Design and synthesis of high-avidity tetravalent glycoclusters as probes for Sambucus sieboldiana agglutinin and characterization of their binding properties

We designed and synthesized three tetravalent sialo-glycoclusters that had different separations between the terminal sialic acids and the linking carboxy groups of the ethylene glycol bis(β-aminoethyl ether)-N,N,N',N'-tetraacetate scaffold to serve as ligands for the sialic acid-binding lectin Sambucus sieboldiana agglutinin (SSA). The interaction between each glycocluster and SSA was characterized by hemagglutination inhibition, quantitative precipitation, and double-diffusion assays. For the precipitation assays, the precipitin curves indicated that the ligands and SSA bound in either a 1:1 or a 1:2 ratio, i.e., stoichiometrically. The strong interactions of these sialo-glycoclusters with SSA could be ascribed to a combination of multivalency and spacer effects. We also assessed the nature of the ligand-SSA complexes by isothermal titration calorimetry and dynamic light scattering. The results of those experiments indicated that formation of intermolecular complexes occurred at less than stoichiometric ratios of ligand to SSA concentrations and that, as the concentrations of the ligands increased, larger cross-linked aggregates formed. Large aggregates that were present concurrently with visible precipitation and with a particle size centered at ~600 to 800 nm were identified by dynamic light scattering.     

A simple chemical example of hierarchical thermodynamic interactions: the protonation equilibria of inorganic polyprotic acids

A general method for formulating complex thermodynamic systems in terms of hierarchical interactions has been developed, and has been applied in a previous analysis to hemoglobin oxygen binding data. Polyprotic acids can be considered a simple chemical model of thermodynamic interaction between ligand binding events. To further illustrate the hierarchical interaction approach it is applied to the analysis of the thermodynamic interactions between proton binding events in inorganic polyprotic acids. pK values for arsenate, carbonate, chromate, phosphate, phosphite, selenite, sulfide and sulfite were recast into hierarchical interaction terms. The intrinsic K(d,h) for protonation ranged from 8.8 x 10(-13) (M) for phosphate to 1.3 x 10(-6) (M) for chromate. Pairwise interactions (K(d,hh)) between protonation events ranged from 1.3 x 10(4) for phosphite to 9.4 x 10(5) for carbonate. Third order interactions (K(d,hhh)) were 0.91 and 0.51 for arsenate and phosphate, respectively, values relatively close to the no interaction value of 1. A principle feature of systems described by hierarchical interactions is that higher order interactions, representing more complex interactions, are less likely to be significant than lower order interactions, and this is further illustrated by these observations from polyprotic acids. The set of significant hierarchical interaction values can be used to predict values for as yet unobserved events, and projected pK values are made for all the polyprotic acids included in this study. Finally, application of this method to the protonation equilibria of water demonstrates a profound pairwise interaction between protonation events (K(d,hh) = 1.3 x 10(17)), which is attributed to oxygen's small size and lack of polarizability.     

Evaporative cooling feature selection for genotypic data involving interactions

MOTIVATION: The development of genome-wide capabilities for genotyping has led to the practical problem of identifying the minimum subset of genetic variants relevant to the classification of a phenotype. This challenge is especially difficult in the presence of attribute interactions, noise and small sample size. METHODS: Analogous to the physical mechanism of evaporation, we introduce an evaporative cooling (EC) feature selection algorithm that seeks to obtain a subset of attributes with the optimum information temperature (i.e. the least noise). EC uses an attribute quality measure analogous to thermodynamic free energy that combines Relief-F and mutual information to evaporate (i.e. remove) noise features, leaving behind a subset of attributes that contain DNA sequence variations associated with a given phenotype. RESULTS: EC is able to identify functional sequence variations that involve interactions (epistasis) between other sequence variations that influence their association with the phenotype. This ability is demonstrated on simulated genotypic data with attribute interactions and on real genotypic data from individuals who experienced adverse events following smallpox vaccination. The EC formalism allows us to combine information entropy, energy and temperature into a single information free energy attribute quality measure that balances interaction and main effects. AVAILABILITY: Open source software, written in Java, is freely available upon request.     

Ionization and charge-transfer: basic data for track structure calculations

It is widely accepted that an understanding of the detailed structure of charged particle tracks is essential for interpreting the mechanistic consequences of energy deposition by high linear energy transfer (LET) radiation. The spatial relationship of events along the path of a charged particle, including excitation, ionization, and charge-transfer, govern subsequent chemical, biochemical, and biological reactions that can lead to adverse biologic effects. The determination of spatial patterns of ionization and excitation relies on a broad range of cross-section data relating the interactions of charged particles to the molecular constituents of the absorbing medium. It is important that these data be absolute in magnitude, comprehensive in scope, and reliable if accurate assessment of track structure parameters is to be achieved. Great strides have been made in the development of this database, understanding the underlying theory, and developing analytic models, particularly for interactions involving electrons and protons with atoms and molecules. The database is less comprehensive for interactions involving heavier charged particles, especially those that carry bound electrons, and for interactions in condensed phase media. Although there has been considerable progress in understanding the physical mechanisms for interactions involving fast heavy ions and atomic targets during the past few years, we still lack sufficient understanding to confidently predict cross-sections for these ions with biologically relevant material. In addition, little is known of the interaction cross-sections for heavy charged particles as they near the end of their track, i.e., for low velocity ions where collision theory is less well developed and where the particle's net charge fluctuates owing to electron capture and loss processes. This presentation focuses on the current status of ionization and charge-transfer data. Compilations, reviews, Internet sources, theoretical models, and recent data applicable to track structure calculations are discussed.     

Rapid non-equilibrium aluminium-ligand interactions: studies on the precipitation of aluminium by laser light scattering, ultrafiltration and centrifugation.

The study aimed to develop simple assays to study aluminium-ligand interactions in natural/biological systems where equilibrium is rarely reached and thus where the initial seconds or hours of interactions are important. The immediate and non-equilibrium precipitation of aluminium hydroxide, in aqueous solution at neutral pH, was therefore studied by laser light scattering (diffraction), ultrafiltration and centrifugation. The interaction of weak ligands, present in the gastrointestinal lumen, on the precipitation of aluminium hydroxide was also investigated. The initial kinetics and particle sizes of precipitated aluminium hydroxide were sensitive to a number of external factors, including the presence of weak ligand (bicarbonate), sheer force (stirring), electrolyte concentration and initial (i.e. added) aluminium concentration. However, after a few seconds (no weak ligand), or several hundred seconds (with weak ligand), the subsequent observed changes to the solid phase were of small magnitude and occurred slowly. Thus, a 25-min window, within 5 and 30 min of pH adjustment, can be used to study the interactions of aluminium-ligand. This may approximate better to most natural systems where unperturbed aluminium-ligand equilibrium must rarely exist.     

Exploration of molecular interactions in cholesterol superlattices: effect of multibody interactions

Experimental evidences have indicated that cholesterol may adapt highly regular lateral distributions (i.e., superlattices) in a phospholipid bilayer. We investigated the formations of superlattices at cholesterol mole fraction of 0.154, 0.25, 0.40, and 0.5 using Monte Carlo simulation. We found that in general, conventional pairwise-additive interactions cannot produce superlattices. Instead, a multibody (nonpairwise) interaction is required. Cholesterol superlattice formation reveals that although the overall interaction between cholesterol and phospholipids is favorable, it contains two large opposing components: an interaction favoring cholesterol-phospholipid mixing and an unfavorable acyl chain multibody interaction that increases nonlinearly with the number of cholesterol contacts. The magnitudes of interactions are in the order of kT. The physical origins of these interactions can be explained by our umbrella model. They most likely come from the requirement for polar phospholipid headgroups to cover the nonpolar cholesterol to avoid the exposure of cholesterol to water and from the sharp decreasing of acyl chain conformation entropy due to cholesterol contact. This study together with our previous work demonstrate that the driving force of cholesterol-phospholipid mixing is a hydrophobic interaction, and multibody interactions dominate others over a wide range of cholesterol concentration.     

Inbreeding–environment interactions increase extinction risk

Being able to accurately estimate the persistence time of populations of endangered plants and animals is central to conservation biology and is of considerable importance in informing land-use decisions. Genetic deterioration (due to inbreeding and random genetic drift) and environmental deterioration (e.g. climate change, pollution and introduced species) clearly contribute to population extinction, however, considerable recent evidence suggests that interactions between genetic deterioration and environmental stress are ubiquitous. The importance of these interactions for potentially reducing persistence times has not been quantified and has not been taken into account by major conservation organizations. Using a computer simulation, we determined that including reasonable estimates of the inbreeding–environment interaction reduces persistence times by 17.5–28.5% (mean=23%) for a wide range of carrying capacities, assumptions concerning the number of lethal equivalents and different regimes for the frequency and magnitude of the stressful environment. We note that the proportional decrease in persistence time with inclusion of the interactions becomes larger (i.e. the interaction becomes more important) as absolute time to extinction gets larger. Thus, inclusion of the interaction is important and surprisingly may be most needed when populations are of intermediate size and are considered relatively safe from environmental and genetic stresses acting independently.     

Molecular motions and hydration of purple membranes and disk membranes studied by neutron scattering

Fast stochastic equilibrium fluctuations (time scale: 10^–10–10^–13 seconds) in purple membranes (PM) and in disk membranes (DM) have been measured with quasielastic incoherent neutron scattering. The comparison of predominantly stochastic motions occurring in purple membranes and in disk membranes revealed qualitatively similar dynamical behaviour. Models of internal motions within restricted volumes have been shown to be useful to fit the spectra from both samples. From fits using these models we found “amplitudes” 15 to 20% larger for motions in DM samples compared to PM samples. This indicates a higher internal flexibility of the DM. Because the dynamical behaviour is very sensitive to the hydration of the protein-lipid complex, we also performed neutron diffraction experiments to determine lamellar spacings as a measure of level of hydration and as a function of temperature. From these studies the interaction of solvent molecules with the surface of the protein-lipid complex appears to be qualitatively similar for both types of membranes. Received: 12 February 1998 / Revised version: 18 March 1998 / Accepted: 27 March 1998     

Probing the “fingers” domain binding pocket of Hepatitis C virus NS5B RdRp and D559G resistance mutation via molecular docking,molecular dynamics simulation and binding free energy calculations

The NS5B RdRp polymerase is a prominent enzyme for the replication of Hepatitis C virus (HCV). During the HCV replication, the template RNA binding takes place in the “fingers” sub-domain of NS5B. The “fingers” domain is a new emerging allosteric site for the HCV drug development. The inhibitors of the “fingers” sub-domain adopt a new antiviral mechanism called RNA intervention. The details of essential amino acid residues, binding mode of the ligand, and the active site intermolecular interactions of RNA intervention reflect that this mechanism is ambiguous in the experimental study. To elucidate these details, we performed molecular docking analysis of the fingers domain inhibitor quercetagetin (QGN) with NS5B polymerase. The detailed analysis of QGN-NS5B intermolecular interactions was carried out and found that QGN interacts with the binding pocket amino acid residues Ala97, Ala140, Ile160, Phe162, Gly283, Gly557, and Asp559; and also forms π?π stacking interaction with Phe162 and hydrogen bonding interaction with Gly283. These are found to be the essential interactions for the RNA intervention mechanism. Among the strong hydrogen bonding interactions, the QGN?Ala140 is a newly identified important hydrogen bonding interaction by the present work and this interaction was not resolved by the previously reported crystal structure. Since D559G mutation at the fingers domain was reported for reducing the inhibition percentage of QGN to sevenfold, we carried out molecular dynamics (MD) simulation for wild and D559G mutated complexes to study the stability of protein conformation and intermolecular interactions. At the end of 50?ns MD simulation, the π?π stacking interaction of Phe162 with QGN found in the wild-type complex is altered into T-shaped π stacking interaction, which reduces the inhibition strength. The origin of the D559G resistance mutation was studied using combined MD simulation, binding free energy calculations and principal component analysis. The results were compared with the wild-type complex. The mutation D559G reduces the binding affinity of the QGN molecule to the fingers domain. The free energy decomposition analysis of each residue of wild-type and mutated complexes revealed that the loss of non-polar energy contribution is the origin of the resistance.

Communicated by Ramaswamy H. Sarma     

Basic aspects of photon transport through matter with respect to track structure formation

After a short summary of the most important physical aspects of photon interaction with matter and of the main elements of photon transport simulation, some basic features of photon tracks in liquid water are discussed. These include the statistical distribution of the number of photon interactions caused during the complete photon slow-down, the corresponding mean value, the distance distribution of photon interactions, and the spectral distribution of secondary electrons or, which is the same, the spectral distribution of the start energy of secondary electron tracks. The latter distribution can easily be interpreted in terms of the track entity concept of Mozumder and Magee, which, therefore, proves to be the most natural concept of track structure analysis in the case of photon irradiation. Received: 20 September 1998 / Accepted in revised form: 30 April 1999     

Weak trophic interactions and the balance of enriched metacommunities

Weak trophic interactions have been shown to promote the stability of ecological food webs characterized by perfect mixing. However, their importance at the landscape level and response to enrichment has not been extensively examined. In this paper we examine the food-web model explored by McCann et al. [1998. Weak trophic interactions and the balance of nature. Nature 395, 794-798]. The model is expanded into a metacommunity construct where local communities are coupled through global or local dispersal. We analyze global and local stability, as well as spatial synchrony in relation to trophic interaction strength and dispersal regimes. Results reveal that weak interactions can operate through two scale-dependent mechanisms: (i) under low local dispersal regimes, local stabilization of each community under weak interactions directly scales-up to global stability. (ii) Under high local dispersal, asynchronous local destabilization associated with weak interactions proves the driver behind global stability. In the face of enrichment, weak trophic interactions are shown to be instrumental in promoting global stability when dispersal is local. These results demonstrate how the importance of weak trophic interactions can be generalized at the landscape level despite contrary local predictions.     

Characteristics of rural dust events shown to impact on asthma severity in Brisbane, Australia

 Wind erosion in arid inland Australia leads to dust plumes which can pass over populated coastal areas in Eastern Australia, such as Brisbane. Such events can lead to concerns about respiratory health problems because they significantly increase the fine particle component of atmospheric aerosols. This paper examines the particulate characteristics of 11 dust events in Brisbane and associations with daily diary records (peak expiratory flow, symptoms) of people with asthma, and hospital emergency attendances for asthma during a number of seasons between 1992 and 1994. These dust events are frequently, but not always, characterised by higher particulate levels and higher ratios of fine to coarse particulates. The results indicate that a number of dust events were significantly associated with changes in asthma severity, but general relationships could not be determined. Given that the phenomenon of wind-blown dust is not isolated to the Australian continent, these findings raise important questions about the effects of wind-blown dust in other parts of the world. Received: 11 June 1997 / Received last revision: 10 September 1998 / Accepted: 25 November 1998     

Development of simulation models for protein folding in a thermal annealing process -I: a simulation of BPTI folding by the pearl necklace model

A model system is proposed to simulate the folding processesof proteins during thermal annealing. This system consists offour subsystems: (i) the pearl necklace model with isotropicinter-residue interactions; (ii) the extended pearl necklacemodel with anisotropic interaction potentials; (iii) moltenglobule phase dynamics; and (iv) final generation of the three-dimensionalstructure of a given protein. In this paper results obtainedwith the pearl necklace model are reported. This model consistsof spherical elements and virtual bonds of 3.8 Å in lengthand is intended to sinudate dynamical processes at relativelyhigh temperature where entropic terms play a dominant role.Inter-residue interactions are composed of spherical soft repulsivepotentials and hydrophobic interactions inherent to respectiveresidues. A simulation of folding processes of BPTI startingfrom the fully extended conformation indicated that intermediates,even at early stages of folding, are not randomly coiled butassume organized structures that resemble, to some extent, thenative conformation.     

Numerical simulation of aldolase tetramer stability

A theoretical study of aldolase tetramer stability, conducted by finite difference Poisson-Boltzmann (FDPB) and modified Tanford-Kirkwood (MTK) techniques using the atomic coordinates of human aldolase, is described. A method for calculating the interaction energy between subunits is proposed. An analysis of the contribution of different energy terms to the stability and oligomeric equilibria (monomer ⇔ dimer ⇔ tetramer) of aldolase is made. It is shown that the loss of solvation energy and electrostatic interactions at very high and low pH-s destabilise the oligomers. These energy terms are compensated over a wide pH range by the stabilization energy due to hydrophobic interactions. It is shown that the aldolase tetramer is energetically more preferable than other oligomers in the pH range from 5 to 11. Subunit-subunit interactions within the tetramer suggest one dimeric form to be the most stable of the possible sub-parts. For this reason the tetramer can be thought of as a “dimer of dimers”. A comparison between our theoretical results and available experimental data shows that the dissociation of the aldolase tetramer below pH 3–4 cooperatively leads to acid denaturation. A second dissociation is predicted to occur at high pH (>12) in addition to the well known acidic dissociation. The analysis suggests that a mutation of His20 or Arg257 to a neutral residue could decrease the pH of the acidic dissociation by approximately 1 pH unit. Received: 16 February 1998 / Revised version: 8 April 1998 / Accepted: 19 April 1998     

Solution structure of halophilic malate dehydrogenase from small-angle neutron and X-ray scattering and ultracentrifugation

Data from small-angle X-ray and neutron scattering and ultracentrifugation experiments on solutions of malate dehydrogenase from Halobacterium maris mortui are analysed together to yield a model for the enzyme particle formed by the protein and its interactions with water and salt in the solvent. The halophilic enzyme is stable only in high concentrations of salt and the model has structural features that are absent from non-halophilic malate dehydrogenase. The complementarity of the information derived from the three experimental methods is discussed extensively and quantitatively. It derives from the fact that mass density (ultracentrifugation), electron density (X-rays) and neutron scattering density are independent of each other. Each method gives a different "view" of the same particle, and an analysis of the combined data provided thermodynamic and structural parameters with, apart from the chemical composition of the solutions, only one other assumption: a constant partial specific volume for water equal to 1.00 cm3 g-1. Both the insights gained by this novel approach and its limitations are carefully pointed out. In solvents between 1 M and 5 M-NaCl, the enzyme forms a particle of invariant volume, consisting of a protein dimer (87,000 g mol-1) with which are associated 0.87 g of water and 0.35 g of salt per gram of protein. The partial specific volume of the protein calculated from the combined experimental data is 0.753(+/- 0.030) cm3 g-1, in good agreement with the value calculated from the amino acid composition. The particle has a radius of gyration of 32 A and an equivalent Stokes radius of 43 A. By combining the data from the X-ray and neutron scattering studies, the radii of gyration of the protein moiety alone and of the associated water and salt distribution were calculated. They are 28 A and about 40 A, respectively. The large-angle scattering curves show that the shapes of the particle and of the protein moiety alone are similar. At very low resolution they can be approximated by an ellipsoid of axial ratio 1:1:0.6 (or 1:1:1.5). At higher resolution, it becomes apparent that the particle has a significantly larger interface with solvent than an homogeneous ellipsoid or globular protein. The model has a globular protein core similar to non-halophilic malate dehydrogenase, with about 20% of the protein extending loosely out of the core, forming the large interface with solvent. The main interactions with water and salt take place on this outer part.     

Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations

Visualization of double stranded DNA in gels with the binding of the fluorescent dye ethidium bromide has been a basic experimental technique in any molecular biology laboratory for >40 years. The interaction between ethidium and double stranded DNA has been observed to be an intercalation between base pairs with strong experimental evidence. This presents a unique opportunity for computational chemistry and biomolecular simulation techniques to benchmark and assess their models in order to see if the theory can reproduce experiments and ultimately provide new insights. We present molecular dynamics simulations of the interaction of ethidium with two different double stranded DNA models. The first model system is the classic sequence d(CGCGAATTCGCG)₂ also known as the Drew–Dickerson dodecamer. We found that the ethidium ligand binds mainly stacked on, or intercalated between, the terminal base pairs of the DNA with little to no interaction with the inner base pairs. As the intercalation at the terminal CpG steps is relatively rapid, the resultant DNA unwinding, rigidification, and increased stability of the internal base pair steps inhibits further intercalation. In order to reduce these interactions and to provide a larger groove space, a second 18-mer DNA duplex system with the sequence d(GCATGAACGAACGAACGC) was tested. We computed molecular dynamics simulations for 20 independent replicas with this sequence, each with ∼27 μs of sampling time. Results show several spontaneous intercalation and base-pair eversion events that are consistent with experimental observations. The present work suggests that extended MD simulations with modern DNA force fields and optimized simulation codes are allowing the ability to reproduce unbiased intercalation events that we were not able to previously reach due to limits in computing power and the lack of extensively tested force fields and analysis tools.     

Interaction rates,vital rates,background fitness and replicator dynamics: how to embed evolutionary game structure into realistic population dynamics

In this paper we are concerned with how aggregated outcomes of individual behaviours, during interactions with other individuals (games) or with environmental factors, determine the vital rates constituting the growth rate of the population. This approach needs additional elements, namely the rates of event occurrence (interaction rates). Interaction rates describe the distribution of the interaction events in time, which seriously affects the population dynamics, as is shown in this paper. This leads to the model of a population of individuals playing different games, where focal game affected by the considered trait can be extracted from the general model, and the impact on the dynamics of other events (which is not neutral) can be described by an average background fertility and mortality. This leads to a distinction between two types of background fitness, strategically neutral elements of the focal games (correlated with the focal game events) and the aggregated outcomes of other interactions (independent of the focal game). The new approach is useful for clarification of the biological meaning of concepts such as weak selection. Results are illustrated by a Hawk–Dove example.     

The Fusion of Membranes and Vesicles: Pathway and Energy Barriers from Dissipative Particle Dynamics

The fusion of lipid bilayers is studied with dissipative particle dynamics simulations. First, to achieve control over membrane properties, the effects of individual simulation parameters are studied and optimized. Then, a large number of fusion events for a vesicle and a planar bilayer are simulated using the optimized parameter set. In the observed fusion pathway, configurations of individual lipids play an important role. Fusion starts with individual lipids assuming a splayed tail configuration with one tail inserted in each membrane. To determine the corresponding energy barrier, we measure the average work for interbilayer flips of a lipid tail, i.e., the average work to displace one lipid tail from one bilayer to the other. This energy barrier is found to depend strongly on a certain dissipative particle dynamics parameter, and, thus, can be adjusted in the simulations. Overall, three subprocesses have been identified in the fusion pathway. Their energy barriers are estimated to lie in the range 8-15 k_BT. The fusion probability is found to possess a maximum at intermediate tension values. As one decreases the tension, the fusion probability seems to vanish before the tensionless membrane state is attained. This would imply that the tension has to exceed a certain threshold value to induce fusion.