The role of electrostatic energy in prediction of obligate protein-protein interactions

Background

Prediction and analysis of protein-protein interactions (PPI) and specifically types of PPIs is an important problem in life science research because of the fundamental roles of PPIs in many biological processes in living cells. In addition, electrostatic interactions are important in understanding inter-molecular interactions, since they are long-range, and because of their influence in charged molecules. This is the main motivation for using electrostatic energy for prediction of PPI types.

Results

We propose a prediction model to analyze protein interaction types, namely obligate and non-obligate, using electrostatic energy values as properties. The prediction approach uses electrostatic energy values for pairs of atoms and amino acids present in interfaces where the interaction occurs. The main features of the complexes are found and then the prediction is performed via several state-of-the-art classification techniques, including linear dimensionality reduction (LDR), support vector machine (SVM), naive Bayes (NB) and k-nearest neighbor (k-NN). For an in-depth analysis of classification results, some other experiments were performed by varying the distance cutoffs between atom pairs of interacting chains, ranging from 5Å to 13Å. Moreover, several feature selection algorithms including gain ratio (GR), information gain (IG), chi-square (Chi2) and minimum redundancy maximum relevance (mRMR) are applied on the available datasets to obtain more discriminative pairs of atom types and amino acid types as features for prediction.

Conclusions

Our results on two well-known datasets of obligate and non-obligate complexes confirm that electrostatic energy is an important property to predict obligate and non-obligate protein interaction types on the basis of all the experimental results, achieving accuracies of over 98%. Furthermore, a comparison performed by changing the distance cutoff demonstrates that the best values for prediction of PPI types using electrostatic energy range from 9Å to 12Å, which show that electrostatic interactions are long-range and cover a broader area in the interface. In addition, the results on using feature selection before prediction confirm that (a) a few pairs of atoms and amino acids are appropriate for prediction, and (b) prediction performance can be improved by eliminating irrelevant and noisy features and selecting the most discriminative ones.

     

Ingredients for protist coexistence: competition, endosymbiosis and a pinch of biochemical interactions

1. The interaction between mutualism, facilitation or interference and exploitation competition is of major interest as it may govern species coexistence. However, the interplay of these mechanisms has received little attention. This issue dates back to Gause, who experimentally explored competition using protists as a model [Gause, G.F. (1935) Vérifications expérimentales de la théorie mathématique de la lutte pour la vie. Actualités Scientifiques et Industrielles, 277]. He showed the coexistence of Paramecium caudatum with a potentially allelopathic species, Paramecium bursaria. 2. Paramecium bursaria hosts the green algae Chlorella vulgaris. Therefore, P. bursaria may benefit from carbohydrates synthesised by the algae. Studying endosymbiosis with P. bursaria is possible as it can be freed of its endosymbiont. In addition, C. vulgaris is known to produce allelochemicals, and P. bursaria may benefit also from allelopathic compounds. 3. We designed an experiment to separate the effects of resource exploitation, endosymbiosis and allelopathy and to assess their relative importance for the coexistence of P. bursaria with a competitor that exploits the same resource, bacteria. The experiment was repeated with two competitors, Colpidium striatum or Tetrahymena pyriformis. 4. Results show that the presence of the endosymbiont enables the coexistence of competitors, while its loss leads to competitive exclusion. These results are in agreement with predictions based on resource equilibrium density of monocultures (R*) supporting the idea that P. bursaria's endosymbiont is a resource provider for its host. When P. bursaria and T. pyriformis coexist, the density of the latter shows large variation that match the effects of culture medium of P. bursaria. Our experiment suggests these effects are because of biochemicals produced in P. bursaria culture. 5. Our results expose the hidden diversity of mechanisms that underlie competitive interactions. They thus support Gauses's speculation (1935) that allelopathic effects might have been involved in his competition experiments. We discuss how a species engaged both in competition for a resource and in costly interference such as allelopathy may counterbalance these costs with a resource-provider endosymbiont.     

Investigating the role of enemies in temporal dynamics: Differential sensitivity, competition and stable coexistence

The impact of herbivores and other pests on plants varies greatly from year to year. Here we develop an analytical model of a temporal niche dynamic as a tool to examine how natural fluctuations in pest (enemy) levels may determine coexistence in competing annual plant species when one but not the other is affected by the pest. We show that the probability and speed with which the resistant drives out the sensitive species, coexists with it, or is driven out by its sensitive competitor depends on the cost of pest-resistance to the unaffected species, the frequency of high pest levels in the habitat and the competitive advantage of the sensitive species when the pest is not actively present. The interaction is regulated primarily by pest impact on relative seedling survival of the two, with relative yield per capita of seeds viable into the following season (effective fecundity) the next most vulnerable life-cycle stage.     

Age-specific coexistence in two-species competition

Sufficient conditions are obtained for the existence and linear stability of stationary age distributions in a two-species competition model with age-dependent mortality and fertility functions.     

Sympatric snow leopards and Tibetan wolves: coexistence of large carnivores with human-driven potential competition

The snow leopard Panthera uncia coexists with the wolf Canis lupus throughout most of its distribution range. We analysed the food habits of snow leopards and wolves in their sympatric range in the Karakoram mountains of Pakistan. A total of 131 genotyped scats (N?=?74, snow leopard; N?=?57, Tibetan wolf) were collected during the cold periods (i.e. winter and spring) of 2011 and 2012 in the Hushey valley. Large mammals, i.e. livestock and ibex, accounted for 84.8 and 83.1% of the diet (relative frequency) of the snow leopard and the wolf, respectively. Domestic prey was the staple of the diet of both snow leopards (66.6%) and wolves (75.1%). Ibex Capra ibex, the only wild ungulate in our study area, contributed 18.2 and 16.9% of relative frequencies in the diets of the snow leopard and the wolf, respectively. In winter, the snow leopard heavily relied on domestic sheep (43.3%) for food, whereas the wolf preyed mainly on domestic goats (43.4%). Differently from other study areas, both snow leopards and wolves showed no apparent prey preference (Jacobs index: snow leopard min. ??0.098, max. 0.102; Tibetan wolf min. ??0.120, max. 0.03). In human depauperate areas, with livestock and only a few wild prey, should competitive interactions arise, two main scenarios could be expected, with either predator as a winner. In both cases, the best solution could primarily impinge on habitat restoration, so that a balance could be found between these predators, who have already coexisted for thousands of years.     

Nucleocytoplasmic transport: a role for nonspecific competition in karyopherin-nucleoporin interactions

Nucleocytoplasmic transport occurs through the nuclear pore complex (NPC), which in yeast is a ~50 MDa complex consisting of ~30 different proteins. Small molecules can freely exchange through the NPC, but macromolecules larger than ~40 kDa must be aided across by transport factors, most of which belong to a related family of proteins termed karyopherins (Kaps). These transport factors bind to the disordered phenylalanine-glycine (FG) repeat domains in a family of NPC proteins termed FG nups, and this specific binding allows the transport factors to cross the NPC. However, we still know little in terms of the molecular and kinetic details regarding how this binding translates to selective passage of transport factors across the NPC. Here we show that the specific interactions between Kaps and FG nups are strongly modulated by the presence of a cellular milieu whose proteins appear to act as very weak competitors that nevertheless collectively can reduce Kap/FG nup affinities by several orders of magnitude. Without such modulation, the avidities between Kaps and FG nups measured in vitro are too tight to be compatible with the rapid transport kinetics observed in vivo. We modeled the multivalent interactions between the disordered repeat binding sites in the FG nups and multiple cognate binding sites on Kap, showing that they should indeed be sensitive to even weakly binding competitors; the introduction of such competition reduces the availability of these binding sites, dramatically lowering the avidity of their specific interactions and allowing rapid nuclear transport.     

Intra‐ and interspecific interactions between aphidophagous ladybirds: the role of prey in predator coexistence

Cannibalism (CANN) and intraguild predation (IGP) may provide energy and nutrients to individuals and eliminate potential competitors. These negative competitive interactions could also affect the coexistence of predatory species. The co‐occurrence of aphidophagous ladybird species in crops creates opportunities for CANN and IGP, especially when aphids become scarce. The Lotka–Volterra model predicts the coexistence of two species if intraspecific competition is stronger than interspecific interference interactions. Cycloneda sanguinea L. and Eriopis connexa (Germar) (both Coleoptera: Coccinellidae) coexist in sweet pepper crops in La Plata (Argentina) consuming mainly Myzus persicae (Sulzer) (Hemiptera: Aphididae). The present study used laboratory experiments to estimate levels of CANN and IGP by adults and larvae on eggs, and by adults on larvae, in both the presence and absence of prey (i.e., M. persicae), to explain the effect of prey on coexistence of these two predators. Levels of CANN by C. sanguinea and E. connexa were high in the absence of aphids, and decreased when prey was present. Intraguild predation was bidirectional and asymmetric. Adults and larvae of E. connexa were more voracious IG predators of C. sanguinea than vice versa, the former being the stronger IG predator and interference competitor. Eriopis connexa always won when larvae of the same instar were compared, whereas the larger larva always won when larvae were of different instars, regardless of species. In the presence of prey, CANN by both species decreased, but IGP by E. connexa on C. sanguinea remained high, suggesting that E. connexa could displace C. sanguinea via interspecific interference competition. Other factors potentially affecting the coexistence of C. sanguinea and E. connexa in sweet pepper crops are discussed.     

Competition and coexistence in plant communities: intraspecific competition is stronger than interspecific competition

Theory predicts that intraspecific competition should be stronger than interspecific competition for any pair of stably coexisting species, yet previous literature reviews found little support for this pattern. We screened over 5400 publications and identified 39 studies that quantified phenomenological intraspecific and interspecific interactions in terrestrial plant communities. Of the 67% of species pairs in which both intra‐ and interspecific effects were negative (competitive), intraspecific competition was, on average, four to five‐fold stronger than interspecific competition. Of the remaining pairs, 93% featured intraspecific competition and interspecific facilitation, a situation that stabilises coexistence. The difference between intra‐ and interspecific effects tended to be larger in observational than experimental data sets, in field than greenhouse studies, and in studies that quantified population growth over the full life cycle rather than single fitness components. Our results imply that processes promoting stable coexistence at local scales are common and consequential across terrestrial plant communities.     

Association between competition and obligate mutualism in a chemostat

In this paper, we consider a simple chemostat model involving two obligate mutualistic species feeding on a limiting substrate. Systems of differential equations are proposed as models of this association. A detailed qualitative analysis is carried out. We show the existence of a domain of coexistence, which is a set of initial conditions in which both species survive. We demonstrate, under certain supplementary assumptions, the uniqueness of the stable equilibrium point which corresponds to the coexistence of the two species.     

Association between competition and obligate mutualism in a chemostat

In this paper, we consider a simple chemostat model involving two obligate mutualistic species feeding on a limiting substrate. Systems of differential equations are proposed as models of this association. A detailed qualitative analysis is carried out. We show the existence of a domain of coexistence, which is a set of initial conditions in which both species survive. We demonstrate, under certain supplementary assumptions, the uniqueness of the stable equilibrium point which corresponds to the coexistence of the two species.     

种间竞争在实蝇入侵中的作用

实蝇是一类危害热带、亚热带水果蔬菜的重要害虫.调查表明,实蝇由入侵引起的种间竞争,一个突出现象就足实蝇种间的入侵具有显著的等级特征,种间竞争性替代具有强烈的方向性,其竞争作用可导致入侵实蝇种群的火绝或者数量的巨大改变.目前有关实蝇种问竞争的等级性模式既未得到进一步研究验证,也未明确其中隐含的作用机制.深入研究实蝇种间竞争的作用机制为检疫性实蝇的风险评估和管理提供参考,同时也为认识农林害虫群落的演替规律提供理论依据.     

The role of sphingomyelin in regulating phase coexistence in complex lipid model membranes: competition between ceramide and cholesterol

The structure, thermotropic phase behavior, dynamic motion and order parameters of bilayer dispersions of egg phosphatidylcholine, egg sphingomyelin, egg ceramide and cholesterol have been determined. The coexistence of gel, liquid-ordered and liquid-disordered structure has been determined by peak fitting analysis of synchrotron X-ray powder patterns. Order parameters and extent of distribution of 16-doxyl-stearic acid spin probe between ordered and disordered environments has been estimated by ESR spectral simulation methods. The presence of ceramide in proportions up to 20 mol% in phosphatidylcholine is characterized by gel-fluid phase coexistence at temperatures up to 46 degrees C depending on the amount of ceramide. Cholesterol tends to destabilize the ceramide-rich domains formed in phosphatidylcholine while sphingomyelin, by formation of stable complexes with ceramide, tends to stabilize these domains. The stability of sphingomyelin-ceramide complexes is evident from the persistence of highly ordered structure probed by ESR spectroscopy and appearance of a sharp wide-angle X-ray reflection at temperatures higher than the gel-fluid transition of ceramide alone in egg phosphatidylcholine bilayers. The competition between ceramide and cholesterol for interaction with sphingomyelin is discussed in terms of control of lipid-mediated signaling pathways by sphingomyelinase and phospholipase A2.     

The effects of intransitive competition on coexistence

Coexistence theory has been developed with an almost exclusive focus on interactions between two species, often ignoring more complex and indirect interactions, such as intransitive loops, that can emerge in competition networks. In fact, intransitive competition has typically been studied in isolation from other pairwise stabilising processes, and thus little is known about how intransitivity interacts with more traditional drivers of species coexistence such as niche partitioning. To integrate intransitivity into traditional coexistence theory, we developed a metric of growth rate when rare, , to identify and quantify the impact of intransitive competition against a backdrop of pairwise stabilising niche differences. Using this index with simulations of community dynamics, we demonstrate that intransitive loops can both stabilise or destabilise species coexistence, but the strength and importance of intransitive interactions are significantly affected by the length and the topology of these loops. We conclude by showing how can be used to evaluate effects of intransitivity in empirical studies. Our results emphasise the need to integrate complex mechanisms emerging from diverse interactions into our understanding of species coexistence.     

Population biology of multispecies helminth infection: competition and coexistence

The role that interspecific interactions play in shaping parasite communities is uncertain. To date, models of competition between helminth species have assumed that interaction occurs through parasite-induced host death. To our knowledge, there has been no theoretical exploration of other forms of competition. We examine models in which competition acts at the point of establishment within the host, and at the time of egg production by the adult worm. The models used are stochastic and we allow hosts to vary in their rate of exposure to infective larvae. We derive the Lotka-Volterra model of competition when exposure is homogenous and thus demonstrate that two helminth species cannot coexist on a single limiting resource. We show that coexistence of species is promoted by heterogeneity in host exposure provided that the rates of exposure to the two species are not perfectly correlated, and, if they are positively correlated, provided that the degree of heterogeneity in host exposure is similar for the two competing helminth species. These results are robust to the mechanism of competition.     

Habitat-dependent competition and the coexistence of Australian heathland rodents

When competing species depress one another's fitness in the habitats that they occupy, their competitive effects will emerge in each species' pattern of density-dependent habitat choice. Thus, a regression analysis of joint densities, corrected by the habitat effect, should reveal the magnitude of interspecific competition. We tested this idea by 1) demonstrating the connection between removal experiments and regression estimates of competition with those obtained from isodars (regressions that implicitly incorporate evolutionarily stable strategies of habitat selection) and 2) evaluating whether interspecific competition inferred from isodars corresponded with the inferences emerging from regression and field experiments. Previous removal experiments on two herbivorous rodents occupying coastal wet heathlands in eastern Australia documented that competition between Rattus lutreolus and Pseudomys gracilicaudatus is asymmetrically biased in favor of the much larger Rattus . The asymmetry in competition was also revealed by regression estimates of competition. Isodar analyses illustrate a habitat-dependent mechanism for the asymmetry. Rattus compete effectively with Pseudomys in both 'wetter' and 'drier' patches of heath whereas Pseudomys appear to exert a competitive effect in only the drier sites. The magnitude of competition measured by a removal experiment in an area with more-or-less equal amounts of both habitats will be biased in favor of Rattus . More generally, one can use the isodar estimates to draw isolegs and isoclines of competitive coexistence. Isoclines for the two Australian rodents imply dynamic equilibria of stable competitive coexistence that vary with plant succession in fire-dominated heathland ecosystems.     

Multiple attractors in host-parasitoid interactions: coexistence and extinction

This paper considers the dynamics of a two-dimensional discrete-time model for host-parasitoid interactions, and shows that the model has two attractors: the fixed point where two species coexist and a boundary cycle where the parasitoid is absent. The analysis with the Liapunov exponent confirms that this kind of bistability is common in this model. The generality of this phenomenon in host-parasitoid interactions is also discussed.     

Three-way interactions between mosquito population,viral strain and temperature underlying chikungunya virus transmission potential

Interactions between pathogens and their insect vectors in nature are under the control of both genetic and non-genetic factors, yet most studies on mosquito vector competence for human pathogens are conducted in laboratory systems that do not consider genetic and/or environmental variability. Evaluating the risk of emergence of arthropod-borne viruses (arboviruses) of public health importance such as chikungunya virus (CHIKV) requires a more realistic appraisal of genetic and environmental contributions to vector competence. In particular, sources of variation do not necessarily act independently and may combine in the form of interactions. Here, we measured CHIKV transmission potential by the mosquito Aedes albopictus in all combinations of six worldwide vector populations, two virus strains and two ambient temperatures (20°C and 28°C). Overall, CHIKV transmission potential by Ae. albopictus strongly depended on the three-way combination of mosquito population, virus strain and temperature. Such genotype-by-genotype-by-environment (G × G × E) interactions question the relevance of vector competence studies conducted with a simpler set of conditions. Our results highlight the need to account for the complex interplay between vectors, pathogens and environmental factors to accurately assess the potential of vector-borne diseases to emerge.     

Dynamics in a discrete two-species competition model: coexistence and over-compensation

The dynamic features of an over-compensating discrete two-species competition system with stable coexistence are recaptured, and it is shown how the probabilities of the different possible ecological scenarios, e.g. coexistence, may be calculated when the assumption of no over-compensation is loosened. A Bayesian methodology for calculating the probability that stable oscillations or chaos may occur in plant populations or communities is outlined. The methodology is exemplified using an experimental population of Arabidopsis thaliana. It is concluded that, when making ecological predictions it is preferable and possibly important to test for the possibility of chaotic population dynamics due to over-compensation rather than assuming a priori that over-compensation does not occur.     

Clutch-size behavior and coexistence in ephemeral-patch competition models

Systems of patchy, ephemeral resources often support surprisingly diverse assemblages of consumer insects. Aggregation of consumer individuals over the landscape of patches has been suggested as one mechanism that can stabilize competition among consumer species. One mechanism for larval aggregation is the laying of eggs in clutches by females traveling among patches to distribute their total fecundity. We use simulation models to explore the consequences, for coexistence of competitors, of larval aggregation that arises from clutch laying. Contrary to some previous treatments, we find that clutch laying can be strongly stabilizing and under certain conditions can be sufficient to allow competitors to coexist stably. We extend these models by considering clutch size as a variable that responds to the abundance of resource patches. Such a relationship might be expected because females should lay their eggs in fewer but larger clutches when the cost of travel among patches is high (because patches are rare). When females adjust clutch size in response to resource abundance, coexistence can be easiest when resource patches are scarce and most difficult when resources are abundant.     

Exploitative competition and coexistence in a parasitoid assemblage

Most insect populations are exploited by a complex of different parasitoid species, providing ample opportunities for competitive interactions among the latter. Despite this, resource-mediated competition (i.e., exploitative competition) among insect parasitoids remains poorly documented in natural systems. Here we propose a novel way to infer the presence of competitive interactions from covariance patterns in parasitism levels, and illustrate the use of this approach on a relatively well-defined and simple host–parasitoid system. The parasitism levels caused by three parasitoid species on a shared host showed a highly consistent negative covariance among samples. With the levels of parasitism by one species increasing, the levels of parasitism attributable to the two others decreased. Importantly, negative covariance between parasitism levels by different species appeared at high abundance, but not at low abundance of the phenologically earlier parasitoid species. This as well as several other lines of evidence indicates the importance of competitive interactions in this system. Feeding biology and phenology of the parasitoids suggest that competition in this parasitoid assemblage is primarily resource-mediated rather than occurring through direct interference. The species attacking earlier stages of the host are competitively superior to those attacking their host later in the season. Better dispersal ability and use of alternative host species by the inferior species could contribute to the coexistence of these competing parasitoids.