Insight on the interaction of polychlorobiphenyl with nucleic acid–base

The interaction between one polychlorobiphenyl (3,3′,4,4′,-tetrachlorobiphenyl, coded PCB77) and the four DNA nucleic acid–base is studied by means of quantum mechanics calculations in stacked conformations. It is shown that even if the intermolecular dispersion energy is the largest component of the total interaction energy, some other contributions play a non negligible role. In particular the electrostatic dipole-dipole interaction and the charge transfer from the nucleobase to the PCB are responsible for the relative orientation of the monomers in the complexes. In addition, the charge transfer tends to flatten the PCB, which could therefore intercalate more easily between DNA base pairs. From these seminal results, we predict that PCB could intercalate completely between two base pairs, preferably between Guanine:Cytosine pairs.

Direct and indirect effects of ant–trophobiont interactions on the reproduction of a hummingbird-pollinated mistletoe

Plant Ecology - Fluid-feeding herbivores directly affect host plants through sap consumption. Moreover, they establish mutualistic relationships with ants, which might generate additional...     

Comment on ‘Thermodynamic database supports deciphering protein–nucleic acid interactions’

Mei and colleagues reported a thermodynamic database, PNATDB for protein-nucleic acid interactions, which contains 12 635 experimentally determined thermodynamic parameters. They claimed that extracting data from existing databases is difficult. ProNAB, which has more than 20 000 experimental data points for binding affinities of protein–nucleic acid complexes and other information, was not discussed.     

Consumer–resource dynamics of indirect interactions in a mutualism–parasitism food web module

Food web dynamics are well known to vary with indirect interactions, classic examples including apparent competition, intraguild predation, exploitative competition, and trophic cascades of food chains. Such food web modules entailing predation and competition have been the focus of much theory, whereas modules involving mutualism have received far less attention. We examined an empirically common food web module involving mutualistic (N ₂) and parasitic (N ₃) consumers exploiting a resource of a basal mutualist (N ₁), as illustrated by plants, pollinators, and nectar robbers. This mutualism–parasitism food web module is structurally similar to exploitative competition, suggesting that the module of two consumers exploiting a resource is unstable. Rather than parasitic consumers destabilizing the module through (?,?) indirect interactions, two mechanisms associated with the mutualism can actually enhance the persistence of the module. First, the positive feedback of mutualism favors coexistence in stable limit cycles, whereby (+,?) indirect interactions emerge in which increases in N ₂ have positive effects on N ₃ and increases in N ₃ have negative effects on N ₂. This (+,?) indirect interaction arising from the saturating positive feedback of mutualism has broad feasibility across many types of food web modules entailing mutualism. Second, optimization of resource exploitation by the mutualistic consumer can lead to persistence of the food web module in a stable equilibrium. The mutualism–parasitism food web module is a basic unit of food webs in which mutualism favors its persistence simply through density-dependent population dynamics, rather than parasitism destabilizing the module.     

Impact of external forces on cyanophage–host interactions in aquatic ecosystems

Cyanobacterial (algal) blooms have by convention been attributed to the excessive level of nutrients from pollution and runoff, which promotes the rapid growth and multiplication of cyanobacteria or algae. The cyanophage (virus) is the natural predator of cyanobacteria (the host). The aim of this review is to unveil certain pressures that disrupt cyanophage–host interactions and the formation of cyanobacterial blooms. This review focuses principally on the impact of greenhouse gases, ozone depletion, solar ultraviolet radiation (SUR) and the role of recently discovered virophages, which coexist with and in turn are the natural predator of phages. The key findings are that the increase in SUR, the mutation of cyanophages and cyanobacteria, along with changing nutrient levels, have combined with virophages to impede cyanophage–host interactions and the resultant viral infection and killing of the cyanobacterial cell, which is a necessary step in controlling cyanobacterial blooms. Consider this a ‘call to action’ for researchers interested in corrective action aimed at evolving aquatic ecosystems.     

Nonlinear dynamics of beam–plasma instability in a finite magnetic field

The nonlinear dynamics of beam–plasma instability in a finite magnetic field is investigated numerically. In particular, it is shown that decay instability can develop. Special attention is paid to the influence of the beam?plasma coupling factor on the spectral characteristics of a plasma relativistic microwave accelerator (PRMA) at different values of the magnetic field. It is shown that two qualitatively different physical regimes take place at two values of the external magnetic field: B ₀ = 4.5 kG (Ω ~ ωB _p ) and 20 kG (Ω _B ? ω_p). For B ₀ = 4.5 kG, close to the actual experimental value, there exists an optimal value of the gap length between the relativistic electron beam and the plasma (and, accordingly, an optimal value of the coupling factor) at which the PRMA output power increases appreciably, while the noise level decreases.     

Electron spin resonance in membrane research: protein–lipid interactions from challenging beginnings to state of the art

Conventional electron paramagnetic resonance (EPR) spectra of lipids that are spin-labelled close to the terminal methyl end of the acyl chains are able to resolve the lipids directly contacting the protein from those in the fluid bilayer regions of the membrane. This allows determination of both the stoichiometry of lipid–protein interaction (i.e., number of lipid sites at the protein perimeter) and the selectivity of the protein for different lipid species (i.e., association constants relative to the background lipid). Spin-label EPR data are summarised for 20 or more different transmembrane peptides and proteins, and 7 distinct species of lipids. Lineshape simulations of the two-component conventional spin-label EPR spectra allow estimation of the rate at which protein-associated lipids exchange with those in the bulk fluid regions of the membrane. For lipids that do not display a selectivity for the protein, the intrinsic off-rates for exchange are in the region of 10 MHz: less than 10× slower than the rates of diffusive exchange in fluid lipid membranes. Lipids with an affinity for the protein, relative to the background lipid, have off-rates for leaving the protein that are correspondingly slower. Non-linear EPR, which depends on saturation of the spectrum at high radiation intensities, is optimally sensitive to dynamics on the timescale of spin-lattice relaxation, i.e., the microsecond regime. Both progressive saturation and saturation transfer EPR experiments provide definitive evidence that lipids at the protein interface are exchanging on this timescale. The sensitivity of non-linear EPR to low frequencies of spin exchange also allows the location of spin-labelled membrane protein residues relative to those of spin-labelled lipids, in double-labelling experiments.     

Theoretical studies on the interaction of proteins and nucleic acid: II. The binding of α-helix to B-DNA

Interactions between B-DNA and homopolymeric α-helices of glycine, alanine, serine, asparagine and aspartic acid have been studied theoretically. The complexation energy has been minimised taking into account the interactions between DNA and the polypeptides as well as the internal energy of the α-helix and the interaction energy of counterions with the complex. The results obtained indicate the important role of strong hydrogen bonds between the peptide side chains and nucleic acid phosphate groups, these bonds being much stronger than specific interactions with the base-pairs. The formation of these structural bonds depends on the size of the α-helix, which in turn determines whether bridging across the major groove is possible. The steric role of the methyl group of thymine in orienting the peptide helix and the role of DNA screening cations in complex stabilization are also significant.     

Nuclear magnetic resonance chromatography: applications of pulse field gradient diffusion NMR to mixture analysis and ligand–receptor interactions

Pulse field gradient (PFG) diffusion NMR spectroscopy is a non-invasive method for the spectroscopic separation and identification of compounds of interest from a mixture. Because it relies on differences in translational diffusion rates to resolve NMR signals from individual components, pulse field gradient NMR is a unique method for analyzing complex mixtures and for detecting intermolecular interactions. A number of multidimensional pulse field gradient NMR experiments have been developed to alleviate the overlap of NMR signals arising from a complex mixture and facilitate component identification. The applications of pulse field gradient NMR for mixture analysis and for the direct identification of high affinity ligands are reviewed.     

Effect of the periodic ripple in an axial confining magnetic field on the Alfvén heating of a cylindrical plasma

In a uniform axial magnetic field, the structure of local Alfvén resonance and the resonant absorption of RF power are governed by collisions, finite ion Larmor radius effects, and electron inertia. It is shown that, in a cylindrical plasma in a constant, periodically rippled, axial magnetic field, the structure of Alfvén resonance and the absorption of RF power can strongly depend on the ripple amplitude. The conditions under which the effect in question is dominant are intrinsic, e.g., to the modular Wendelstein stellarators.     

On the possibility of reflection of Alfvén waves in a curvilinear magnetic field

The propagation of Alfvén waves in a plasma immersed in a curvilinear magnetic field is investigated by using a 2D model. The waves are described by a 1D equation that formally coincides with the equation for the case of a quasi-uniform straight magnetic field with a modified Alfvén velocity that takes into account the longitudinal dependence of the Lame coefficients. It is shown that toroidal and poloidal Alfvén modes depend differently on the magnetic-field geometry. In the case of a 2D plane-parallel configuration of the magnetic field, poloidal modes are efficiently reflected from regions where the magnetic field lines sharply converge or diverge. This effect can result in the formation of open-field-line Alfvén quasi-resonators.     

Erratum to: An in silico biomechanical analysis of the stent–esophagus interaction

Biomechanics and Modeling in Mechanobiology - In the original publication of the article, Tables 2 and 3 were published with error. The correct tables are provided below (Tables 2, 3). The...     

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions

A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to the formation of a small region of positive electrostatic potential opposite the covalent bond to the halogen, called the ‘sigma hole.’ Empirical force fields in which the electrostatic interactions are represented by atom-centered point charges cannot capture this effect because halogen atoms usually carry a negative charge and therefore interact unfavorably with other electronegative atoms. A strategy to overcome this problem is to attach a positively charged virtual particle to the halogen. In this work, we extend the additive CHARMM General Force Field (CGenFF) to include such interactions in model systems of phenyl-X, with X being Cl, Br or I including di- and trihalogenated species. The charges, Lennard-Jones parameters, and halogen-virtual particle distances were optimized to reproduce the orientation dependence of quantum mechanical interaction energies with water, acetone, and N-methylacetamide as well as experimental pure liquid properties and relative hydration free energies with respect to benzene. The resulting parameters were validated in molecular dynamics simulations on small-molecule crystals and on solvated protein–ligand complexes containing halogenated compounds. The inclusion of positive virtual sites leads to better agreement across experimental observables, including preservation of ligand binding poses as a direct result of the improved representation of halogen bonding.     

Dynamics of plasma−dust structures formed in a trap created in the narrowing of a current channel in a magnetic field

The geometry and dynamics of plasma?dust structures in a longitudinal magnetic field is studied experimentally. The structures are formed in a glow-discharge trap created in the double electric layer produced as a result of discharge narrowing by means of a dielectric insert introduced in the discharge tube. Studies of structures formed in the new type of glow-discharge trap are of interest from the standpoint of future experiments with complex plasmas in superstrong magnetic fields in which the dust component is magnetized. Different types of dielectric inserts were used: conical and plane ones with symmetric and asymmetric apertures. Conditions for the existence of stable dust structures are determined for dust grains of different density and different dispersity. According to the experimental results, the angular velocity of dust rotation is ≥10 s^–1, which is the fastest type of dust motion for all types of discharges in a magnetic field. The rotation is interpreted by analyzing the dynamics of individual dust grains.