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At least 487 records · Page 27Linked to original sources
PubMed2001

Transmembrane alpha-helices in the gap junction membrane channel: systematic search of packing models based on the pair potential function.

Recent progress in the field of electron cryo-microscopy and image analysis has shown that there is an overwhelming need to interpret medium resolution (5 to 10 A) three-dimensional maps. Traditional methods of fitting amino acid residues into electron density using molecular modeling programs must be supplemented with further analysis. We have used a potential of mean force (PMF) method, derived from Boltzmann statistics in protein structure, to generate models for the packing of alpha-helices, using pairwise potentials between amino acid residues. The approach was tested using the three-dimensional map of a recombinant cardiac gap junction membrane channel provided by electron cryo-crystallography (Unger et al., 1997; 1999a, 1999b) which had a resolution of 7.5 A in the membrane plane and 21 A in the vertical direction. The dodecameric channel was formed by the end-to-end docking of two hexamers, each of which displayed 24 rods of density in the membrane interior, which was consistent with an alpha-helical conformation for the four transmembrane domains of each connexin subunit. Based on the three-dimensional map and the amino acid sequence for the 4 transmembrane domains determined by hydropathy analysis, we used the modeling utility SymServ (Macke et al., 1998) to build hexameric connexons with 24 transmembrane alpha-helices. Canonical alpha-helices were aligned to the axes of the rods of density and translated along the density so that the center of masses coincided. The PMF function was used to evaluate 162,000 conformations for each of the 24 possible alpha-helical packing models. Since the different packing models yielded different energy distributions, the pair potential function appears to be a promising tool for evaluating the packing of alpha-helices in membrane proteins. The analysis will be refined by energy calculations based on the expectations that the outer boundary of the channel will be formed by hydrophobic residues in contact with the lipids.

Connexins↗
PubMed2003

An image-based finite difference model for simulating restricted diffusion.

Water diffusion in tissues is generally restricted and often anisotropic. Neural tissue is of particular interest, since it is well known that injury alters diffusion in a characteristic manner. Both Monte Carlo simulations and approximate analytical models have previously been reported in attempts to predict water diffusion behavior in the central nervous system. These methods have relied on axonal models, which assume simple geometries (e.g., ellipsoids, cylinders, and square prisms) and ignore the thickness of the myelin sheath. The current work describes a method for generating models using synthetic images. The computations are based on a 3D finite difference (FD) approximation of the diffusion equation. The method was validated with known analytic solutions for diffusion in a cylindrical pore and in a hexagonal array of cylinders. Therefore, it is envisioned that, by exploiting histologic images of neuronal tissues as input model, current method allows investigating the water diffusion behavior inside biological tissues and potentially assessing the status of neural injury and regeneration.

Axons↗
PubMed1997

The influenza A virus M2 channel: a molecular modeling and simulation study.

The M2 protein of influenza virus forms ion channels activated by low pH which are proton permeable and play a key role in the life cycle of the virus. M2 is a 97-residue integral membrane protein containing a single transmembrane (TM) helix. M2 is present as disulfide-linked homotetramers. The TM domain of M2 has been modeled as a bundle of four parallel M2 helices. The helix bundle forms a left-handed supercoil surrounding a central pore. Residue H37 has been implicated in the mechanism of low-pH activation of the channel. Models generated with H37 in a fully deprotonated state exhibit a pore occluded by a ring of H37 side chains oriented toward the lumen of the pore. Models with H37 in a fully protonated state no longer exhibit such occlusion of the pore, as the H37 side chains adopt a more interfacial location. Extended molecular dynamics simulations with water molecules within and at the mouths of the pores support this distinction between the H37-deprotonated and H37-protonated models. These simulations suggest that only in the H37-protonated model is there a continuous column of water extending the entire length of the central pore. A mechanism for activation of M2 by low pH is presented in which the H37-deprotonated model corresponds to the "closed" form of the channel, while the H37-protonated model corresponds to the "open" form. A switch from the closed to the open form of the channel occurs if H37 is protonated midway through a simulation. The open channel is suggested to contain a wire of H-bonded water molecules which enables proton permeability.

Computer Simulation↗
PubMed2003

Advanced modeling environment for developing and testing FES control systems.

Realistic models of neuromusculoskeletal systems can provide a safe and convenient environment for the design and evaluation of controllers for functional electrical stimulation (FES) prior to clinical trials. We have developed a set of integrated musculoskeletal modeling tools to facilitate the model building process. Simulink models of musculoskeletal systems are created using two software packages developed in our laboratory, Musculoskeletal Modeling in Simulink (MMS) and virtual muscle, in addition to one software package available commercially, SIMM (Musculographics Inc., USA). MMS converts anatomically accurate musculoskeletal models generated by SIMM into Simulink(R) blocks. It also removes run-time constraints on kinetic simulations in SIMM, and allows the development of complex musculoskeletal models without writing a line of code. Virtual muscle builds realistic Simulink models of muscles responding to either natural recruitment or FES. Models of sensorimotor control systems can be developed using various Matlab (Mathworks Inc., USA) toolboxes and integrated easily with these musculoskeletal blocks in the graphical environment of Simulink.

Computer Simulation↗
PubMed2002

Conformational-relaxation models of single-enzyme kinetics.

Fluorescent spectroscopy experiments with single-enzyme molecules yield a large volume of statistical data that can be analyzed and interpreted using stochastic models of enzyme action. Here, we present two models, each based on the mechanism that an enzyme molecule must pass through a sequence of conformational transformations to complete its catalytic turnover cycle. In the simplest model, only one path leading to the release of product is present. In contrast to this, two different catalytic paths are possible in the second considered model. If a cycle is started from an active state, immediately after the previous product release, it follows a different conformational route and is much shorter. Our numerical investigations show that both models generate non-Markovian molecular statistics. However, their memory landscapes and distributions of cycle times are significantly different. The memory landscape of the double-path model bears strong similarity to the recent experimental data for horseradish peroxidase.

Catalysis↗
PubMed2001

Three-dimensional virtual-reality surgical planning and soft-tissue prediction for orthognathic surgery.

Complex maxillofacial malformations continue to present challenges in analysis and correction beyond modern technology. The purpose of this paper is to present a virtual-reality workbench for surgeons to perform virtual orthognathic surgical planning and soft-tissue prediction in three dimensions. A resulting surgical planning system, i.e., three-dimensional virtual-reality surgical-planning and soft-tissue prediction for orthognathic surgery, consists of four major stages: computed tomography (CT) data post-processing and reconstruction, three-dimensional (3-D) color facial soft-tissue model generation, virtual surgical planning and simulation, soft-tissue-change preoperative prediction. The surgical planning and simulation are based on a 3-D CT reconstructed bone model, whereas the soft-tissue prediction is based on color texture-mapped and individualized facial soft-tissue model. Our approach is able to provide a quantitative osteotomy-simulated bone model and prediction of postoperative appearance with photorealistic quality. The prediction appearance can be visualized from any arbitrary viewing point using a low-cost personal-computer-based system. This cost-effective solution can be easily adopted in any hospital for daily use.

Humans↗
PubMed2002

Pharmacodynamics and pharmacogenomics of methylprednisolone during 7-day infusions in rats.

An array of adverse steroid effects was examined on a whole body, tissue, and molecular level. Groups of male adrenalectomized Wistar rats were subcutaneously implanted with Alzet mini-pumps giving zero-order release rates of 0, 0.1, and 0.3 mg/kg/h methylprednisolone for 7 days. The rats were sacrificed at various times during the 7-day infusion period. A two-compartment model with a zero order input could adequately describe the kinetics of methylprednisolone upon infusion. Blood lymphocyte counts dropped to a minimum by 6 h and were well characterized by the cell trafficking model. The time course of changes in body and organ (liver, spleen, thymus, gastrocnemius muscle, and lungs) weights was described using indirect response models. Markers of gene-mediated steroid effects included hepatic cytosolic free receptor density, receptor mRNA, tyrosine aminotransferase (TAT) mRNA, and TAT levels. Our fifth-generation model of acute corticosteroid pharmacodynamics was used to predict the time course of receptor/gene-mediated effects. An excellent agreement between the expected and observed receptor dynamics suggested that receptor events and mRNA autoregulation are not altered upon 7-day methylprednisolone dosing. However, the model indicated a decoupling between the receptor and TAT dynamics with this infusion. The strong tolerance seen in TAT mRNA induction could be partly accounted for by receptor down-regulation. An amplification of translation of TAT mRNA to TAT and/or a reduction in the enzyme degradation rate could account for the observed exaggerated TAT activity. Our results exemplify the importance of biological signal transduction variables in controlling receptor/gene-mediated steroid responses during chronic dosing.

Adrenalectomy↗
PubMed1992

A model for the generation of movements requiring endpoint precision.

A model is proposed in which movement accuracy is regulated by means of corrective actions taken at discrete intervals throughout the course of a movement. A movement, as represented by its tangential velocity profile, cna be decomposed into a series of one or more submovements. Each submovement consists of a prototype velocity profile which can be scaled in magnitude and duration. For planar two-joint movements, we demonstrate that these submovements can be mathematically represented either in terms of velocity profiles or in terms of the underlying joint torque profiles. In either case, the submovements superimpose linearly to produce the composite movement. The model provides a very good fit to tangential velocity profiles recorded from human subjects during three-dimensional arm movements with constraints on accuracy and speed. The model assumes that when a submovement is present, its onset is associated with a change in the direction of the hand path and/or a zero crossing or inflection in at least one of the components of the velocity vector. The model is consistent with a strategy in which precision is achieved by periodic discrete actions which redirect the moving arm in order to bring the hand closer to the target. Since submovements were also observed in slow movements where accuracy constraints had been relaxed, we hypothesize that the strategy of superimposing a series of submovements to make one composite movement may be a general one. We suggest that it would be particularly appropriate for the process of learning a new motor skill.

Adult↗
PubMedDate not supplied

Graphical and stereolithographic models of the developing human heart lumen.

Scaled physical models can be useful in analyzing stage-specific hemodynamics in the embryonic human heart to address correlations between early physical stressors and myocardial wall responses. We generated models of the cardiac blood space from reconstructions of four digitized human embryo images from Carnegie Collection at the Armed Forces Institute of Pathology. From physical scale models manufactured by stereolithography, compliant sleeves can be created for flow dynamics studies. This novel use of Carnegie collection images and graphical modeling software provides tools for broadening our understanding of normal and aberrant heart formation.

Embryonic and Fetal Development↗
PubMed1996

The within-host cellular dynamics of bloodstage malaria: theoretical and experimental studies.

The properties of a mathematical model of bloodstage infection with a single strain of malaria were investigated. Analysing the cell population dynamics in the absence of a host immune response we demonstrate a relationship between host and parasite parameters that defines a criterion for the successful invasion and persistence of the parasite. Important parameters are the rates of merozoite production and death and those of erythrocyte production, death and invasion. We present data from experiments designed to evaluate the erythrocyte invasion rate in a rodent malaria system. The model generates patterns of parasitaemia in good qualitative agreement with those seen in Plasmodium berghei infections. The sole force behind the rise and fall in parasitaemia in the model without immunity is the density of susceptible erythrocytes, suggesting that resource availability is an important determinant of the initial pattern of infection in vivo. When we incorporate a simple immune response into the model we find that immunity against the infected cell is much more effective at suppressing parasite abundance than immunity against the merozoite. Simulations reveal oscillating temporal patterns of parasite abundance similar to P. c. chabaudi infection, challenging the concept that antigenic variation is the sole mechanism behind recrudescing patterns of infection.

Animals↗
PubMed2002

Beyond phrenology: what can neuroimaging tell us about distributed circuitry?

Unsupervised models of how the brain identifies and categorizes the causes of its sensory input can be divided into two classes: those that minimize the mutual information (i.e., redundancy) among evoked responses and those that minimize the prediction error. Although these models have the same goal, the way that goal is attained, and the functional architectures required, are fundamentally different. This review describes the differences, in the functional anatomy of sensory cortical hierarchies, implied by the two models. We then consider how neuroimaging can be used to disambiguate between them. The key distinction reduces to whether backward connections are employed by the brain to generate a prediction of sensory inputs. To ascertain whether backward influences are evident empirically requires a characterization of functional integration among brain systems. This review summarizes the approaches to measuring functional integration in terms of effective connectivity and proceeds to address the question posed by the theoretical considerations. In short, it will be shown that the conjoint manipulation of bottom-up and top-down inputs to an area can be used to test for interactions between them, in elaborating cortical responses. The conclusion, from these sorts of neuroimaging studies, points to the prevalence of top-down influences and the plausibility of generative models of sensory brain function.

Animals↗
PubMed1991

Theoretical considerations in relation to the treatment of brain tumours by means of local hyperthermia generated by ultrasound fields.

Brain tumours comprise a significant fraction of all tumours in the human body. Despite the development of technology in clinical oncology, these tumours still present a difficult challenge. The margin between destruction of tumour and damage to normal tissue is narrow in the brain. The price paid for producing tissue damage outside the tumour is high in terms of quality of survival. Results of many experiments with ultrasound hyperthermia show that this new technique is successful for treating certain types of malignant tumours. In the case of brain tumours, applying focused fields should have the advantage of selectively destroying the tumour and leaving surrounding tissues intact. Previous attempts at applying ultrasound to the field of neurosurgery are reviewed. Those factors which have effects on the generation of thermal fields in brain tissues are considered in relation to the possible treatment of human brain tumours. Calculated thermal fields in a 2-D brain model generated by an applicator built in our laboratory are also presented.

Brain↗
PubMed1983

Effects of circulating renin substrate on renal function in isolated perfused rat kidney.

The effects of two different amounts of pure rat angiotensinogen were investigated in a closed circuit isolated perfused rat kidney. In response to angiotensinogen, circulating levels of angiotensin I (AI) and angiotensin II (AII) immunoreactive materials were found to increase in a time and dose-dependent manner. Vasoconstrictor and renin inhibitory effects were observed in parallel with the increase in AII. Glomerular filtration rate decreased after administration of angiotensinogen to a greater extent than renal flow and filtration fraction. The characterization by high performance liquid chromatography of peptides generated showed the liberation of AI, des-Asp1AI, AII and des-Asp1AII (AIII). These findings demonstrate that administration of angiotensinogen in an isolated perfused kidney model generates AI and that renal converting enzyme and aminopeptidases are able to convert AI to AII, AI to des-Asp1AI, and des-Asp1AI and/or AII to AIII. Changes in circulating level of angiotensinogen influence the activity of the renin-angiotensin system and, therefore, renal function.

Angiotensin I↗
PubMed1986

On the effect of the intracellular calcium-sensitive K+ channel in the bursting pancreatic beta-cell.

Based on the observation that the calcium-activated K+ channel in the pancreatic islet cells can also be activated by the membrane potential, we have formulated a mathematical model for the electrical activity in the pancreatic beta-cell. Our model contains two types of ionic channels, which are active above the subthreshold glucose concentration in the limit-cycle region: a Ca2+-activated, voltage-gated K+ channel and voltage-gated Ca2+ channel. Numerical simulation of the model generates bursts of electrical activity in response to a variation of kCa, the rate constant for sequestration of intracellular calcium ions. The period and duration of the bursts in response to kCa are in good agreement with experiment. The model predicts that a combined spike and burst pattern can be created using only single species of inward and outward currents, the inactivation kinetics (i.e., h) in the inward current is not a necessary condition for the generation of the pattern, and a given pattern or intensity of electrical activity may produce different levels of intracellular Ca2+ depending on the set of certain electrical parameters.

Animals↗
PubMed1992

A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems.

Under physiological conditions, many polypeptide chains spontaneously fold into discrete and tightly packed three-dimensional structures. The folded polypeptide chain conformation is believed to represent a minimum Gibbs energy of the system, governed by the weak interactions that operate between the amino acid residues and between the residues and the solvent. A semiempirical molecular thermodynamic model is proposed to represent the Gibbs energy of folding of aqueous homopolypeptide systems. The model takes into consideration both the entropy contribution and the enthalpy contribution of folding homopolypeptide chains in aqueous solutions. The entropy contribution is derived from the Flory-Huggins expression for the entropy of mixing. It accounts for the entropy loss in folding a random-coiled polypeptide chain into a specific polypeptide conformation. The enthalpy contribution is derived from a molecular segment-based Non-Random Two Liquid (NRTL) local composition model [H. Renon and J. M. Prausnitz (1968) AIChE J., Vol. 14, pp. 135-142; C.-C. Chen and L. B. Evans (1986) AIChE J., Vol. 32, pp. 444-454], which takes into consideration of the residue-residue, residue-solvent, and solvent-solvent binary physical interactions along with the local compositions of amino acid residues in aqueous homopolypeptides. The UNIFAC group contribution method [A. Fredenslund, R. L. Jones, and J. M. Prausnitz (1975) AIChE J., 21, 1086-1099; A. Fredenslund, J. Gmehling, and P. Rasmussen (1977) Vapor-Liquid Equilibrium Using UNIFAC, Elsevier Scientific Publishing Company, Amsterdam], developed originally to estimate the excess Gibbs energy of solutions of small molecules, was used to estimate the NRTL binary interaction parameters. The model yields a hydrophobicity scale for the 20 amino acid side chains, which compares favorably with established scales [Y. Nozaki and C. Tanford (1971) Journal of Biological Chemistry, Vol. 46, pp. 2211-2217; E. B. Leodidis and T. A. Hatton (1990) Journal of Physical Chemistry, Vol. 94, pp. 6411-6420]. In addition, the model generates qualitatively correct thermodynamic constants and it accurately predicts thermodynamically favorable folding of a number of aqueous homopolypeptides from random-coiled states into alpha-helices. The model further facilitates estimation of the Zimm-Bragg helix growth parameter s and the nucleation parameter sigma for amino acid residues [B. H. Zimm and J. K. Bragg (1959) Journal of Chemical Physics, Vol. 31, pp. 526-535]. The calculated values of the two parameters fall into the ranges suggested by Zimm and Bragg.

Models, Molecular↗
PubMed1995

Optimisation of transcutaneous cardiac pacing by three-dimensional finite element modelling of the human thorax.

The goal of the study is to determine by finite element analysis (FE) the optimal electrode placement, size and electrolyte resistivity that minimise the pain experienced by patients during successful transcutaneous cardiac pacing (TCP). The three-dimensional FE model generated for this purpose has 55,388 nodes, 50,913 hexahedral elements and simulated 16 different organs and tissues, as well as the properties of the electrolyte. The model uses a non-uniform mesh with an average spatial resolution of 0.8 cm in all three dimensions. To validate this model, the voltage across 3 cm2 Ag-AgCl electrodes is measured when currents of 5 mA at 50 kHz are injected into a subject's thorax through the same electrodes. For the same electrode placements and sizes and the same injected current, the FE analysis produced results in good agreement with the experimental data. The optimisation analysis tested seven different electrode placements, five different electrode sizes and six different electrolyte resistivities. The analysis indicates that the anterior-posterior electrode placement, electrode sizes of about 90 cm2 and electrolytes with resistivity of about 800 omega.cm yield the most uniform current distribution through the skin, thus having the best chances to minimise the pain delivered to the patient during successful TCP. The anterior-anterior electrode placement is the second most efficient.

Cardiac Pacing, Artificial↗
PubMed1995

[Geometrical modeling of the spine and the thorax for the biomechanical analysis of scoliotic deformities using the finite element method].

In order to study the biomechanical behavior of the whole human spine and thorax, as well as orthopaedic treatment effects, a new generation model is proposed, which includes a precise functional representation of the posterior part of the spine, while respecting computational capabilities. This paper presents the geometrical aspects of this model. The latter is built using an hybrid method which combines steroradiographic 3-D reconstructions of the spine and thorax [1] to serial CT scan 3-D reconstructions of typical human vertebrae and sternum [4] and published morphometric data of ribs [2, 3]. These anatomical structures were deformed in order to fit as well as possible the personalized data of scoliotic patients using geometrical transformations as well as interpolation or extrapolation techniques. In the posterior part, articular facets are modelled and parameterized as elementary surface shapes (plane, cylinder, sphere). For the articular facet geometry of a given normal subject, results revealed that the zygapophyseal facets are better represented by planes for T1 to T11 and by portions of cylinders for T12 to L5, which is in concordance with the literature [5, 6]. Evaluation of this modelling approach was done on 2 cadaveric vertebral segments. Parametric data obtained from the model were compared to precise measurements done on the vertebrae using a 3-D digitizer, and concordance was found. These personalized geometric informations were then used to build a finite element model [7], which will be useful to study scoliotic deformities as well as personalized orthopaedic treatments.

Humans↗
PubMed1993

Extending the multiple indicator dilution method to include slow intracellular diffusion.

The traditional multiple indicator dilution (MID) method is extended to incorporate cytoplasmic concentration gradients due to slow intracellular diffusion of the permeable molecule. The new model is governed by a system of partial differential equations that are solved using Laplace transformation. An analysis of the transformed solution shows that the traditional MID method is a special case of the extended model. We then use simulation analysis to show that the traditional MID model and the new diffusion model generate similar outflow curves. However, when the traditional MID equations were used to analyze outflow curves generated using a system in which intracellular diffusion is slow compared to other transport processes, the recovered rate constants for the transmembrane and excretion processes were incorrect. The diffusion model permits estimation of the rate of intracellular transport of amphipathic molecules from suitable indicator dilution data.

Animals↗