The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process.     

Hypochlorous acid-induced stress on human spermatozoa. A model for inflammation in the male genital tract

The fertilising ability of human spermatozoa may be impaired by inflammations of the genital tract, although details of these processes are still unknown. Hypochlorous acid (HOCl), an important product of myeloperoxidase released from stimulated neutrophils, induces a concentration-dependent increase in externalisation of phosphatidylserine in ejaculated human spermatozoa as revealed by fluorescence-activated cell sorting (FACS) analysis. The increase of annexin-V binding cells starts already at about 10(-5) mol/l HOCl, while a formation of lysophosphatidylcholines as detected by matrix-assisted laser desorption and ionisation time-of-flight mass spectrometry (MALDI-TOF MS) is only found at HOCl concentrations higher than 10(-4) mol/l. Thus, changes in lipid composition of spermatozoa are unlikely responsible for the phosphatidylcholine (PS)-externalisation. These data gave concomitant evidence that HOCl itself leads to a dramatic damage of the cell membrane. Thus, the neutrophil-derived HOCl contributes to the deterioration of spermatozoa leading to diminished fertilisation ability.     

Anchoring a cationic ligand: the structure of the Fab fragment of the anti-morphine antibody 9B1 and its complex with morphine

The crystal structures of an anti-morphine antibody 9B1 (to 1.6A resolution) and its complex with morphine (to 2.0 A resolution) are reported. The morphine-binding site is described as a shallow depression on the protein surface, an unusual topology for a high-affinity ( Ka approximately 10(9) M(-1)) antibody against a small antigen. The polar part of the ligand is exposed to solvent, and the cationic nitrogen atom of the morphine molecule is anchored at the bottom of the binding site by a salt-bridge to a glutamate side-chain. Additional affinity is provided by a double cation-pi interaction with two tryptophan residues. Comparison of the morphine complex with the structure of the free Fab shows that a domain closure occurs upon binding of the ligand.     

Crossing scales,crossing disciplines: collective motion and collective action in the Global Commons

Two conflicting tendencies can be seen throughout the biological world: individuality and collective behaviour. Natural selection operates on differences among individuals, rewarding those who perform better. Nonetheless, even within this milieu, cooperation arises, and the repeated emergence of multicellularity is the most striking example. The same tendencies are played out at higher levels, as individuals cooperate in groups, which compete with other such groups. Many of our environmental and other global problems can be traced to such conflicts, and to the unwillingness of individual agents to take account of the greater good. One of the great challenges in achieving sustainability will be in understanding the basis of cooperation, and in taking multicellularity to yet a higher level, finding the pathways to the level of cooperation that is the only hope for the preservation of the planet.     

Proteins as micro viscosimeters: Brownian motion revisited

Translational and rotational diffusion coefficients of proteins in solution strongly deviate from the Stokes–Einstein laws when the ambient viscosity is induced by macromolecular co-solutes rather than by a solvent of negligible size as was assumed by A. Einstein one century ago for deriving the laws of Brownian motion and diffusion. Rotational and translational motions experience different micro viscosities and both become a function of the size ratio of protein and macromolecular co-solute. Possible consequences upon fluorescence spectroscopy observations of diffusing proteins within living cells are discussed.     

Comment: analyses of models of ion actions under the combined action of AC and DC magnetic fields

I show that the interaction of weak DC and ELF magnetic fields with contained ions cannot generate significant biological effects through changing the character of the ion orbits.     

Molecular dynamics study of major urinary protein-pheromone interactions: a structural model for ligand-induced flexibility increase

Recently, two independent (15)N NMR relaxation studies indicated that in contrast to the decreased flexibility expected for induced-fit interactions, the backbone flexibility of major urinary protein isoform I (MUP-I) slightly increased upon complex formation with its natural pheromone 2-sec-butyl-4,5-dihydrothiazol. We have investigated the subtle details of molecular interactions by molecular dynamics simulations in explicit solvent. The calculated order parameters S(2) for a free- and ligand-bound protein supply evidence that mobility in various regions of MUP-I can be directly related to small conformational changes of the free- and complexed protein resulting from modifications of the hydrogen bonding network.     

Exploring patterns of interspecific variation in quantitative traits using sequential phylogenetic eigenvector regressions

A number of metrics have been developed for estimating phylogenetic signal in data and to evaluate correlated evolution, inferring broad-scale evolutionary and ecological processes. Here, we proposed an approach called phylogenetic signal-representation (PSR) curve, built upon phylogenetic eigenvector regression (PVR). In PVR, selected eigenvectors extracted from a phylogenetic distance matrix are used to model interspecific variation. In the PSR curve, sequential PVR models are fitted after successively increasing the number of eigenvectors and plotting their R(2) against the accumulated eigenvalues. We used simulations to show that a linear PSR curve is expected under Brownian motion and that its shape changes under alternative evolutionary models. The PSR area, expressing deviations from Brownian motion, is strongly correlated (r= 0.873; P < 0.01) with Blomberg's K-statistics, so nonlinear PSR curves reveal if traits are evolving at a slower or higher rate than expected by Brownian motion. The PSR area is also correlated with phylogenetic half-life under an Ornstein-Uhlenbeck process, suggesting how both methods describe the shape of the relationship between interspecific variation and time since divergence among species. The PSR curve provides an elegant exploratory method to understand deviations from Brownian motion, in terms of acceleration or deceleration of evolutionary rates occurring at large or small phylogenetic distances.