Simulation of diffusion time of small molecules in protein crystals

A simple model for evaluation of diffusion times of small molecule into protein crystals has been developed, which takes into account the physical and chemical properties both of protein crystal and the diffusing molecules. The model also includes consideration of binding and the binding affinity of a ligand to the protein. The model has been validated by simulation of experimental set-ups of several examples found in the literature. These experiments cover a wide range of situations: from small to relatively large diffusing molecules, crystals having low, medium, or high protein density, and different size. The reproduced experiments include ligand exchange in protein crystals by soaking techniques. Despite the simplifying assumptions of the model, theoretical and experimental data are in agreement with available data, with experimental diffusion times ranging from a few seconds to several hours. The method has been used successfully for planning intermediate cryotrapping experiments in maltodextrin phosphorylase crystals.     

An approach in mathematical modeling of an upflow packed-bed reactor for enzymatic hydrolysis of wheat straw

The behavior of a packed-bed reactor for enzymatic hydrolysis of pretreated wheat straw has been described by means of a mathematical model. The flow pattern has been evaluated by residence time distribution experiments. Small deviations from ideal plug flow behavior were found using the dispersion model. The kinetic model proposed for enzymatic hydrolysis of cellulosic fraction of pretreated wheat straw has been derived from batch experimental data. Variations of enzyme concentration throughout the straw bed have been approximately described using a ramp variation of adsorbed enzyme. The final explains qualitatively the experimental results.     

The human thermoregulation range within the neutral zone.

A mathematical and physical model of thermoregulatory mechanisms has been derived and experimental data are presented for the elements of the model. The thermoregulatory range within the neutral zone has been analyzed by regression analysis of the experimental data. The optimal globe temperature and the adaptational shifts in temperature for winter and summer are also given.     

Multiplicity of auto-oscillations and steady states in an open reaction catalyzed by E. coli phosphofructokinase. Quantitative model

A quantitative mathematical model of two-substrate reaction catalized by phosphofructokinase from E. coli has been investigated. The model takes into account the tetrameric enzyme structure and resulting kinetic peculiarities of the reaction catalized, in particular, iso-and alosteric effects of ADP on enzyme activity. Fitting of the model parameters to experimental data allowed to approximate these data with good accuracy. The ranges of admitted rates of fructose-6-phosphate input and ATP regeneration at which autooscillations and multiple steady-states occur in the system have been calculated. A minimal open system with three enzymes has been proposed for experimental demonstration of the autooscillatory behaviour.     

Homology modelling of the human eukaryotic initiation factor 5A (eIF-5A).

Homology modelling of the human eIF-5A protein has been performed by using a multiple predictions strategy. As the sequence identity between the target and the template proteins is nearly 30%, which is lower than the commonly used threshold to apply with confidence the homology modelling method, we developed a specific predictive scheme by combining different sequence analyses and predictions, as well as model validation by comparison to structural experimental information. The target sequence has been used to find homologues within sequence databases and a multiple alignment has been created. Secondary structure for each single protein has been predicted and compared on the basis of the multiple sequence alignment, in order to evaluate and adjust carefully any gap. Therefore, comparative modelling has been applied to create the model of the protein on the basis of the optimized sequence alignment. The quality of the model has been checked by computational methods and the structural features have been compared to experimental information, giving us a good validation of the reliability of the model and its correspondence to the protein structure in solution. Last, the model was deposited in the Protein Data Bank to be accessible for studies on the structure-function relationships of the human eIF-5A.     

Sticky chain model for shear response of red blood cells

A sticky chain model has been proposed to describe the unfolding of spectrin network under applied mechanical loads. With the model, the response of a red blood cell (RBC) under static and cyclic shear loading has been predicted, which agrees qualitatively with relevant experimental results.     

Kinetic modeling of lactose hydrolysis with an immobilized beta-galactosidase from Kluyveromyces fragilis

The kinetic model of the hydrolysis of lactose with a beta-galactosidase from Kluyveromyces fragilis immobilized on a commercial silica-alumina (KA-3, from Südchemie) has been determined. A wide experimental range of the main variables has been employed: temperature, concentrations of substrate, and products and concentration of enzyme. The runs were performed in a complex buffer with the salt composition of milk. The effect of pH and temperature on the stability and the activity of the enzyme have been studied. The optimum pH for the enzyme activity was, approximately, seven. The immobilized enzyme was more stable than the free one at acidic pH, but more instable at basic pH. The maximum temperature used for the hydrolysis runs performed to select the kinetic model was 40 degrees C, so inactivation of the enzyme during the kinetic runs has been avoided. Agitation, concentration of enzyme in the solid and particle size were selected to ensure that the overall rate was that of the chemical reaction. Eleven kinetic models were proposed to fit experimental data, from first order to more complex ones, such as those taking into account inhibition by one of the compounds involved in the hydrolysis reaction. Applying statistical and physical criteria, a Michaelis-Menten model with a competitive inhibition by galactose has been selected. The model is able to fit the experimental data correctly in the wide experimental range studied. Finally, the model obtained is compared to the one selected in a previous work for the hydrolysis of lactose with the free enzyme.     

A Tissue-Level Electromechanical Model of the Left Ventricle: Application to the Analysis of Intraventricular Pressure

The ventricular pressure profile is characteristic of the cardiac contraction progress and is useful to evaluate the cardiac performance. In this contribution, a tissue-level electromechanical model of the left ventricle is proposed, to assist the interpretation of left ventricular pressure waveforms. The left ventricle has been modeled as an ellipsoid composed of twelve mechano-hydraulic sub-systems. The asynchronous contraction of these twelve myocardial segments has been represented in order to reproduce a realistic pressure profiles. To take into account the different energy domains involved, the tissue-level scale and to facilitate the building of a modular model, multiple formalisms have been used: Bond Graph formalism for the mechano-hydraulic aspects and cellular automata for the electrical activation. An experimental protocol has been defined to acquire ventricular pressure signals from three pigs, with different afterload conditions. Evolutionary Algorithms have been used to identify the model parameters in order to minimize the error between experimental and simulated ventricular pressure signals. Simulation results show that the model is able to reproduce experimental ventricular pressure. In addition, electro-mechanical activation times have been determined in the identification process. For example, the maximum electrical activation time is reached, respectively, 96.5, 139.3 and 131.5 ms for the first, second, and third pigs. These preliminary results are encouraging for the application of the model on non-invasive data like ECG, arterial pressure or myocardial strain.     

Dipalmitoylphosphatidylcholine membranes modified with zeaxanthin: numeric study of membrane organisation

The model of a dipalmitoylphosphatidylcholine (DPPC) bilayer containing a xanthophyll pigment zeaxanthin (ZEA) is proposed. The model is based on the ten-state Pink-Green-Chapman model of a lipid monolayer. The Monte Carlo method of computer simulation has been applied. Our model of the lipid membrane consists of two lipid monolayers with ZEA molecules spanning the lipid bilayer. The concentration of ZEA molecules is assumed to be conserved. Within the model, the interactions between lipid monolayers in a bilayer exist through ZEA molecules only. The experimental data concerning the aggregation of ZEA in DPPC from the literature and from our research were applied as a criterion to fit the model parameters. The model gives the dependences of the main phase transition temperature on ZEA/DPPC molar ratio, the percentage of ZEA in a monomeric form on ZEA/DPPC molar ratio and on temperature. The dependences obtained within the model and the experimental ones are in qualitative agreement. The influence of intermolecular interaction parameters on ZEA aggregation has been discussed. The differences between the model and the experimental results concerning mainly the pattern of ZEA aggregation have been discussed. Analyses of the lipid microconfiguration allow to advance the hypothesis concerning the influence of ZEA on the membrane permeability.     

An allelism test for quantitative trait genes

Analytical modeling has been used to test assumptions on the mode of inheritance of a quantitative trait in the course of diallel crossing between pure lines that are sufficient for adequacy of a simple regression model. This model frequently proved to be adequate in analysis of numerous data on diallel crossings of wheat and maize. An allelism test for quantitative trait genes has been suggested. Computer simulation has been used to estimate the effect of random experimental errors and deviations from the model assumptions.     

Effectiveness of a polyvalent corpuscular Pseudomonas aeruginosa vaccine, antibiotics and their combinations in experimental chronic Pseudomonas aeruginosa infection

The data on the development of the experimental model of P. aeruginosa chronic infection in mice, produced by their intraperitoneal inoculation with the infective agent, and on the study of the properties of this model are presented. The model has been used in the experimental study of the preventive action of P. aeruginosa polyvalent corpuscular vaccine. The comparative study, carried out with the use of the proposed model, has been made with a view to evaluating the effectiveness of different methods for the treatment of P. aeruginosa chronic septic infection by means of antibiotics (polymixin B and tobramycin), P. aeruginosa polyvalent corpuscular vaccine and their combination. The combined use of this vaccine with antibiotics (polymixin B or tobramycin) has proved to give the most pronounced curative effect with respect to P. aeruginosa chronic infection.     

The origin of adaptive mutants: Random or nonrandom?

Several recent reports have claimed that adaptive mutants in bacteria and yeast are induced by selective conditions. The results of these reports suggest that mutants can arise nonrandomly with respect to fitness, contrary to what has been widely accepted. In several cases that have received careful experimental reexamination, however, the detection of seemingly nonrandom mutation has been explained as an experimental artifact. In the remaining cases, there is no evidence to suggest that cells have the capacity to direct or choose which genetic variants will arise. Instead, current models propose processes by which genetic variants persist as mutations only if they enable cell growth and DNA replication. Most of these models are apparently contradicted by experimental data. One model, the hypermutable state model, has recently received limited circumstantial support. However, in this model the origin of adaptive mutants is random; the apparent nonrandomness of mutation is merely a consequence of natural selection. The critical distinction between the origin of genetic variation (mutation) and the possible consequence of that variation (selection) has been neglected by proponents of directed mutation.     

Stochastic simulation of processive and oscillatory sliding using a two-headed model for axonemal dynein

Computer simulations have been used in an attempt to understand experimental observations of processive and oscillatory sliding by one or a few axonemal dyneins. A simple two-headed model has been examined using stochastic simulation methods. To explain the experimental observations, the model must be capable of taking backward steps, as well as forward steps, and there must be hysteresis in switching between forward or backward stepping. When the effects of Brownian movement on motor strain are included, it is not possible to obtain oscillations as regular as the experimental records by using motor strain to regulate switching between forward or backward stepping.     

Computer simulation of complex formation between plastocyanine and cytochrome f in thylakoid lumen

The diffusion of the protein plastocyanine and complex formation between plastocyanine and cytochrome f (a subunit of a cytochrome b6/f complex) in the chloroplast thylakoid lumen has been studied. A 3D computer simulation model of diffusion and binding of plastocyanine and cytochrome f has been constructed, which considers their electrostatic interaction. Based on the experimental data, the parameters of the model for complex formation between plastocyanine and cytochrome f in solution have been estimated. The dependence of the rate of plastocyanine-cytochrome f reaction on the size of the luminal space has been studied. It was shown that the contraction of the luminal space leads to a decrease in the reaction rate, which is in agreement with the experimental data on the inhibition of the reaction under hyperosmotic stress.     

Floral organ identity: 20 years of ABCs

One of the early successes of the application of molecular genetics to study plant development was the discovery of a series of genes that act together, in an apparently simple combinatorial model, to specify the identity of the different organs of a flower. Widely known as the ABC model, this framework for understanding has been investigated and modified over the course of the last two decades. The cast list of genes has been defined and, as other chapters in this volume will show, great progress has been made in understanding how they are regulated, how they act together, what they do and how they have contributed to the evolution of the flower in its varied forms. In this introductory review to the volume we will review the derivation and elaboration of the most current version of the ABC model, highlighting the modifications that have been necessary to ensure it fits the available experimental data. We will highlight the remaining difficulties in fitting the current model to the experimental data and propose a further modification to enable it to regain its applicability.     

Metabolic dynamics in the human red cell. Part IV--Data prediction and some model computations

The biochemical information on the basic cellular determinants of the human red cell has been compiled into a comprehensive model of the red cell metabolic machinery. This model gives a consistent interpretation--both qualitative and quantitative--of the experimental findings. The predicted steady states and the dynamic states of the model are compared with the experimental findings, and the utility of this model is demonstrated.     

A model for the rate of enzymatic hydrolysis of cellulose in heterogeneous solid–liquid systems

Hydrolysis of cellulose by cellulase enzymes has been studied in a stirred batch reactor at 50°C. A kinetic model has been devised by which the behaviour of such a reaction could be described. The model has been developed on the basis of shrinking particle theory and Langmuir isotherm concept. The applicability of the model has been tested by comparing the experimental results for diverse reaction systems, obtained in the present study or taken from the literature, and those predicted from the model. The degree of agreement was within ±2–11%.     

Anion activation of dopamine beta-hydroxylase: a kinetic model

1. A theoretical analysis has been made of the mechanism of anion activation of dopamine beta-hydroxylase on the basis of accumulated experimental data. A model is presented that accounts for the numerous different effects of activating anions on the enzyme kinetics. This model has a general validity, since it holds for any of the kinetic mechanisms thus far proposed for dopamine beta-hydroxylase. 2. It has been shown that the results of this analysis have direct implications for the experimental conditions to be used in the study of the dopamine beta-hydroxylase reaction. 3. The present analysis has proved that, under appropriate assumptions, theoretical treatment of nonessential activation, so far limited to the single-substrate case, can be easily extended to steady-state multireactant enzymes.     

丙型肝炎病毒感染实验动物模型的研究进展

丙型肝炎病毒（HCV）感染是导致人类慢性病毒性肝炎、肝硬化和肝癌的最主要病因之一。由于缺乏合适的HCV感染实验动物模型,使得针对HCV感染更为有效的疗法及疫苗的研发滞后。黑猩猩是HCV感染研究的最佳实验动物,但由于其来源有限、价格昂贵及临床症状等诸多问题,其应用受限,因此发展新的实验动物模型用于HCV感染相关的基础和应用研究迫在眉睫。近年来,以啮齿类等动物为替代模型取得了不少进展,应用转基因等实验技术使替代动物感染了HCV,并成功应用于多个学科领域的研究。本文分析了HCV自然感染的实验动物、自然感染和非自然感染的替代实验动物在致病机制研究、药物评价和疫苗研发应用中的优缺点及未来研究趋势。