Circular proteins in plants - Solution structure of a novel macrocyclic trypsin inhibitor from Momordica cochinchinensis

Much interest has been generated by recent reports on the discovery of circular (i.e. head-to-tail cyclized) proteins in plants. Here we report the three-dimensional structure of one of the newest such circular proteins, MCoTI-II, a novel trypsin inhibitor from Momordica cochinchinensis, a member of the Cucurbitaceae plant family. The structure consists of a small beta -sheet, several turns, and a cystine knot arrangement of the three disulfide bonds. Interestingly, the molecular topology is similar to that of the plant cyclotides (Craik, D. J., Daly, N. L., Bond, T., and Waine, C. (1999) J. Mol. Biol, 294, 1327-1336), which derive from the Rubiaceae and Violaceae plant families, have antimicrobial activities, and exemplify the cyclic cystine knot structural motif as part of their circular backbone. The sequence, biological activity, and plant family of MCoTI-II are all different from known cyclotides. However, given the structural similarity, cyclic backbone, and plant origin of MCoTI-II, we propose that MCoTI-II can be classified as a new member of the cyclotide class of proteins. The expansion of the cyclotides to include trypsin inhibitory activity and a new plant family highlights the importance and functional variability of circular proteins and the fact that they are more common than has previously been believed, Insights into the possible roles of backbone cyclization have been gained by a comparison of the structure of MCoTI-II with the homologous acyclic trypsin inhibitors CMTI-I and EETI-II from the Cucurbitaceae plant family.

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Analytical solution to the zero-inertia problem for surge flow phenomena in nonprismatic channels

Surge flow phenomena. e.g.. as a consequence of a dam failure or a flash flood, represent free boundary problems. ne extending computational domain together with the discontinuities involved renders their numerical solution a cumbersome procedure. This contribution proposes an analytical solution to the problem, It is based on the slightly modified zero-inertia (ZI) differential equations for nonprismatic channels and uses exclusively physical parameters. Employing the concept of a momentum-representative cross section of the moving water body together with a specific relationship for describing the cross sectional geometry leads, after considerable mathematical calculus. to the analytical solution. The hydrodynamic analytical model is free of numerical troubles, easy to run, computationally efficient. and fully satisfies the law of volume conservation. In a first test series, the hydrodynamic analytical ZI model compares very favorably with a full hydrodynamic numerical model in respect to published results of surge flow simulations in different types of prismatic channels. In order to extend these considerations to natural rivers, the accuracy of the analytical model in describing an irregular cross section is investigated and tested successfully. A sensitivity and error analysis reveals the important impact of the hydraulic radius on the velocity of the surge, and this underlines the importance of an adequate description of the topography, The new approach is finally applied to simulate a surge propagating down the irregularly shaped Isar Valley in the Bavarian Alps after a hypothetical dam failure. The straightforward and fully stable computation of the flood hydrograph along the Isar Valley clearly reflects the impact of the strongly varying topographic characteristics on the How phenomenon. Apart from treating surge flow phenomena as a whole, the analytical solution also offers a rigorous alternative to both (a) the approximate Whitham solution, for generating initial values, and (b) the rough volume balance techniques used to model the wave tip in numerical surge flow computations.

Conformations of platypus venom C-type natriuretic peptide in aqueous solution and sodium dodecyl sulfate micelles

Nuclear magnetic resonance spectroscopy was used to investigate the conformations of the platypus venom C-type natriuretic peptide A (OvCNPa) in aqueous solutions and in solutions containing sodium dodecyl sulfate (SDS) micelles. The chemically synthesized OvCNPa showed a substantial decrease in flexibility in aqueous solution at 10 degreesC, allowing the observation of medium- and long-range nuclear Overhauser enhancement (NOE) connectivities. Three-dimensional structures calculated using these data showed flexible and reasonably well-defined regions, the locations of which were similar in the two solvents. In aqueous solution, the linear part that spans residues 3-14 was basically an extended conformation while the cyclic portion, defined by residues 23-39, contained a series of beta-turns. The overall shape of the cyclic portion was similar to that observed for an atrial natriuretic peptide (ANP) variant in aqueous solution. OvCNPa adopted a different conformation in SDS micelles wherein the N-terminal region, defined by residues 2-10, was more compact, characterised by turns and a helix, while the cyclic region had turns and an overall shape that was fundamentally different from those structures observed in aqueous solution. The hydrophobic cluster, situated at the centre of the ring of the structure in aqueous solution, was absent in the structure in the presence of SDS micelles. Thus, OvCNPa interacts with SDS micelles and can possibly form ion-channels in cell membranes. (C) 2002 Elsevier Science Ltd. All rights reserved.

Analytical solution for tidal propagation in a coupled semi-confined/phreatic coastal aquifer

An analytical solution is derived for tidal fluctuations in a coupled coastal aquifer system consisting of a semi-confined aquifer, a thin semi-permeable layer and a phreatic aquifer. Based on the solution, we study the interactions (via leakage) between the confined and unconfined aquifers in response to tides. The results show that, under certain conditions, leakage from the confined aquifer can affect considerably the tidal water table fluctuation in the phreatic aquifer and vice versa. Ignoring these effects could lead to errors in estimating aquifer properties based on tidal signals. (C) 2002 Elsevier Science Ltd. All rights reserved.

A director theory for visco-elastic folding instabilities in multilayered rock

A model for finely layered visco-elastic rock proposed by us in previous papers is revisited and generalized to include couple stresses. We begin with an outline of the governing equations for the standard continuum case and apply a computational simulation scheme suitable for problems involving very large deformations. We then consider buckling instabilities in a finite, rectangular domain. Embedded within this domain, parallel to the longer dimension we consider a stiff, layered beam under compression. We analyse folding up to 40% shortening. The standard continuum solution becomes unstable for extreme values of the shear/normal viscosity ratio. The instability is a consequence of the neglect of the bending stiffness/viscosity in the standard continuum model. We suggest considering these effects within the framework of a couple stress theory. Couple stress theories involve second order spatial derivatives of the velocities/displacements in the virtual work principle. To avoid C-1 continuity in the finite element formulation we introduce the spin of the cross sections of the individual layers as an independent variable and enforce equality to the spin of the unit normal vector to the layers (-the director of the layer system-) by means of a penalty method. We illustrate the convergence of the penalty method by means of numerical solutions of simple shears of an infinite layer for increasing values of the penalty parameter. For the shear problem we present solutions assuming that the internal layering is oriented orthogonal to the surfaces of the shear layer initially. For high values of the ratio of the normal-to the shear viscosity the deformation concentrates in thin bands around to the layer surfaces. The effect of couple stresses on the evolution of folds in layered structures is also investigated. (C) 2002 Elsevier Science Ltd. All rights reserved.

Estimation of crystalline phase present in the glucose crystal-solution mixture by water activity measurement

The amount of crystalline fraction present in monohydrate glucose crystal-solution mixture up to 110% crystal in relation to solution (crystal:solution=110:100) was determined by water activity measurement. It was found that the water activity had a strong linear correlation (R-2=0.994) with the amount of glucose present above saturation. Difference in the water activities of the crystal-solution mixture (a(w1)) and the supersaturated solution (a(w2)) by re-dissolving the crystalline fraction allowed calculation of the amount of crystalline phase present (DeltaG) in the mixture by an equation DeltaG=846.97(a(w1)-a(w2)). Other methods such as Raoult's, Norrish and Money-Born equations were also tested for the prediction of water activity of supersaturated glucose solution. (C) 2003 Swiss Society of Food Science and Technology. Published by Elsevier Science Ltd. All rights reserved.

Seedling responses of four Australian tree species to toxic concentrations of manganese in solution culture

Little is known about the responses of Australian plants to excess metal, including Mn. It is important to remedy this lack of information so that knowledgeable decisions can be made about managing Mn contaminated sites where inhabited by Australian vegetation. Acacia holosericea, Melaleuca leucadendra, Eucalyptus crebra and Eucalyptus camaldulensis were grown in dilute solution culture for 10 weeks. The seedlings ( 42 days old) were exposed to six Mn treatments viz., 1, 8, 32, 128, 512 and 2048 muM. The order of tolerance to toxic concentrations of Mn was A. holosericea congruent to = E. crebra < M. leucadendra < E. camaldulensis, the critical external concentrations being approximately 5.1, 5.0, 21 and 330 muM, respectively. The critical tissue Mn concentrations for the youngest fully expanded leaf and total shoots were, respectively, 265 and 215 mug g(-1) DM for A. holosericea, 445 and 495 mug g(-1) DM for M. leucadendra, 495 and 710 mug g(-1) DM for E. crebra and 7230 and 6510 mug g(-1) DM for E. camaldulensis. The high tolerance of E. camaldulensis ( as opposed to the sensitivity of E. crebra) to excess Mn raises concern about fauna feeding on the plant and is consistent with hypotheses suggesting the Eucalyptus subgenus Symphomyrtus is particularly tolerant of stress, including excess Mn. The results from this paper provide the first comprehensive combination of growth responses, critical external concentrations, critical tissue concentrations and plant toxicity symptoms for three important Australian genera, viz., Eucalyptus, Acacia and Melaleuca, for use in the management of Mn toxic sites.

Effect of honey types and concentration on starch gelatinization

The complex and variable composition of honey, depending on source, season and processing, means different honey samples could cause variation in the characteristics of the finished product. The objective of this study was to determine how the minor components present in honey affect starch gelatinization. A Rapid Visco Analyser was used to measure changes in viscosity when unmodified maize starch was gelatinized in a honey or model sugar solution. When honey was compared to equivalent blends of sugars, there was an increase in starch viscosity with increasing levels of addition. However, at the same level, honey gave a lower viscosity than the blends of sugars. Honeys from different sources (differing in pH and amylase activity) show a varied effect on starch gelatinization, with starch viscosity increasing with addition level for six of the honeys, but decreasing with increasing addition level for two honey samples. Varying the pH also produced variation in starch gelatinization patterns between honey types. Between pH 3.0 and 4.0, starch viscosity was similar for all four honey types studied, while above this pH there were differences between all honey types. As expected, starch viscosity decreased as the solution pH neared the optimum for honey amylase activity (pH 5.3-5.6), though it did not increase as the pH moved away from the honey amylase activity optimum. Differences between honey samples, and between honey and a model sugar mixture, in their effect on starch gelatinization was attributed to honey amylase activity and the composition and concentration of minor organic compounds present. Crown Copyright (C) 2003 Published by Elsevier Ltd. on behalf of Swiss Society of Food Science and Technology

Stability property of matchings is a natural solution concept in coalitional market games

Stability of matchings was proved to be a new cooperative equilibrium concept in Sotomayor (Dynamics and equilibrium: essays in honor to D. Gale, 1992). That paper introduces the innovation of treating as multi-dimensional the payoff of a player with a quota greater than one. This is done for the many-to-many matching model with additively separable utilities, for which the stability concept is defined. It is then proved, via linear programming, that the set of stable outcomes is nonempty and it may be strictly bigger than the set of dual solutions and strictly smaller than the core. The present paper defines a general concept of stability and shows that this concept is a natural solution concept, stronger than the core concept, for a much more general coalitional game than a matching game. Instead of mutual agreements inside partnerships, the players are allowed to make collective agreements inside coalitions of any size and to distribute his labor among them. A collective agreement determines the level of labor at which the coalition operates and the division, among its members, of the income generated by the coalition. An allocation specifies a set of collective agreements for each player.

The pareto-stability concept is a natural solution concept for discrete matching markets with indifferences

In a decentralized setting the game-theoretical predictions are that only strong blockings are allowed to rupture the structure of a matching. This paper argues that, under indifferences, also weak blockings should be considered when these blockings come from the grand coalition. This solution concept requires stability plus Pareto optimality. A characterization of the set of Pareto-stable matchings for the roommate and the marriage models is provided in terms of individually rational matchings whose blocking pairs, if any, are formed with unmatched agents. These matchings always exist and give an economic intuition on how blocking can be done by non-trading agents, so that the transactions need not be undone as agents reach the set of stable matchings. Some properties of the Pareto-stable matchings shared by the Marriage and Roommate models are obtained.

Integrability and exact solution of an electronic model with long range interactions

We present an electronic model with long range interactions. Through the quantum inverse scattering method, integrability of the model is established using a one-parameter family of typical irreducible representations of gl(211). The eigenvalues of the conserved operators are derived in terms of the Bethe ansatz, from which the energy eigenvalues of the Hamiltonian are obtained.

Generation of Naphthoquinone Radical Anions by Electrospray Ionization: Solution, Gas-Phase, and Computational Chemistry Studies

Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(center dot-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q + 15](-) was described as being a reaction between the solvent system and the radical anion, Q(center dot-).The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses.