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Computer modelling studies of the covalent interactions between DNA and the enantiomers of anti-7,8-diol,9,10-epoxy-benzo[a]pyrene.

The molecular structures of adducts between the + and - enantiomers of 7,8-diol 9,10-epoxy benzo[a]pyrene and a double-stranded model for DNA, have been examined by empirical energy calculations. Low-energy structures were only obtained for A form, and not B form DNA. Both + and - adducts are of approximately equal energy. Some structural differences in the orientation of the BP chromophore in the two adducts were found.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

Binding, internalization, and intracellular processing of protein ligands. Derivation of rate constants by computer modeling.

Information about ligand binding, dissociation, internalization, and intracellular processing and about receptor turnover, processing, and insertion into the membrane is contained in the time-dependent changes in concentrations of membrane-associated and internalized ligand. Single experiments similar in design to those typically performed for Scatchard analyses of binding data conducted at physiological temperature and in the absence of inhibitors of ligand-receptor complex internalization and degradation can provide kinetic data sufficient to permit derivation of all the respective rate constants by numerical methods. We developed an analytical solution of the kinetic model which assumes that all of these processes follow first order kinetics. The model represents interactions of surface receptors (R)s, the surface ligand-receptor complex (LR)s and internalized receptor-ligand complex (LR)I: d[R]S/dt = Vr - kt[R]S - ka[L] [R]S + kd [LR]S; d[LR]S/dt = ka[L] [R]S - kd[LR]S - ke[LR]S; d[LR]I/dt = ke[LR]S - kh[LR]I; Vr is the constant rate of insertion of receptors into the membrane, kt is the internalization rate constant for free receptors, ka and kd are association and dissociation rate constants for ligand-surface receptor interaction, ke is the internalization rate constant for ligand-receptor complexes, and kh is the intracellular ligand decomposition rate constant. The interaction of radioiodinated human recombinant interferon-alpha 2a with the human alveolar lung carcinoma cell line, A549, was adequately accounted for by the model. The rate constants, numerically derived from time-dependent concentrations of surface-bound and internalized ligand of other systems taken from the literature, were in agreement with values of these rate constants individually measured by steady-state experiments. In cases where the fate of internalized radioactivity was more complex than assumed by the model, the parameters ka, kt, (kd + ke) and Vr could be derived from the time dependence of [LR]S.

Adenocarcinoma↗

The role of aspartic acid 143 in E. coli tRNA-guanine transglycosylase: insights from mutagenesis studies and computational modeling.

tRNA guanine transglycosylase (TGT) is a tRNA-modifying enzyme which catalyzes the posttranscriptional exchange of guanine in position 34 of tRNA(Y,H,N,D) with the modified base queuine in eukaryotes or its precursor, preQ(1) base, in eubacteria. Thus, TGT must recognize the guanine in tRNA and the free base queuine or preQ(1) to catalyze this exchange. The crystal structure of Zymomonas mobilis TGT with preQ(1) bound suggests that a key aspartate is critically involved in substrate recognition. To explore this, a series of site-directed mutants of D143 in Escherichia coli TGT were made and characterized to investigate heterocyclic substrate recognition. Our data confirm that D143 has significant impact on K(M) of guanine; however, the trend in the K(M) data (D143A < D143N < D143S < D143T) is unexpected. Computational studies were used to further elucidate the interactions between guanine and the D143 mutants. A homology model of E. coli TGT was created, and the role of D143 was investigated by molecular dynamic simulations of guanine bound to the wild-type and D143-mutant TGTs. To validate the model systems against our kinetic data, free energies of binding were fit using the linear interaction energy (LIE) method. This is a unique application of the LIE method because the same ligand is bound to several mutant proteins rather than one protein binding several ligands. The atomic detail gained from the simulations provided a better understanding of the binding affinities of guanine with the mutant TGTs, revealing that water molecules enter the active site and hydrogen bond to the ligand and compensate for lost protein-ligand interactions. The trend of binding affinity for wild-type > D143A > D143N > D143S > D143T appears to be directly related to the degree of hydrogen bonding available to guanine in the binding site.

Aspartic Acid↗

Computer modelling of aldosterone regulation in patients on regular hemodialysis.

To evaluate the relative influence of changes in plasma renin activity, potassium, ACTH, and sodium concentrations on the secretion of aldosterone, a multifactorial analysis was performed on different sets of investigations in anephric as well as non-nephrectomized patients on regular hemodialysis. During steady-state conditions the relationship between the stimulating effect of each of these factors and combinations between these factors and the resultant plasma aldosterone concentration was analyzed. Linear models could not explain all variations in plasma aldosterone, especially not a variation found within patients. The stimulus-response curve is therefore probably non-linear and at least one or more additional factors may take part in the aldosterone regulation.

Adolescent↗

No parallel fiber volleys in the cerebellar cortex: evidence from cross-correlation analysis between Purkinje cells in a computer model and in recordings from anesthetized rats.

Purkinje cells aligned on the medio-lateral axis share a large proportion of their approximately 175,000 parallel fiber inputs. This arrangement has led to the hypothesis that movement timing is coded in the cerebellum by beams of synchronously active parallel fibers. In computer simulations I show that such synchronous activation leads to a narrow spike cross-correlation between pairs of Purkinje cells. This peak was completely absent when shared parallel fiber input was active in an asynchronous mode. To determine the presence of synchronous parallel fiber beams in vivo I recorded from pairs of Purkinje cells in crus IIa of anesthetized rats. I found a complete absence of precise spike synchronization, even when both cells were strongly modulated in their spike rate by trains of air-puff stimuli to the face. These results indicate that Purkinje cell spiking is not controlled by volleys of synchronous parallel fiber inputs in the conditions examined. Instead, the data support a model by which granule cells primarily control Purkinje cell spiking via dynamic population rate changes.

Action Potentials↗

Computer modeling of wound gape following radial keratotomy.

BACKGROUND: The edges of radial keratotomy incisions remain separated by epithelium or new collagen. To determine if the amount of gape of the incision edges agrees with the induced corneal flattening, two mathematical models of the cornea were studied. METHODS: A finite element model of the eye was constructed; radial incisions through Bowman's membrane and stroma were simulated, as well as incisions confined to the stroma but not involving Bowman's or Descemet's membranes. Geometrical calculations were also performed in a second morphologic model of a spherical shell. RESULTS: The finite element and geometrical models agree closely on the corneal curvature change for a given incision gape. Both models predict that linear intrastromal incisions that do not involve Bowman's layer would not produce significant corneal flattening. CONCLUSIONS: Corneal flattening after radial keratotomy is closely related to incision gape, mediated through structural weakening of the cornea. Purely intrastromal radial incisions, as might be created with Nd:YAG lasers, prevent wound gape and would not appear to be a promising technique for flattening the cornea.

Computer Simulation↗

Design considerations and computer modeling related to the development of molecular scaffolds and peptide mimetics for combinatorial chemistry.

A critical issue in drug discovery utilizing combinatorial chemistry as part of the discovery process is the choice of scaffolds to be used for a proper presentation, in a three-dimensional space, of the critical elements of structure necessary for molecular recognition (binding) and information transfer (agonist/ antagonist). In the case of polypeptide ligands, considerations related to the properties of various backbone structures (alpha-helix, beta-sheets, etc.; phi, psi space) and those related to three-dimensional presentation of side-chain moieties (topography; chi (chi) space) must be addressed, although they often present quite different elements in the molecular recognition puzzle. We have addressed aspects of this problem by examining the three-dimensional structures of chemically different scaffolds at various distances from the scaffold to evaluate their putative diversity. We find that chemically diverse scaffolds can readily become topographically similar. We suggest a topographical approach involving design in chi space to deal with these problems.

Animals↗

[ECT versus transcranial magnetic stimulation (TMS): preliminary data of computer modeling].

The essential issue of electroshock therapy (ECT) is the activity of physical stimulus, i.e., the electric current, on the disturbed structures of the brain. ECT sessions--when chronically applied for evoking antidepressive effects--are responsible for the appearance of excessive incitement in the neuronal net in the brain tissue in a form of self-sustaining after-discharge (SSAD) (convulsive attack characteristic for ECT). The study presents the computer research on basic biophysical phenomena of electroshock therapy (flow of electric current in the structures of the head just before convulsive attack). Five-layer 3-D model of the head was created in OPERA-3D (Vector Fields Ltd., Oxford), general 3 dimensional issues solver. Geometrical dimensions and electrophysical properties of each layer correspond with natural properties. The model was subjected to the action of electric stimulation (parameters identical to those applied in clinical conditions). Analysis of the flow in particular layers revealed the crawling/spreading effect present not only in the scalp layer but also in the layer of cerebrospinal fluid. The effect is conditioned by "deeper situated" lesser conduction of electricity-respectively skull bones, brain tissue. Crawling effect is the reason why only 5-15% of the electricity applied on the surface of the head reaches the surface of the brain. Electro-stimulation examinations also showed that the values of the so called density of the current in layers of brain tissue balanced between 1-10 mA/mm2. The current parameters of ECT were effective in evoking subsequent convulsive attack and safe for the brain tissue. The model was subjected to the action of magnetic stimulation according to the parameters of neurologic technique of transcranial magnetic stimulation (TMS). ELECTRA module was used to solve wire-current issues. The examination showed more regular distribution of current vectors in all layers of the head. The density of cerebral cortex was 0.1-1 mA/mm2, confirming markedly lesser current charge than that observed during ECT. The problem of magnetic stimulation efficacy in irritating deep structures of the brain demands further studies.

Electroconvulsive Therapy↗

The effect of nerve cuff geometry on interference reduction: a study by computer modeling.

The effect of nonlinearity in the extrafascicular field in tripolar electrode cuffs on interference pick-up was investigated. It was concluded that the interference is sensitive to electrode separation, especially in short cuffs. This suggests that significant improvements can be obtained by placing the end electrodes a few mm from the cuff ends.

Computer Simulation↗

[Costs and effectiveness of diagnosis and treatment of patients with dyspepsia, determined with the aid of a computer model].

A theoretical investigation was carried out to determine whether the use of an antibody test for Helicobacter pylori (HP) and the use of bismuth oxide with optional antibiotics, would be cost effective in the diagnosis and treatment of patients with dyspepsia. With literature data on therapeutic effectiveness a computer simulation was carried out. A quick antibody test reduced the number of gastroscopic investigations necessary. Gastroscopic investigation still had to be carried out for patients suffering from non-HP-related dyspepsia. This strategy not only reduced costs, but enabled the general practitioner to start treating the patient immediately. The treatment of a HP-related gastritis with histamine receptor blockers (cimetidine, ranitidine) proved less effective than treatment with bismuth oxide, and more expensive. The treatment with bismuth oxide combined with antibiotics, the so called triple treatment, proved to be the most effective, however disproportionately more expensive. Although the interpretation of the serological test is not without problems, treating dyspepsia with bismuth oxide, especially when the HP serological test result is positive, is the cheaper option and achieves the required effectiveness.

Bismuth↗

Thermodynamic molecular switch in sequence-specific hydrophobic interaction: two computational models compared.

We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in DeltaCp(o)(T)reaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related K(eq). We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273-333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed. The change in inherent chemical bond energy at 0 K, DeltaH(o)(T0) is 7.53 kcal mol(-1) compared with 2.4 kcal mol(-1), while is 365 K as compared with 355 K, for the Nemethy-Scheraga and Planck-Benzinger model, respectively. At , the thermal agitation energy is about five times greater than DeltaH(o)(T0) in the Planck-Benzinger model, that is 465 K compared to 497 K in the Nemethy-Scheraga model. The results imply that the negative Gibbs free energy minimum at a well-defined , where TDeltaS(o) = 0 at about 355 K, has its origin in the sequence-specific hydrophobic interactions, which are highly dependent on details of molecular structure. The Nemethy-Scheraga model shows no evidence of the thermodynamic molecular switch that we have found to be a universal feature of biological interactions. The Planck-Benzinger method is the best known for evaluating the innate temperature-invariant enthalpy, DeltaH(o)(T0), and provides for better understanding of the heat of reaction for biological molecules.

Chemical Phenomena↗

Multi-scale computational model of fuel homeostasis during exercise: effect of hormonal control.

A mathematical model of the whole-body metabolism is developed to predict fuel homeostasis during exercise by using hormonal control over cellular metabolic processes. The whole body model is composed of seven tissue compartments: brain, heart, liver, GI (gastrointestinal) tract, skeletal muscle, adipose tissue, and "other tissues". Each tissue compartment is described by dynamic mass balances and major cellular metabolic reactions. The glucagon-insulin controller is incorporated into the whole body model to predict hormonal changes during exercise. Moderate [150 W power output at 60% of peak oxygen consumption (VO(2max))] exercise for 60 min was implemented by increasing ATP utilization rates in heart and skeletal muscle. Arterial epinephrine level was given as an input function, which directly affects heart and skeletal muscle metabolism and indirectly other tissues via glucagon-insulin controller. Model simulations were validated with experimental data from human exercise studies. The exercise induced changes in hormonal signals modulated metabolic flux rates of different tissues in a coordinated way to achieve glucose homeostasis, demonstrating the efficacy of hormonal control over cellular metabolic processes. From experimental measurements of whole body glucose balance and arterial substrate concentrations, this model could predict the dynamic changes of hepatic glycogenolysis and gluconeogenesis, which are not easy to measure experimentally, suggesting the higher contribution of glycogenolysis ( approximately 75%). In addition, it could provide dynamic information on the relative contribution of carbohydrates and lipids for fuel oxidation in skeletal muscle. Model simulations indicate that external fuel supplies from other tissue/organ systems to skeletal muscle become important for prolonged exercise emphasizing the significance of interaction among tissues. In conclusion, this model can be used as a valuable complement to experimental studies due to its ability to predict what is difficult to measure directly, and usefulness to provide information about dynamic behaviors.

Adaptation, Physiological↗

Computer model of action potential of mouse ventricular myocytes.

We have developed a mathematical model of the mouse ventricular myocyte action potential (AP) from voltage-clamp data of the underlying currents and Ca2+ transients. Wherever possible, we used Markov models to represent the molecular structure and function of ion channels. The model includes detailed intracellular Ca2+ dynamics, with simulations of localized events such as sarcoplasmic Ca2+ release into a small intracellular volume bounded by the sarcolemma and sarcoplasmic reticulum. Transporter-mediated Ca2+ fluxes from the bulk cytosol are closely matched to the experimentally reported values and predict stimulation rate-dependent changes in Ca2+ transients. Our model reproduces the properties of cardiac myocytes from two different regions of the heart: the apex and the septum. The septum has a relatively prolonged AP, which reflects a relatively small contribution from the rapid transient outward K+ current in the septum. The attribution of putative molecular bases for several of the component currents enables our mouse model to be used to simulate the behavior of genetically modified transgenic mice.

Action Potentials↗

Computer modeling of two inorganic pyrophosphatases.

The yeast Saccharomyces cerevisiae has two inorganic pyrophosphatases that are structurally related. One, PPA1, is a cytoplasmic enzyme. The other, PPA2, is located in the mitochondria and appears to be energy-linked. The sequence similarity of PPA1 and PPA2 is about 66% and the identity is about 50%. All amino acids known to be important for catalysis are conserved, except one glutamate which is substituted by an aspartate in PPA2. The structures of PPA2 and the cytoplasmic PPase from Schizosaccharomyces pombe were modeled based on the three dimensional structure of PPA1. Two cysteines in PPA2 and one in the S. pombe enzyme are located at the catalytic cleft. Four residues form an unique insertion near the entrance of the catalytic cleft in the mitochondrial enzyme.

Amino Acid Sequence↗

Mechanism of Ca++ release from the sarcoplasmic reticulum: a computer model.

The proposed model describes myocyte calcium (Ca++) cycling, emphasizing the kinetics of sarcoplasmic reticulum (SR) Ca++ release channels. The suggested SR channel regulating mechanism includes two types of Ca++ binding sites: (1) low affinity sites with high binding rates, regulating the opening of Ca++ channels and (2) high affinity sites with low binding rates, which regulate their closing. The amount of Ca++ released from the SR and the peak value of Ca++ ion concentration [Ca++] in the cytoplasm were found to depend on the rate of the increase of [Ca++], similar to Ca++ induced Ca++ release experiments. The model describes spontaneous release of Ca++ from overloaded SR. The dependence of the control mechanism on the activating and inactivating sites is substantiated by simulations of ryanodine intervention, providing results similar to experimental results. Simulations under conditions of isolated SR vesicles produced Ca++ release results similar to measured data. Consequently, it is suggested that the recovery of Ca++ release channels represents the rate limiting factor in the process of mechanical restitution.

Animals↗

A patient-specific computational model of fluid-structure interaction in abdominal aortic aneurysms.

It is generally believed that knowledge of the wall stress distribution could help to find better rupture risk predictors of abdominal aortic aneurysms (AAAs). Although AAA wall stress results from combined action between blood, wall and intraluminal thrombus, previously published models for patient-specific assessment of the wall stress predominantly did not include fluid-dynamic effects. In order to facilitate the incorporation of fluid-structure interaction in the assessment of AAA wall stress, in this paper, a method for generating patient-specific hexahedral finite element meshes of the AAA lumen and wall is presented. The applicability of the meshes is illustrated by simulations of the wall stress, blood velocity distribution and wall shear stress in a characteristic AAA. The presented method yields a flexible, semi-automated approach for generating patient-specific hexahedral meshes of the AAA lumen and wall with predefined element distributions. The combined fluid/solid mesh allows for simulations of AAA blood dynamics and AAA wall mechanics and the interaction between the two. The mechanical quantities computed in these simulations need to be validated in a clinical setting, after which they could be included in clinical trials in search of risk factors for AAA rupture.

Aortic Aneurysm, Abdominal↗

Computer modelling of radiation-induced bystander effect.

Radiation-induced genomic instability and bystander effects are now well established consequences of exposure of living cells to ionising radiation. It has been observed that cells not directly hit by radiation tracks may still exhibit radiation effects. We present a quantitative modelling of the radiation-induced bystander effect based on a diffusion model of spreading the bystander signal. The model assumes the bystander factor to be aprotein of low molecular weight, given out by the hit cell, diffusing in the medium and reacting with non-hit cells. The model calculations successfully predict the results of cell survival in an irradiated conditioned medium. The model predicts the shape of dose-effect relationship for cell survival and oncogenic transformation induced by broad-beam and micro-beam irradiation by alpha-particles.

Bystander Effect↗

Properties of human motoneurones and their synaptic noise deduced from motor unit recordings with the aid of computer modelling.

This paper reviews two new facets of the behaviour of human motoneurones; these were demonstrated by modelling combined with analysis of long periods of low-frequency tonic motor unit firing (sub-primary range). 1) A novel transformation of the interval histogram has shown that the effective part of the membrane's post-spike voltage trajectory is a segment of an exponential (rather than linear), with most spikes being triggered by synaptic noise before the mean potential reaches threshold. The curvature of the motoneurone's trajectory affects virtually all measures of its behaviour and response to stimulation. The 'trajectory' is measured from threshold, and so includes any changes in threshold during the interspike interval. 2) A novel rhythmic stimulus (amplitude-modulated pulsed vibration) has been used to show that the motoneurone produces appreciable phase-advance during sinusoidal excitation. At low frequencies, the advance increases with rising stimulus frequency but then, slightly below the motoneurones mean firing rate, it suddenly becomes smaller. The gain has a maximum for stimuli at the mean firing rate (the 'carrier'). Such behaviour is functionally important since it affects the motoneurone's response to any rhythmic input, whether generated peripherally by the receptors (as in tremor) or by the CNS (as with cortical oscillations). Low mean firing rates favour tremor, since the high gain and reduced phase advance at the 'carrier' reduce the stability of the stretch reflex.

Animals↗