Effects of convective and dispersive migration on the linear stability of a two species system with mutualistic interactions and functional response

In this paper, effects of convective and dispersive migration on the linear stability of the equilibrium state of a two species system with mutualistic interactions and functional response have been investigated. In both finite and semi-infinite habitats, it has been shown that the otherwise stable equilibrium state without dispersal remains so with dispersal also, both under flux and reservior conditions. In the case of finite habitat, the degree of stability increases as dispersal coefficients of the two species increase. The effect of convective migration also is to stabilize the equilibrium state in this case.     

Exploring local and non-local interactions for protein stability by structural motif engineering

In order to probe the relative contribution of local and non-local interactions to the thermodynamic stability of proteins, we have devised an experimental approach based on a combination of motif engineering and sequence shuffling. Candidate chain segments in an immunoglobulin V(L) domain were identified whose conformation is proposed to be dominated by non-local interactions. Locally interacting structural motifs of a different conformation were then constructed as replacements, by introducing motif consensus sequences. We find that all nine replacements we constructed systematically reduce the folding cooperativity. By comparing this destabilising effect with the folding transitions of shuffled sequences for three of these motifs, we estimate the contribution of local, native interactions to the free energy of folding. Our results suggest that local and non-local interactions contribute to stability by an approximately equal amount, but that local interactions stabilise by increasing the resistance to denaturation while non-local interactions increase folding cooperativity. The systematic loss of stability by sequence shuffling in these host-guest experiments suggests that the designed interactions indeed are present in the native state, thus consensus sequence engineering may be a useful tool in structure design, but non-local interactions must be taken into account for global stability engineering. Statistical approaches are powerful tools for engineering protein structure and stability, but an analysis based on local sequence propensities alone does not adequately represent the balance of sequence and context in protein structures.     

Effects of convective and dispersive interactions on the stability of two species

The evolution and local stability of a system of two interacting species in a finite two-dimensional habitat is investigated by taking into account the effects of self- and cross-dispersion and convection of the species. In absence of cross-dispersion, an equilibrium state which is stable without dispersion is always stable with dispersion provided that the dispersion coefficients of the two species are equal. However, when the dispersion coefficients of the two species are different, the possibility of self-dispersive instability arises. It is also pointed out that the cross-dispersion of species may lead to stability or instability depending upon the nature and the magnitude of the cross-dispersive interactions in comparison to the self-dispersive interactions. The self-convective movement of species increases the stability of the equilibrium state and can stabilize an otherwise unstable equilibrium state. The effect of cross-convection (in absence of self-dispersion and self-convection) is to stabilize the equilibrium state in a prey-predator model with positive cross-dispersion coefficients for the prey species. Finally, it is shown that if the system is stable under homogeneous boundary conditions it remains so under non-homogeneous boundary conditions.     

Effects of phosphatidylethanolamine glycation on lipid-protein interactions and membrane protein thermal stability

Non-enzymatic glycation of biomolecules has been implicated in the pathophysiology of aging and diabetes. Among the potential targets for glycation are biological membranes, characterized by a complex organization of lipids and proteins interacting and forming domains of different size and stability. In the present study, we analyse the effects of glycation on the interactions between membrane proteins and lipids. The phospholipid affinity for the transmembrane surface of the PMCA (plasma-membrane Ca(2+)-ATPase) was determined after incubating the protein or the phospholipids with glucose. Results show that the affinity between PMCA and the surrounding phospholipids decreases significantly after phosphospholipid glycation, but remains unmodified after glycation of the protein. Furthermore, phosphatidylethanolamine glycation decreases by approximately 30% the stability of PMCA against thermal denaturation, suggesting that glycated aminophospholipids induce a structural rearrangement in the protein that makes it more sensitive to thermal unfolding. We also verified that lipid glycation decreases the affinity of lipids for two other membrane proteins, suggesting that this effect might be common to membrane proteins. Extending these results to the in vivo situation, we can hypothesize that, under hyperglycaemic conditions, glycation of membrane lipids may cause a significant change in the structure and stability of membrane proteins, which may affect the normal functioning of membranes and therefore of cells.     

Effects of solute-solute interactions on protein stability studied using various counterions and dendrimers

Much work has been performed on understanding the effects of additives on protein thermodynamics and degradation kinetics, in particular addressing the Hofmeister series and other broad empirical phenomena. Little attention, however, has been paid to the effect of additive-additive interactions on proteins. Our group and others have recently shown that such interactions can actually govern protein events, such as aggregation. Here we use dendrimers, which have the advantage that both size and surface chemical groups can be changed and therein studied independently. Dendrimers are a relatively new and broad class of materials which have been demonstrated useful in biological and therapeutic applications, such as drug delivery, perturbing amyloid formation, etc. Guanidinium modified dendrimers pose an interesting case given that guanidinium can form multiple attractive hydrogen bonds with either a protein surface or other components in solution, such as hydrogen bond accepting counterions. Here we present a study which shows that the behavior of such macromolecule species (modified PAMAM dendrimers) is governed by intra-solvent interactions. Attractive guanidinium-anion interactions seem to cause clustering in solution, which inhibits cooperative binding to the protein surface but at the same time, significantly suppresses nonnative aggregation.     

Breeding migration and population stability

We have modeled habitat shift for reproduction to examine the relationship between the timing of migration and population stability, by modifying Takimoto’s (Am Nat 162:93–109, 2003) consumer–resource model with a consumer’s ontogenetic niche shift. We found that equilibrium was always locally unstable if migration occurs at a fixed time or level of energy storage, whereas it could be stable if the timing of migration was adaptively flexible to maximize reproductive output. The general conditions for stability were safer breeding rather than feeding habitat and abundant resources at the feeding habitat. These results imply that both adopting an adaptive plastic strategy in the timing of migration and choosing to migrate from a rich feeding habitat to a safe breeding habitat can contribute to population stability. We also found that reduced reproductive success with delays in migration, and the survival rate after reproduction, had complicated effects on stability, depending on resource availability at the feeding habitat. The equilibrium was more likely to be stable when reproduction success was only slightly (or greatly) reduced or survival rate was high (or low) if the feeding habitat was rich (or poor). These are significant predictions for ecological study of migrating animals.     

Protein stability and hydrophobic interactions

The paper summarizes results of calorimetric studies of protein denaturation and of dissolution of non-polar substances in water. The analysis of the available experimental data shows that the positive contribution of the hydrophobic interactions in stabilization of the protein compact state is due to van der Waals interactions between the protein non-polar groups, while the contribution of water solvation by these groups, in spite of the widely spread opinion, appears to be always negative. This destabilizing action of water solvation on the protein increases as the temperature decreases, and at a significantly low temperature causes unfolding of the compact structure of protein, i. e. cold denaturation.     

Implications of spatial pattern and local density on community-level interactions

Explaining the causes of regular multi annual oscillations (cycles) in animal populations has been a major problem for ecology, partly due to a lack of methodological rigor. In this paper we show how the analysis of R-functions, the functional relationship between the per capita rate of change of a species and components of its environment, can be used to detect the causes of population cycles. Analysis of the R-functions enables one to separate cycles due to negative feedback between species (endogenous causes) from those forced by one-way effects (exogenous causes). We illustrate the approach by reference to the spruce needle-miner inhabiting Danish spruce plantations, and conclude that population cycles in this insect are probably caused by interactions with two species of parasitic hymenoptera.     

Global stability of predator-prey interactions

Summary A Lyapunov function is given that extends functions used by Volterra, Goh, and Hsu to a wide class of predator-prey models, including Leslie type models, and a biological interpretation of this function is given. It yields a simple stability criterion, which is used to examine the effect on stability of intraspecific competition among both prey and predators, of a refuge for the prey, and of Holling type II and type III functional responses. Although local stability analysis of these specific models has been done previously, the Lyapunov function facilitates study of global stability and domains of attraction and provides a unified theory which depends on the general nature of the interactions and not on the specific functions used to model them.     

The effect of protein stability on protein-monoglyceride interactions

We have previously shown that proteins such as beta-lactoglobulin and lysozyme insert into monoglyceride monolayers and are able to induce an L(beta) to coagel phase transition in monoglyceride bilayers. These studies gave a first indication that protein stability could be an important factor for these interactions. This study therefore aims at further investigating the potential role of protein stability on protein-monoglyceride interactions. To this end we studied the interaction of stable and destabilized alpha-lactalbumin with monostearoylglycerol. Our results show that protein stability is important for the insertion of proteins into a monostearoylglycerol monolayer, such that the lower the stability of the protein the better the protein inserts. In marked contrast to beta-lactoglobulin and lysozyme we found that destabilized alpha-lactalbumin does not induce the L(beta) to coagel phase transition in monoglyceride bilayers. We propose that this is due to an increased surface coverage by the protein which could result from the unfolding of the protein upon binding to the interface.     

Protein-protein interactions, cytoskeletal regulation and neuronal migration

Neuronal migration, like the migration of many cell types, requires an extensive rearrangement of cell shape, mediated by changes in the cytoskeleton. The genetic analysis of human brain malformations has identified several biochemical players in this process, including doublecortin (DCX) and LIS1, mutations of which cause a profound migratory disturbance known as lissencephaly ('smooth brain') in humans. Studies in mice have identified additional molecules such as Cdk5, P35, Reelin, Disabled and members of the LDL superfamily of receptors. Understanding the cell biology of these molecules has been a challenge, and it is not known whether they function in related biochemical pathways or in very distinct processes. The last year has seen rapid advances in the biochemical analysis of several such molecules. This analysis has revealed roles for some of these molecules in cytoskeletal regulation and has shown an unexpected conservation of the genetic pathways that regulate neuronal migration in humans and nuclear movement in simple eukaryotic organisms.     

Evolution of migration under kin selection and local adaptation

We present here a stochastic two-locus, two-habitat model for the evolution of migration with local adaptation and kin selection. One locus determines the migration rate while the other causes local adaptation. We show that the opposing forces of kin competition and local adaptation can lead to the existence of one or two convergence stable migration rates, notably depending on the recombination rate between the two loci. We show that linkage between migration and local adaptation loci has two antagonist effects: when linkage is tight, cost of local adaptation increases, leading to smaller equilibrium migration rates. However, when linkage is tighter, the population structure at the migration locus tends to be very high because of the indirect selection, and thus equilibrium migration rates increases. This result, qualitatively different from results obtained with other models of migration evolution, indicates that ignoring drift or the detail of the genetic architecture may lead to incorrect conclusions.     

Effects of prostaglandins on leukocyte migration

Artificially synthetized prostaglandins (PGE₁, PGE₂ PGF_1α, and PGF_2α) were found, using Boyden's chamber, to induce significant migration of polymorphonuclear leukocytes (PMNs) of the rabbit; PGF_2α had greater effects than PGE₁ or E₂. A typical dose dependent relationship was found between the PMNs migration and PGF_2α concentrations. Indomethacin pretreatments of rabbits did not significantly alter the PMNs migration indicating that PGs synthetized in vivo was not involved in the migration.PGF_2α was placed in the lower compartment opposite to PMNs and also in the upper compartment together with PMNs. No significant difference was found in the number of migrated PMNs between the two experimental conditions. PGs diffusion occurred across the millipore filter separating the two compartments where the concentrations were almost equal at the end of 3 hours incubation. It was thus concluded that PGs effects are to induce random PMNs movements rather than to initiate chemotactic directional migration.     

Inter-residue interactions in protein folding and stability

During the process of protein folding, the amino acid residues along the polypeptide chain interact with each other in a cooperative manner to form the stable native structure. The knowledge about inter-residue interactions in protein structures is very helpful to understand the mechanism of protein folding and stability. In this review, we introduce the classification of inter-residue interactions into short, medium and long range based on a simple geometric approach. The features of these interactions in different structural classes of globular and membrane proteins, and in various folds have been delineated. The development of contact potentials and the application of inter-residue contacts for predicting the structural class and secondary structures of globular proteins, solvent accessibility, fold recognition and ab initio tertiary structure prediction have been evaluated. Further, the relationship between inter-residue contacts and protein-folding rates has been highlighted. Moreover, the importance of inter-residue interactions in protein-folding kinetics and for understanding the stability of proteins has been discussed. In essence, the information gained from the studies on inter-residue interactions provides valuable insights for understanding protein folding and de novo protein design.     

Global stability, local stability and permanence in model food webs

The dynamical theory of food webs has been based typically on local stability analysis. The relevance of local stability to food web properties has been questioned because local stability holds only in the immediate vicinity of the equilibrium and provides no information about the size of the basin of attraction. Local stability does not guarantee persistence of food webs in stochastic environments. Moreover, local stability excludes more complex dynamics such as periodic and chaotic behaviors, which may allow persistence. Global stability and permanence could be better criteria of community persistence. Our simulation analysis suggests that these three stability measures are qualitatively consistent in that all three predict decreasing stability with increasing complexity. Some new predictions on how stability depends on food web configurations are generated here: a consumer-victim link has a smaller effect on the probabilities of stability, as measured by all three stability criteria, than a pair of recipient-controlled and donor-controlled links; a recipient-controlled link has a larger effect on the probabilities of local stability and permanence than a donor-controlled link, while they have the same effect on the probability of global stability; food webs with equal proportions of donor-controlled and recipient-controlled links are less stable than those with different proportions.     

Amazing stability of phosphate-quaternary amine interactions

We have previously used MALDI mass spectrometry to highlight ammonium- or guanidinium-aromatic interactions via cation-pi bonding and ammonium- or guanidinium-phosphate interactions through salt bridge formation. In the present work, the gas-phase stability and dissociation pathways of the interaction between phosphorylated peptides and compounds containing quaternary amines are demonstrated using electrospray ionization mass spectrometry. The presence of one quaternary amine in a compound is enough to form a noncovalent complex with a phosphorylated residue. However, if two quaternary amines are present in one molecule, the electrostatic interactions of the quaternary amines with the phosphate results in a "covalent-like" stability, and these bonds can withstand fragmentation by collision-induced dissociation at energies similar to those that fragment covalent bonds. Such interactions are important in accounting for physiological, pathophysiological, and pharmacological effects of many therapeutic compounds and small molecules containing quaternary amines or phosphates.     

Impact of intra-subunit domain-domain interactions on creatine kinase activity and stability

Creatine kinase (CK) is a key enzyme in vertebrate excitable tissues. In this research, five conserved residues located on the intra-subunit domain-domain interface were mutated to explore their role in the activity and structural stability of CK. The mutations of Val72 and Gly73 decreased both the activity and stability of CK. The mutations of Cys74 and Val75, which had no significant effect on CK activity and structure, gradually decreased the stability and reactivation of CK. Our results suggested that the mutations might modify the correct positioning of the loop contributing to domain-domain interactions, and result in decreased stability against denaturation.     

Prolonged diapause and the stability of host-parasitoid interactions

We investigated the effect on host-parasitoid dynamics of prolonged diapause, a feature of the life history of many animals living in unpredictable environments, by modifying the classical May (J. Anim. Ecol. 47 (1978) 833) host-parasitoid model. We considered three patterns of development of host and parasitoid: (a) prolonged parasitoid diapause controlled by host physiology, (b) parasitoid interference in host development, preventing parasitized hosts from prolonging diapause, and (c) host diapause independent of parasitoid attack. We found that single-year prolonged diapause shifted the boundaries of the May model towards a slight increase in stability. Longer periods of diapause prolongation had a stronger influence, but this influence remained modest if we considered realistic parameter values. In contrast to other recent studies, our results suggest that prolonged diapause does not necessarily compensate for the destabilizing effects of time lags on the influence of parasitoids on population dynamics.