ProPose: a docking engine based on a fully configurable protein–ligand interaction model

Virtual high-throughput screening of molecular databases and in particular high-throughput protein–ligand docking are both common methodologies that identify and enrich hits in the early stages of the drug design process. Current protein–ligand docking algorithms often implement a program-specific model for protein–ligand interaction geometries. However, in order to create a platform for arbitrary queries in molecular databases, a new program is desirable that allows more manual control of the modeling of molecular interactions.For that reason, ProPose, an advanced incremental construction docking engine, is presented here that implements a fast and fully configurable molecular interaction and scoring model. This program uses user-defined, discrete, pharmacophore-like representations of molecular interactions that are transformed on-the-fly into a continuous potential energy surface, allowing for the incorporation of target specific interaction mechanisms into docking protocols in a straightforward manner. A torsion angle library, based on semi-empirical quantum chemistry calculations, is used to provide minimum energy torsion angles for the incremental construction algorithm. Docking results of a diverse set of protein–ligand complexes from the Protein Data Bank demonstrate the feasibility of this new approach.As a result, the seamless integration of pharmacophore-like interaction types into the docking and scoring scheme implemented in ProPose opens new opportunities for efficient, receptor-specific screening protocols. Figure ProPose — a fully configurable protein-ligand docking program — transforms pharmacophores into a smooth potential energy surface.This revised version was published online in October 2004 with corrections to the Graphical Abstract.     

Fluid–structure interaction in a fully coupled three-dimensional mitral–atrium–pulmonary model

This paper aims to investigate detailed mechanical interactions between the pulmonary haemodynamics and left heart function in pathophysiological situations (e.g. atrial fibrillation and acute mitral regurgitation). This is achieved by developing a complex computational framework for a coupled pulmonary circulation, left atrium and mitral valve model. The left atrium and mitral valve are modelled with physiologically realistic three-dimensional geometries, fibre-reinforced hyperelastic materials and fluid–structure interaction, and the pulmonary vessels are modelled as one-dimensional network ended with structured trees, with specified vessel geometries and wall material properties. This new coupled model reveals some interesting results which could be of diagnostic values. For example, the wave propagation through the pulmonary vasculature can lead to different arrival times for the second systolic flow wave (S2 wave) among the pulmonary veins, forming vortex rings inside the left atrium. In the case of acute mitral regurgitation, the left atrium experiences an increased energy dissipation and pressure elevation. The pulmonary veins can experience increased wave intensities, reversal flow during systole and increased early-diastolic flow wave (D wave), which in turn causes an additional flow wave across the mitral valve (L wave), as well as a reversal flow at the left atrial appendage orifice. In the case of atrial fibrillation, we show that the loss of active contraction is associated with a slower flow inside the left atrial appendage and disappearances of the late-diastole atrial reversal wave (AR wave) and the first systolic wave (S1 wave) in pulmonary veins. The haemodynamic changes along the pulmonary vessel trees on different scales from microscopic vessels to the main pulmonary artery can all be captured in this model. The work promises a potential in quantifying disease progression and medical treatments of various pulmonary diseases such as the pulmonary hypertension due to a left heart dysfunction.

     

Is a fluid-mosaic model of biological membranes fully relevant? Studies on lipid organization in model and biological membranes

The basic concept of the fluid-mosaic model of Singer and Nicolson, an essential point of which is that the membrane proteins are floating in a sea of excess lipid molecules organized in the lipid bilayer, may be misleading in understanding the movement of membrane components in biological membranes that show distinct domain structure. It seems that the lipid bilayer is an active factor in forming the membrane structure, and the lipid composition is responsible for the presence of domains in the membrane. The main role in the process of domain formation is played by cholesterol and sphingolipids. The results presented here show that in a binary mixture of cholesterol and unsaturated phospholipids, cholesterol is segregated out from the bulk unsaturated liquid-crystalline phase. This forms cholesterol-enriched domains or clustered cholesterol domains due to the lateral nonconformability between the rigid planar ring structure of cholesterol and the rigid bend of the unsaturated alkyl chain at double bond position. These cholesterol-enriched domains may be stabilized by the presence of saturated alkyl chains of sphingomyelin or glycosphingolipids, and also by specific proteins which selectively locate in these domains and stabilize them as a result of protein-protein interaction. Such lipid domains are called "rafts" and have been shown to be responsible both for signal transduction to and from the cell and for protein sorting. We also looked at whether polar carotenoids, compounds showing some similarities to cholesterol and affecting membrane properties in a similar way, would also promote domain formation and locate preferentially in one of the lipid phases. Our preliminary data show that in the presence of cholesterol, lutein (a polar carotenoid) may segregate out from saturated lipid regions (liquid-ordered phase) and accumulate in the regions rich in unsaturated phospholipids forming carotenoid-rich domains there. Conventional and pulse EPR (electron paramagnetic resonance) spin labeling techniques were employed to assess the molecular organization and dynamics of the raft-constituent molecules and of the raft itself in the membrane.     

Studies on the oxidation–reduction systems of the erythrocyte

1. Starvation for 3 days produces a decrease in methaemoglobin-reductase and glutathione-reductase activities, but it does not alter the glucose 6-phosphate-dehydrogenase activity of the rat erythrocyte. 2. The feeding of a protein-free diet for 11 days causes greater changes in the first two enzymes and also a diminution of the third. Under this experimental condition slight decreases in protein and haemoglobin contents were noted. 3. The experimental animals did not show methaemoglobinaemia, probably because the activity of methaemoglobin diaphorase is preserved. 4. The GSH content was not affected but the stability of the tripeptide in the presence of an oxidizing agent was diminished.     

Microscopical and Spectroscopic Studies on the Fluorescence of a Daunomycin–aluminum Complex

In this study, the spectroscopic features and microscopical applications of the fluorescent daunomycin-Al3+ complex have been analyzed. In the presence of Al3+, the absorption spectrum of daunomycin showed a deep bathochromic shift and new peaks at 529 and 566nm, whereas the fluorescence emission was considerably modified. The emission of daunomycin alone (peak at 560nm under optimal excitation at 470nm) decreased continuously from 0.5 to 24h after addition of Al3+ ions, and a new emission peak appeared at 580nm (optimal excitation at 530nm). Under the fluorescence microscope using green exciting light, nuclei from chicken blood smears and paraffin sections of rat embryos stained with daunomycin showed a weak emission, which greatly increased after treatment with Al3+ ions. The bright and stable fluorescence of chromatin DNA induced by daunomycin-Al3+ could be a valuable labelling method in fluorescence microscopy and DNA cytochemistry.     

Studies on the cyanophytes of Cuba 4–6

The article comprises three subsequently published studies of the taxonomy of Cuban cyanophyte/cyanobacterial flora: (4)Lyngbyopsis willei: This oscillatorialean genus and species, described byGardner (1927) from mountain creeks in Puerto Rico, was found more than 50 years later in similar localities in Cuba. The morphological variability of the Cuban populations is described and similarity with the genusSchizothrix (sect.Inactis) discussed. —(5)Cylindrospermum-species: The morphological variability of twenty-oneCylindrospermum-populations collected in Cuba was studied, documented by graphical methods and compared with the published data. Four new taxa were recognized (C. minutissimum v.rinoi, C. zonatum, C. bourrellyi, andC. desikacharyi). The other populations belong to the variation ranges ofC. breve, C. minutissimum, C. michailovskoense, andC. muscicola v.kashmiriense.— (6)Gomphosphaerioideae-species: Fifty eight populations (9 species) of the subfamilyGomphosphaerioideae (Microcystaceae, Chroococcales) from freshwater biotopes of Cuba were evaluated: Four planktic species with a probable cosmopolitan distribution were found (Coelosphaerium kuetzinginianum, C. minutissimum, Snowella lacustris andCoelomoron pusillus), and from the genusCoelomoron Buell two new species,C. microcystoides andC. vestitus were described. The tropical planktic speciesWoronichinia fremyi forms occasionally water blooms in larger reservoirs. Two tropical species from the genusGomphosphaeria Kütz, were recognized,G. multiplex (Nyg.) c. n. andG. semen-vitis sp. n.     

Red blood cell simulation using a coupled shell–fluid analysis purely based on the SPH method

Biomechanics and Modeling in Mechanobiology - In this paper, a novel 3D numerical method has been developed to simulate red blood cells (RBCs) based on the interaction between a shell-like solid...     

Studies on the UV spectrum of poly(γ-glutamic acid) based on development of a simple quantitative method

A simple and valid ultraviolet (UV) spectrophotometric method for the determination of poly(γ-glutamic acid) is developed. The method is based on the UV absorption spectrum of γ-PGA in aqueous solution, which exhibits a maximum absorption wavelength at 216 nm. The results obtained were comparable to those obtained with the reported high-performance liquid chromatography (HPLC) method according to ICH guidelines. Under the proposed procedure, the calibration graph is linear over the range of 20-200 μg/ml with regression correlation coefficient of 0.9997. Precision (%R.S.D.<1.50) and recovery (%R.>99.29%) are good. The limit of detection (LOD) and limit of quantitation (LOQ) are 0.39 and 1.19 μg/ml, respectively. These results agree well with those of HPLC method. Its spectrum properties studies showed that the spectrum of γ-PGA remarkably changed with an increase in temperature due to γ-PGA was digested into glutamate monomer. In spite of this, the determining procedure could carried out in a wide temperature range (25-50°C). In addition, the method is not influenced by the molecular weight, but the measurement system need to control in pH 3.0-10.0 and ionic strength not more than 0.5M. The proposed method is applied successfully for high-throughput quantification of poly(γ-glutamic acid) in biological samples. The advantages of the UV method are simplicity of operation, rapidity, sensitive, low-cost and high-throughput.     

A stochastic model for the spatial distribution of species based on an aggregation–repulsion rule

The heterogeneity associated with the spatial distribution of organisms is an awkward problem in ecology because this heterogeneity directly depends on the sampling scale. To specify the scope of the influence of sampling scale on the level of species aggregation, we need data sets that entail excessive sampling costs in situ. To find a solution for this problem, we can use models to simulate patterns of organisms. These models are often very complex models that take into account heterogeneity of habitats and displacement or longevity of studied species. In this article, we introduce a new stochastic model to simulate patterns for one taxon and we want this model to be parsimonious, i.e., with few parameters and able to simulate observed patterns. This model is based on an aggregation–repulsion rule. This aggregation–repulsion rule is defined by two parameters. On a large scale, the number of aggregates present on the pattern is the first parameter. On a smaller scale, the level of aggregation–repulsion among individuals is determined by a probability distribution. These two parameters are estimated from field data set in a robust way so that the simulated patterns reflect the observed heterogeneity. We apply this model to entomological data: four Diptera families, namely the Sciaridae, Phoridae, Cecidomyiidae, and Empididae. The field data for the Phoridae family are used to simulate sampling using different trap sizes. We record changes in the coefficient of variation (C) as a function of the sampling scale, and we can suggest to ecologists emergence traps of 0.6 m², in other words a square 77 × 77 cm trap, to obtain a C value under 20%. Received: February 28, 2000 / Accepted: October 14, 2000     

Poincaré plot interpretation using a physiological model of HRV based on a network of oscillators

In this paper, we develop a physiological oscillator model of which the output mimics the shape of the R-R interval Poincaré plot. To validate the model, simulations of various nervous conditions are compared with heart rate variability (HRV) data obtained from subjects under each prescribed condition. For a variety of sympathovagal balances, our model generates Poincaré plots that undergo alterations strongly resembling those of actual R-R intervals. By exploiting the oscillator basis of our model, we detail the way that low- and high-frequency modulation of the sinus node translates into R-R interval Poincaré plot shape by way of simulations and analytic results. With the use of our model, we establish that the length and width of a Poincaré plot are a weighted combination of low- and high-frequency power. This provides a theoretical link between frequency-domain spectral analysis techniques and time-domain Poincaré plot analysis. We ascertain the degree to which these principles apply to real R-R intervals by testing the mathematical relationships on a set of data and establish that the principles are clearly evident in actual HRV records.     

A process-based coupled model of stomatal conductance–photosynthesis–transpiration during leaf ontogeny for water-saving irrigated rice

Photosynthesis Research - Process-based coupled model of stomatal conductance–photosynthesis–transpiration was developed to estimate simultaneously stomatal conductance gsw,...     

Studies on the boronation of methyl-β-d-cellobioside—a cellulose model

The conversion of phenylboronic acid (PBA) with methyl-β-d-cellobioside (Me-β-d-clb) and cellodextrins (DP_w 12) was investigated to gain a basic understanding of the interactions of boric acid derivatives with oligo- and polyglucans. By means of MS and NMR experiments, it was possible to show a first stage formation of a six-membered ring at C-4 and C-6 of the non-reducing glucose occurs as in the case of monosaccharides. If the amount of reagent is increased the formation of seven-membered rings at the secondary OH moieties is observed. Even the existence of two of these large ring-systems in the direct neighborhood was found. Application of an excess of boronation reagent led to dimerization reactions of Me-β-d-clb via the primary reducing glucose residue as confirmed by DOSY NMR studies. Preliminary ¹³C NMR studies for the interaction of cellodextrins with PBA in DMSO solution confirmed a functionalization at the trans-1,2-diol moieties of these oligomers. The amount of reagent applied may either was shown to lead to soluble products or to insoluble cross-linked material.     

Studies on the Effect of Water-Soluble Polymers on Drug–Cyclodextrin Complex Solubility

The effect of complexation of irbesartan (IRB), a practically water-insoluble drug, with cyclodextrins in presence of different concentrations of water-soluble polymers (PEG 4000 and PVP K-90) on the dissolution rate of the drug has been investigated. Phase solubility studies were carried out to evaluate the solubilizing power of βCD in association with water-soluble polymers towards IRB and to determine the apparent stability constant (K _S) of the complexes. Improvement in K _S value for ternary complexes (IRB–βCD–polymers) clearly proved the benefit on the addition of water-soluble polymer to increase complexation efficiency. The dissolution rate of the drug from ternary systems containing PEG 4000 and PVP K-90 was higher as compared to the binary system. An optimum increase in the dissolution rate of the drug was observed at a polymer concentration of 5% w/w for PVP K-90 and 10% w/w for PEG 4000. DSC, FTIR, SEM, and XRD studies were carried out to characterize the complexes.     

Remarks on the number of persistent states to a fragmented predator–prey model system

We consider a predator–prey model system for spatially distributed species over patches. Each predator species has a unique preferred patch (shelter and reproduction site) and travel for chasing prey. Its individuals are split into resident from the preferred patch and travelers. Further there is at most one resident predator species per patch. Depending on the availability of local anthropized resources not related to local prey on the preferred patch, one distinguishes between well-fed and starving predators. We assume prey species do not disperse at the predator scale.In this study we are interested in the number of persistent stationary states for the resulting ordinary differential equations model system. There exists at most one persistent predator–prey stationary state when there is exactly one starving resident predators per patch provided all functional responses to predation are Lotka–Volterra like or when a single starving resident predators is available. Else multiple persistent predator–prey stationary state are likely to exist. A specific emphasis is put on toy-model systems with 2 or 3 patches. Slow–fast dynamical methodology is also used for locally asymptotically stable purposes.Numerical experiments suggest that several scalings may govern the dynamics at stabilization.     

Studies on the mechanism of estrogen biosynthesis in the rat ovary–I

Methods were evaluated for obtaining a reliable, active estrogen synthetase (aromatase) system from the rat ovary for mechanistic studies. Short terrn treatment with luteinizing hormone and follicle stimulating hormone in various combinations did not produce appreciable stimulation, whereas long term treatment (8–16 days) with pregnant mare's serum gonadotropin increased activity in homogenates up to nine fold per mg wet wt of tissue. A similar increase per mg protein was noted in the 105,000_g microsomal fraction where the bulk of the activity was found. Various conditions for preparing and incubating the aromatase were evaluated to obtain optimal enzyme activity. The potencies of six steroids as aromatase inhibitors were compared in the rat ovarian and human placental microsomal systems. In all cases except one the results were comparable.