Prediction of localization and interactions of apoptotic proteins

During apoptosis several mitochondrial proteins are released. Some of them participate in caspase-independent nuclear DNA degradation, especially apoptosis-inducing factor (AIF) and endonuclease G (endoG). Another interesting protein, which was expected to act similarly as AIF due to the high sequence homology with AIF is AIF-homologous mitochondrion-associated inducer of death (AMID). We studied the structure, cellular localization, and interactions of several proteins in silico and also in cells using fluorescent microscopy. We found the AMID protein to be cytoplasmic, most probably incorporated into the cytoplasmic side of the lipid membranes. Bioinformatic predictions were conducted to analyze the interactions of the studied proteins with each other and with other possible partners. We conducted molecular modeling of proteins with unknown 3D structures. These models were then refined by MolProbity server and employed in molecular docking simulations of interactions. Our results show data acquired using a combination of modern in silico methods and image analysis to understand the localization, interactions and functions of proteins AMID, AIF, endonuclease G, and other apoptosis-related proteins.     

Advantageous indirect interactions in systems of competition

Ecological foodwebs display complex networks of species interactions. Here we discuss how two species, whether directly interacting or not, can crucially affect each other 'indirectly' through their mutual associations with intermediary species. A technique is presented for quantifying these "indirect effects", so that a simple measure emerges for the degree of overall harm or advantage that a particular species encounters from another in the context of a given foodweb. If the system is one of pure competition, the "direct" interaction between any two species is of course harmful to both. But when the method is applied to such systems it predicts that, if all interactions are allowed for including the indirect, in a large proportion of pair interactions at least one species will be deriving benefit from the other. Computer-generated samples confirm that this proportion is accurately predicted. The many pathways for indirect interaction can thus often reverse the direct connection, so that competing species achieve an interaction here called 'Advantageous in A Community Context' (ACC).     

On quantitative measures of indirect interactions

Indirect effects, whether density-mediated (DMII) or trait-mediated (TMII), have been recognized as potentially important drivers of community dynamics. However, empirical studies that have attempted to detect TMII or to quantify the relative strength of DMII and TMII in short-term studies have used a range of different metrics. We review these studies and assess both the consistency of a variety of different metrics and their robustness to (or ability to detect) ecological phenomena such as the dependence of forager behaviour on conspecific density. Quantifying indirect effects over longer time scales when behaviour and population density vary is more challenging, but also necessary if we really intend to incorporate indirect effects into predictions of long-term community dynamics; we discuss some problems associated with this effort and conclude with general recommendations for quantifying indirect effects.     

Prediction of protein-protein interactions in dengue virus coat proteins guided by low resolution cryoEM structures

Background  

Dengue virus along with the other members of the flaviviridae family has reemerged as deadly human pathogens. Understanding the mechanistic details of these infections can be highly rewarding in developing effective antivirals. During maturation of the virus inside the host cell, the coat proteins E and M undergo conformational changes, altering the morphology of the viral coat. However, due to low resolution nature of the available 3-D structures of viral assemblies, the atomic details of these changes are still elusive.     

Sulphur-aromatic interactions in proteins

The geometry of sulphur-aromatic interactions in globular proteins has been analysed using crystallographic data derived from 36 proteins, solved to resolutions of 2 Å or better. About half of all sulphur atoms from cyst(e)ine and methionine residues are in contact ( 6 Å from ring centroid) with an aromatic ring (phenylalanine, tyrosine or tryptophan). Compared to carbon and nitrogen atoms the interacting sulphur atoms express an affinity towards the edge of the aromatic rings, and avoid the region above the ring in the vicinity of the π-electrons. This preference is similar to that previously found for oxygen atoms around phenylalanine rings, and may be electrostatic in origin.

Sulfw-aromatic interaction Protein Side-chain contact Cyst(e)ine Methionine Packing     

Amino-aromatic interactions in proteins

Geometric analysis of 33 refined high-resolution protein crystal structures (2 A or higher) demonstrates that side-chain amino groups interact with aromatic side chains. Positively charged or delta(+) amino groups of lysine, arginine, asparagine, glutamine and histidine are preferentially located within 6 A of the ring centroids of phenylalanine, tyrosine and tryptophan, where they make van der Waals' contact with the delta(-) pi-electrons and avoid the delta(+) ring edge. This geometric pattern is different from the distribution expected due to random close packing of side chains in a protein. It is opposite to oxygen- and sulfur-aromatic interactions, similar to aromatic-aromatic interactions, and almost certainly electrostatic in origin.     

Parasitism proteins in nematode-plant interactions

The current battery of candidate parasitism proteins secreted by nematodes to modify plant tissues for parasitism includes cell-wall-modifying enzymes of potential prokaryotic origin, multiple regulators of host cell cycle and metabolism, proteins that can localize to the plant cell nucleus, potential suppressors of host defense, mimics of plant molecules, and a relatively large cadre of predicted novel nematode parasitism proteins. Phenotypic effects of expressing nematode parasitism proteins in transformed plant tissues, protein-protein interaction assays, and RNA-mediated interference (RNAi) analyses are currently providing exciting evidence of the biological role of candidate nematode secreted parasitism proteins and identifying potential novel means of developing transgenic resistance to nematodes in crops.     

Motifs in bipartite ecological networks: uncovering indirect interactions

Indirect interactions play an essential role in governing population, community and coevolutionary dynamics across a diverse range of ecological communities. Such communities are widely represented as bipartite networks: graphs depicting interactions between two groups of species, such as plants and pollinators or hosts and parasites. For over thirty years, studies have used indices, such as connectance and species degree, to characterise the structure of these networks and the roles of their constituent species. However, compressing a complex network into a single metric necessarily discards large amounts of information about indirect interactions. Given the large literature demonstrating the importance and ubiquity of indirect effects, many studies of network structure are likely missing a substantial piece of the ecological puzzle. Here we use the emerging concept of bipartite motifs to outline a new framework for bipartite networks that incorporates indirect interactions. While this framework is a significant departure from the current way of thinking about bipartite ecological networks, we show that this shift is supported by analyses of simulated and empirical data. We use simulations to show how consideration of indirect interactions can highlight differences missed by the current index paradigm that may be ecologically important. We extend this finding to empirical plant–pollinator communities, showing how two bee species, with similar direct interactions, differ in how specialised their competitors are. These examples underscore the need to not rely solely on network‐ and species‐level indices for characterising the structure of bipartite ecological networks.     

Energetics of charge-charge interactions in proteins

Electrostatic interactions between pairs of atoms in proteins are calculated with a model based on the linearized Poisson-Boltzmann equation. The equation is solved accurately by a method that takes into account the detailed shape of the protein. This paper presents applications to several systems. Experimental data for the interaction of ionized residues with an active site histidine in subtilisin BPN' allow the model to be tested, using various assumptions for the electrical properties of the protein and solvent. The electrostatic stabilization of the active site thiolate of rhodanese is analyzed, with attention to the influence of alpha-helices. Finally, relationships between electrostatic potential and charge-charge distance are reported for large and small globular proteins. The above results are compared with those of simpler electrostatic models, including Coulomb's law with both a distance-dependent dielectric constant (epsilon = R) and a fixed dielectric constant (epsilon = 2), and Tanford-Kirkwood theory. The primary conclusions are as follows: 1) The Poisson-Boltzmann model agrees with the subtilisin data over a range of ionic strengths; 2) two alpha-helices generate a large potential in the active site of rhodanese; 3) epsilon = R overestimates weak electrostatic interactions but yields relatively good results for strong ones; 4) Tanford-Kirkwood theory is a useful approximation to detailed solutions of the linearized Poisson-Boltzmann equation in globular proteins; and 5) the modified Tanford-Kirkwood theory over-screens the measured electrostatic interactions in subtilisin.     

The role of indirect interactions in structuring tropical insect communities

Apparent competition is a form of indirect interaction among species that can potentially structure biological communities. In insect communities, parasitoid-mediated apparent competition has been proposed as a particularly important structuring force. We argue that short-term apparent competition may be less important in structuring insect communities in tropical regions, compared with temperate regions. This prediction arises because, compared with temperate insects, tropical insects that share natural enemies are more likely to be isolated in both space and time.     

Prediction of physical protein-protein interactions

Many essential cellular processes such as signal transduction, transport, cellular motion and most regulatory mechanisms are mediated by protein-protein interactions. In recent years, new experimental techniques have been developed to discover the protein-protein interaction networks of several organisms. However, the accuracy and coverage of these techniques have proven to be limited, and computational approaches remain essential both to assist in the design and validation of experimental studies and for the prediction of interaction partners and detailed structures of protein complexes. Here, we provide a critical overview of existing structure-independent and structure-based computational methods. Although these techniques have significantly advanced in the past few years, we find that most of them are still in their infancy. We also provide an overview of experimental techniques for the detection of protein-protein interactions. Although the developments are promising, false positive and false negative results are common, and reliable detection is possible only by taking a consensus of different experimental approaches. The shortcomings of experimental techniques affect both the further development and the fair evaluation of computational prediction methods. For an adequate comparative evaluation of prediction and high-throughput experimental methods, an appropriately large benchmark set of biophysically characterized protein complexes would be needed, but is sorely lacking.     

Size-dependent trait-mediated indirect interactions among sea urchin herbivores

Despite their importance in community interactions, nonlethalindirect effects of predators are not well understood in manymarine food webs. In this study, I found that within a guildof herbivorous sea urchins, small urchins (Strongylocentrotusdroebachiensis and small Strongylocentrotus franciscanus) alteredgrazing rates in the presence of the predatory sea star (Pycnopodiahelianthoides) and were highly preferred by the predator. Incontrast, large urchins (adult S. franciscanus) did not significantlyalter grazing in the presence of cues from the sea star and,when immobile, were less frequently attacked by the predator.However, the sea star's preference (active predator choice)was obscured by sea urchin mobility, that is, small S. franciscanuswas only most preferred when unable to escape. These resultssuggest that by identifying the relative threat of predationfacing guild members and the degree to which individuals transmittrait-mediated indirect interactions, these indirect effectsmay be predictably incorporated in community interactions.     

Using indirect protein-protein interactions for protein complex prediction

Protein complexes are fundamental for understanding principles of cellular organizations. As the sizes of protein-protein interaction (PPI) networks are increasing, accurate and fast protein complex prediction from these PPI networks can serve as a guide for biological experiments to discover novel protein complexes. However, it is not easy to predict protein complexes from PPI networks, especially in situations where the PPI network is noisy and still incomplete. Here, we study the use of indirect interactions between level-2 neighbors (level-2 interactions) for protein complex prediction. We know from previous work that proteins which do not interact but share interaction partners (level-2 neighbors) often share biological functions. We have proposed a method in which all direct and indirect interactions are first weighted using topological weight (FS-Weight), which estimates the strength of functional association. Interactions with low weight are removed from the network, while level-2 interactions with high weight are introduced into the interaction network. Existing clustering algorithms can then be applied to this modified network. We have also proposed a novel algorithm that searches for cliques in the modified network, and merge cliques to form clusters using a "partial clique merging" method. Experiments show that (1) the use of indirect interactions and topological weight to augment protein-protein interactions can be used to improve the precision of clusters predicted by various existing clustering algorithms; and (2) our complex-finding algorithm performs very well on interaction networks modified in this way. Since no other information except the original PPI network is used, our approach would be very useful for protein complex prediction, especially for prediction of novel protein complexes.     

Direct and indirect transgenerational effects alter plant-herbivore interactions

Theory suggests that environmental effects with transgenerational consequences, including rapid evolution and maternal effects, may affect the outcome of ecological interactions. However, indirect effects occur when interactions between two species are altered by the presence of a third species, and can make the consequences of transgenerational effects difficult to predict. We manipulated the presence of insect herbivores and the competitor Medicago polymorpha in replicated Lotus wrangelianus populations. After one generation, we used seeds from the surviving Lotus to initiate a reciprocal transplant experiment to measure how transgenerational effects altered ecological interactions between Lotus, Medicago, and insect herbivores. Herbivore leaf damage and Lotus fecundity were dependent on both parental and offspring environmental conditions. The presence of insect herbivores and Medicago in the parental environment resulted in transgenerational changes in herbivore resistance, but these effects were non-additive, likely as a result of indirect effects in the parental environment. Indirect transgenerational effects interacted with more immediate ecological indirect effects to affect Lotus fecundity. These results suggest that explanations of ecological patterns require an understanding of transgenerational effects and that these effects may be difficult to predict in species-rich, natural communities where indirect effects are prevalent.     

Prediction of C alpha-H...O and C alpha-H...pi interactions in proteins using recurrent neural network

In this study, an attempt has been made to develop a method for predicting weak hydrogen bonding interactions, namely, C alpha-H...O and C alpha-H...pi interactions in proteins using artificial neural network. Both standard feed-forward neural network (FNN) and recurrent neural networks (RNN) have been trained and tested using five-fold cross-validation on a non-homologous dataset of 2298 protein chains where no pair of sequences has more than 25% sequence identity. It has been found that the prediction accuracy varies with the separation distance between donor and acceptor residues. The maximum sensitivity achieved with RNN for C alpha-H...O is 51.2% when donor and acceptor residues are four residues apart (i.e. at delta D-A = 4) and for C alpha-H...pi is 82.1% at delta D-A = 3. The performance of RNN is increased by 1-3% for both types of interactions when PSIPRED predicted protein secondary structure is used. Overall, RNN performs better than feed-forward networks at all separation distances between donor-acceptor pair for both types of interactions. Based on the observations, a web server CHpredict (available at http://www.imtech.res.in/raghava/chpredict/) has been developed for predicting donor and acceptor residues in C alpha-H...O and C alpha-H...pi interactions in proteins.     

Trait and density mediated indirect interactions in simple food webs

This article compares indirect trait-mediated interactions in simple resource–consumer–predator food webs with those that are density-mediated. It focuses on two well documented responses of consumers to predation risk: decrease in consumer activity and habitat switch. These behavioral effects are transmitted to resources and they cause similar indirect effects as those which are mediated by density changes in consumers. Two indirect interactions are studied in this article: trophic cascades, and apparent competition. Results for density only, trait only and combined density and trait mediated interactions are compared and discussed with respect to manipulation with predator density (top-down manipulation) and resource environmental capacity (bottom-up manipulation). The article shows that trait-mediated effects on species equilibrial densities are similar to those of density-mediated, but they are often highly non-linear. Thus, they may have potential for even stronger impact on food webs than those which are density mediated.