Tryptophan interactions of gramicidin A′ channels in lipids: a time-resolved fluorescence study

The evolution of the incorporation of cation transport channels into lysolecithin micelles by gramicidin A was followed by measuring the ns time-resolved fluorescence of the tryptophan residues. In all samples, the tryptophan fluorescence could be resolved into three exponentially decaying components. The three decay times ranged from 6 to 8 ns, 1.8 to 3 ns, and 0.3 to 0.8 ns, depending on the emission wavelength. The fractional fluorescence of each component changed with incubation time. The long lifetime component had a reduced contribution to the total fluorescence while the short decay time component increased. The fluorescence spectra could be resolved into three distinct fluorescent components having maxima at 340 nm, 330 nm and 323 nm after 90 min of incubation, and 335 nm, 325 nm and 320 nm after 24 h of incubation. These maxima were, respectively, associated with the long, medium and short decay components. The fluorescence decay behaviour was interpreted as representing three families of tryptophans, the short lifetime component being due to a stacking interaction between tryptophan residues. The variation with incubation time suggests a two-step process in the channel-lipid organization. The first is associated with the conformational change of the polypeptide as it takes up a left-handed helical head-to-head dimer structure in the lipid. The second step is proposed to involve changes originating from membrane assembly and intermolecular interactions between channels as they form hexameric clusters.     

Supramolecular organization of lysophosphatidylcholine-packaged gramicidin A′

Heat derived gramicidin A′/l-α-lysophosphatidylcholine complexes were separated on a sucrose gradient to form two fractions: Fraction A which had an approximately constant Gramicidin A′ to phospholipid ratio of 8 to 10 lipid molecules per Gramicidin A′ molecule and Fraction B which had a larger but variable ratio. Fluorescence and circular dichroism studies confirmed Fraction A to be a lipid-incorporated channel state. Electron microscopic studies, using uranyl acetate negative staining, showed fraction A to be a membranous state with the formation of bilayer vesicles, that is, the interaction of peptide and phospholipid micelles causes the lipid to reorganize into a bilayer structure. Freeze-fracture replicas of the channel incorporated state demonstrated the presence of a supramolecular organization of particles exhibiting a tendency to form rows with a 50–60 Å periodicity along the row and with 70–80 Å distance between rows. An idealized working model for the incorporated state is presented.     

Fluorescence quenching in model membranes An analysis of the local phospholipid environments of diphenylhexatriene and gramicidin A′

Interactions between the fluorophors diphenylhexatriene or gramicidin A′ and lipids are examined using a spin-labeled phosphatidylcholine as a fluorescence quenching probe. It is found that in phospholipid vesicles of mixed lipid composition at temperatures where phospholipids are completely in the liquid crystal phase, several different species of phosphatidylcholines are randomly distributed around the fluorophors. In vesicles of mixed lipid composition which can undergo thermally induced phase separations, the fluorescence quenching observed at lower temperatures reflects a non-random distribution of lipids around each fluorophor. This observation is explained in terms of the partition of fluorophor between a spin-labeled lipid-rich liquid crystal phase, and a spin-labeled lipiddepleted gel phase. Gramicidin A′ strongly favors partition into the liquid crystal phase, whereas diphenylhexatriene partitions about equally between the two lipid phases. A method is described utilizing fluorescence quenching for the calculation of the partition coefficient for a fluorophor. The partition coefficients so calculated are shown to be in good agreement with previously reported values derived from other methods. It is also shown that Ca²⁺-induced lipid phase separations can be monitored by fluorescence quenching.     

A nonlocal kinetic model for predator–prey interactions

We extend the aggregation model from Fetecau (2011) by adding a field of vision to individuals and by including a second species. The two species, assumed to have a predator–prey relationship, have dynamics governed by nonlocal kinetic equations that include advection and turning. The latter is the main mechanism for aggregation and orientation, which results from interactions among individuals of the same species as well as predator–prey relationships. We illustrate numerically a diverse set of predator–prey behaviors that can be captured by this model. We show that a prey’s escape outcome depends on the social interactions between its group members, the prey’s field of vision and the sophistication of the predator’s hunting strategies.     

A model for the coevolution of resistance and virulence in coupled host—parasitoid interactions

A coevolutionary model is developed of the interaction between a host and an internal parasitoid, where the outcome of parasitism depends upon the extent to which individual hosts invest in resistance mechanisms and individual parasitoids in countermeasures (virulence). The host and parasitoid are assumed to have coupled population dynamics (of Nicholson–Bailey form) and to be composed of a series of asexual clones with different levels of resistance and virulence. Investment in resistance and virulence mechanisms is assumed to be costly. The model has two main outcomes. First, if resistance is relatively costly compared to virulence, the host may be selected not to invest in resistance mechanisms despite parasitoid investment in virulence, in effect trading off the risks of parasitism against the savings in costs. A number of cases which appear to correspond to this result have been reported. Second, for most other feasible parameter values, an arms race occurs between host and parasitoid, until effective resistance becomes so costly that the host abandons defence. This abandonment is followed by a reduction in parasitoid virulence and the cycle begins again. These cycles may explain reports of persistent additive genetic variation in resistance and virulence, and may also contribute towards population dynamic stability.     

Data mining for protein–protein interactions in invertebrate model organisms

Well-annotated genome databases are available for many invertebrate species, notably the fruitfly, Drosophila melanogaster, and the nematode, Caenorhabditis elegans. An adequate interpretation of this information at the biological level requires the exploration of the interactions between the gene products. Knowledge of protein interactions and the components of cell signalling pathways in the fly and worm are particularly valuable as hypotheses can be rapidly tested using the powerful genetic toolkits available. Invertebrates offer additional experimental advantages when attempting to characterise protein–protein interactions (PPIs). Their relatively small genome size compared to mammals helps to reduce missed interactions due to redundancy, and their function can be addressed using forward (mutants) and reverse (RNA interference) genetics. However, the researcher looking for evidence of PPIs for a protein of interest is faced with the challenge of extracting interaction data from sources that are highly varied, such as the results of microarray experiments in the unstructured text of research papers. This challenge is greatly reduced by a range of public databases of curated information, as well as publicly available, enhanced search engines, which can provide either direct experimental evidence for a PPI, or valuable clues for generating new hypotheses.     

Importance of the tryptophans of gramicidin for its lipid structure modulating activity in lysophosphatidylcholine and phosphatidylethanolamine model membranes. A comparative study employing gramicidin analogs and a synthetic α-helical hydrophobic polypeptide

The importance of the tryptophan residues of gramicidin for the lipid structure modulating activity of this pentadecapeptide was investigated by studying the interaction of gramicidin analogs A, B, C (which have a tryptophan, phenylalanine and tyrosine in position 11, respectively) and tryptophan-N-formylated gramicidin (in which the four tryptophan residues have been formylated) with several phospholipid systems. In addition in α-helical model pentadecapeptide (P15) was studied to further test the specificity of the gramicidin-lipid interaction. DSC experiments showed that all the gramicidin analogs produced a significant decrease in the gel to liquid-crystalline transition enthalpy of dipalmitoylphosphatidylcholine. The P15 peptide was much less effective in this respect. In dielaidoylphosphatidylethanolamine the gel → liquid-crystalline transition enthalpy was much less affected by the incorporation of these molecules. In this lipid system tryptophan-N-formylated gramicidin was found to be the most ineffective. ³¹P-NMR and small angle X-ray diffraction experiments showed that the ability of the peptides to induce bilayer structures in palmitoyllysophosphatidylcholine and H_II phase promotion in dielaidoylphosphatidylethanolamine systems follows the order: gramicidin A′ (natural mixture) ≈gramicidin A > gramicidin B ≈ gramicidin C > tryptophan-N-formylated gramicidin > P15. These results support the hypothesis that the shape of gramicidin and its aggregational behaviour, in which the tryptophan residues play an essential role, are major determinants in the unique lipid structure modulating activity of gramicidin.     

A “micromere model” of cell-cell interactions in sea urchin early embryos

It has been shown that isolation of sea urchin blastomeres before the post-division adhesion leads mainly to the formation of equal blastomeres at the stage of 4th cleavage division, whereas isolation after adhesion results in the formation of micromeres simultaneous with that in intact embryos. Similar results were obtained in five sea urchin species. It has been concluded that there exists a critical point in the cleavage process, when blastomeres exchange information that determines the further cleavage pattern. It has been shown with this “micromere model” that serotonin and its analogs influence the cleavage pattern of half-embryos. These data have served as a basis for the hypothesis of “protosynapse,” a bilaterally symmetric structure in which the blastomeres are not only source and target of the signal but also a passive obstacle to leakage of the signal substance from the interblastomere cleft to the milieu. Such a structure may also specify the primary asymmetry of the blastomeres. The micromere model may be useful in specific pharmacological screening.     

Angiotensin as a model for hormone — receptor interactions

Proton magnetic resonance and chemical reactivity studies have demonstrated the presence of a tyrosine charge relay system in angiotensin which is analogous to the serine charge relay system present at the active site of serine proteases. Receptor activation by angiotensin can be explained by electronic effects deriving from an interaction of the charge relay system with stacking of the histidine and phenylalanine rings. Experiments with serine protease inhibitors suggest the possibility that mechanistic features of the interaction of angiotensin with its receptors may apply to other phenoxyl hormones including certain peptides, steroids and catecholamines.     

Physicochemical interactions of amyloid β-peptide with lipid bilayers

The aggregation and deposition onto neuronal cells of amyloid β-peptide (Aβ) is central to the pathogenesis of Alzheimer's disease. Accumulating evidence suggests that membranes play a catalytic role in the aggregation of Aβ. This article summarizes the structures and properties of Aβ in solution and the physicochemical interaction of Aβ with lipid bilayers of various compositions. Reasons for discrepancies between results by different research groups are discussed. The importance of ganglioside clusters in the aggregation of Aβ is emphasized. Finally, a hypothetical physicochemical cascade in the pathogenesis of the disease is proposed.     

Brachypodium as an emerging model for cereal–pathogen interactions

Background Cereal diseases cause tens of billions of dollars of losses annually and have devastating humanitarian consequences in the developing world. Increased understanding of the molecular basis of cereal host–pathogen interactions should facilitate development of novel resistance strategies. However, achieving this in most cereals can be challenging due to large and complex genomes, long generation times and large plant size, as well as quarantine and intellectual property issues that may constrain the development and use of community resources. Brachypodium distachyon (brachypodium) with its small, diploid and sequenced genome, short generation time, high transformability and rapidly expanding community resources is emerging as a tractable cereal model.Scope Recent research reviewed here has demonstrated that brachypodium is either susceptible or partially susceptible to many of the major cereal pathogens. Thus, the study of brachypodium–pathogen interactions appears to hold great potential to improve understanding of cereal disease resistance, and to guide approaches to enhance this resistance. This paper reviews brachypodium experimental pathosystems for the study of fungal, bacterial and viral cereal pathogens; the current status of the use of brachypodium for functional analysis of cereal disease resistance; and comparative genomic approaches undertaken using brachypodium to assist characterization of cereal resistance genes. Additionally, it explores future prospects for brachypodium as a model to study cereal–pathogen interactions.Conclusions The study of brachypodium–pathogen interactions appears to be a productive strategy for understanding mechanisms of disease resistance in cereal species. Knowledge obtained from this model interaction has strong potential to be exploited for crop improvement.     

A spatial theory for characterizing predator–multiprey interactions in heterogeneous landscapes

Trophic interactions in multiprey systems can be largely determined by prey distributions. Yet, classic predator–prey models assume spatially homogeneous interactions between predators and prey. We developed a spatially informed theory that predicts how habitat heterogeneity alters the landscape-scale distribution of mortality risk of prey from predation, and hence the nature of predator interactions in multiprey systems. The theoretical model is a spatially explicit, multiprey functional response in which species-specific advection–diffusion models account for the response of individual prey to habitat edges. The model demonstrates that distinct responses of alternative prey species can alter the consequences of conspecific aggregation, from increasing safety to increasing predation risk. Observations of threatened boreal caribou, moose and grey wolf interacting over 378 181 km² of human-managed boreal forest support this principle. This empirically supported theory demonstrates how distinct responses of apparent competitors to landscape heterogeneity, including to human disturbances, can reverse density dependence in fitness correlates.     

A physiologically based model of pest–natural enemy interactions

The population dynamic processes in aphids and mites are very similar, because the two groups show strong similarities in their biology. Resource limitation, density-dependent emigration and natural enemies are major factors controlling aphid and mite populations, but an assessment of their relative importance has proven difficult. We used a physiologically based simulation model to investigate the relative impact of the three factors on aphid pest populations. The present simulation model includes winter wheat, three aphid species, Metopolophium dirhodum (Wlk.), Rhopalosiphum padi (L.) and Sitobion avenae (F.) (Hom.: Aphididae) and three parasitoids, Aphelinus abdominalis Dalman (Hym.: Apheliniidae), Aphidius rhopalosiphi De Stefani-Perez and Praon volucre (Hal.) (Hym.: Aphidiidae). We derived and parameterized the model from literature data and validated it against independent field data. The study showed that resource limitation and density-dependent alate production restricts aphid numbers in the field. The mortality due to parasitoids increased late in the season and reduced the peak aphid numbers only moderately. The modelling approach we used is appropriate for simulating other pest–natural enemy systems, such as the spider mite–predatory mite system. Using an object-oriented modelling framework as a template, acarologists can now efficiently develop the simulation model of their choice. This revised version was published online in November 2006 with corrections to the Cover Date.     

The effect of cholesterol and gramicidin A′ on the carbonyl groups of dimyristoylphosphatidylcholine dispersions

Proton-enhanced carbon-13 magnetic resonance measurements have been made of the natural abundance carbon-13 carbons in hydrated L_α phase dispersions of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) codispersed with cholesterol or with the polypeptide gramicidin A′. The carbonyl group spectrum consists of a superposition of two peaks derived from the two carbonyl sites within the lipid. In the L_α phase of DMPC both carbonyl sites contribute axially symmetric spectra, one with a chemical shift anisotropy of –29 ppm and the other with a chemical shift anisotropy of less than –5 ppm. The chemical shift anisotropy of the broader carbonyl resonance was found to increase with increasing cholesterol content. However, in DMPC dispersions with gramicidin A′, the chemical shift anisotropy of the broader carbonyl signal initially increased slightly from that of pure DMPC and then decreased with increasing concentrations of gramicidin A′. The width of the narrower spectral component was essentially unaltered by cholesterol or gramicidin A′. The presence of a narrow component at all concentrations of cholesterol or gramicidin A′ suggests that it is unlikely that any significant conformational changes have occurred at the carbonyl level of the bilayer. We propose that the major effect of cholesterol or gramicidin A′ is to alter the molecular order parameter, S_mol, which reflects the range of angles through which the local molecular long axis of the phospholipid is tumbling.     

A mate to die for? A model of conditional monogyny in cannibalistic spiders

Monogynous males in various species actively limit themselves to mating with a single female in their lifetime. Whereas previous models have considered monogyny as an obligate mating strategy, here we explore the potential of monogyny to evolve as a context‐specific (conditional) behavior. Using a state‐dependent dynamic game model based on the biology of the cannibalistic spider Argiope bruennichi, we confirm that conditional monogyny can evolve under broad conditions, including an even sex ratio. We predict that males should make a terminal investment when mating with large, virgin females, especially if population density is low and the encounter occurs late in the season. We encourage empirical tests for the existence of conditional monogyny in all species where monogyny occurs in the absence of strict morphological constraints that would make it obligatory.