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At least 1,387 records · Page 77Linked to original sources
PubMed1996

Computer model of a bovine type I collagen microfibril.

Collagens are a family of structural proteins of the extracellular matrix. The fibril-forming collagens are the major structural proteins of skin, cartilage, bone, blood vessel walls and internal organs. In addition to biological function, the collagens provide natural structural frameworks that are utilized in the medical, food and leather industries. Many schemes for the organization of type I collagen into triple helices, microfibrils and fibrils have been proposed during the past 30 years. Here, the development of a molecular model of a bovine type I collagen "Smith' microfibril is described. In cross-section, this model exhibits a symmetrical, pentagonal grouping of five triple helices. The model comprises 15 polypeptide chains having 315 residues each. This model is large enough to allow a comparison of its gross structural features with images of stained collagen obtained by electron microscopy, yet small enough to be manipulated on a minicomputer or work-station. The model is useful for (among others) studies of structure-function relationships in collagen, exploring folding pathways, predicting the efficacy of potential crosslinking agents or chemical modifications, and designing synthetic collagen-like materials or modifications for specific applications.

Amino Acid Sequence↗
PubMed1999

A computer model of human thermoregulation for a wide range of environmental conditions: the passive system.

A dynamic model predicting human thermal responses in cold, cool, neutral, warm, and hot environments is presented in a two-part study. This, the first paper, is concerned with aspects of the passive system: 1) modeling the human body, 2) modeling heat-transport mechanisms within the body and at its periphery, and 3) the numerical procedure. A paper in preparation will describe the active system and compare the model predictions with experimental data and the predictions by other models. Here, emphasis is given to a detailed modeling of the heat exchange with the environment: local variations of surface convection, directional radiation exchange, evaporation and moisture collection at the skin, and the nonuniformity of clothing ensembles. Other thermal effects are also modeled: the impact of activity level on work efficacy and the change of the effective radiant body area with posture. A stable and accurate hybrid numerical scheme was used to solve the set of differential equations. Predictions of the passive system model are compared with available analytic solutions for cylinders and spheres and show good agreement and stable numerical behavior even for large time steps.

Algorithms↗
PubMed1995

A computer model for time-based simulation of electrophoresis systems with freely defined initial and boundary conditions.

A PC-based program has been developed that allows the user to perform one-dimensional computer simulations of electrophoresis systems with freely definable initial- and boundary conditions. The program can handle n constituents with n pK-values and calculates constituent concentrations and derived parameters as a function of time. Results are displayed graphically on screen and are stored as data files for graphical hard-copy processing.

Computer Simulation↗
PubMed1990

Peptides related to the active fragment of "proline rich polypeptide", an immunoregulatory protein of the ovine colostrum. Spectroscopic and computer modeling studies.

The preferred solution conformation of the PRP-hexapeptide (Tyr-Val-Pro-Leu-Phe-Pro) and of some of its structural analogues was investigated by NMR-spectroscopy, spectrofluorimetry and computer simulation technic. It was found that the preferred conformation is characterized by cis'-conformation of Pro3 and the gamma-turn on the Leu4-residue: for Val2 and Phe5 a beta-structure seems to be privileged. In such a conformation Val2 and Leu4 residues occupy exactly the same positions in space as residues i and i + 3 in an alpha-helix. It suggests that the PRP-hexapeptide can interact with receptor protein inducing or stabilizing its helical conformation by "knobs into holes" packing.

Amino Acid Sequence↗
PubMed1995

Application of a computer model to predict optimum slaughter end points for different biological types of feeder cattle.

A bioeconomic model was developed to predict slaughter end points of different genotypes of feeder cattle, where profit/rotation and profit/day were maximized. Growth, feed intake, and carcass weight and composition were simulated for 17 biological types of steers. Distribution of carcass weight and proportion in four USDA quality and five USDA yield grades were obtained from predicted carcass weights and composition. Average carcass value for each genotype was calculated from these distributions under four carcass pricing systems that varied from value determined on quality grade alone to value determined on yield grade alone. Under profitable market conditions, rotation length was shorter and carcass weights lighter when the producer's goal was maximum profit/day, compared with maximum profit/rotation. A carcass value system based on yield grade alone resulted in greater profit/rotation and in lighter and leaner carcasses than a system based on quality grade alone. High correlations ( > .97) were obtained between breed profits obtained with different sets of input/output prices and carcass price discount weight ranges. This suggests that breed rankings on the basis of breed profits may not be sensitive to changes in input/output market prices. Steers that were on a grower-stocker system had leaner carcasses, heavier optimum carcass weight, greater profits, and less variation in optimum carcass weights between genotypes than steers that were started on a high-energy finishing diet at weaning. Overall results suggest that breed choices may change with different carcass grading and value systems and postweaning production systems. This model has potential to provide decision support in marketing fed cattle.

Abattoirs↗
PubMed1999

Computational modeling of the rate limiting step in low molecular weight protein tyrosine phosphatase.

Hydrolysis of the phosphoenzyme intermediate is the second and rate limiting step of the reaction catalyzed by the protein tyrosine phosphatases (PTPs). The cysteinyl phosphate thioester bond is cleaved by nucleophilic displacement where an active site water molecule attacks the phosphorus atom. Starting from the crystal structure of the low molecular weight PTP, we study the energetics of this reaction utilizing the empirical valence bond method in combination with molecular dynamics and free energy perturbation simulations. The reactions of the wild-type as well as the D129A and C17S mutants are modeled. For the D129A mutant, which lacks the general acid/base residue Asp-129, an alternative reaction mechanism is proposed. The calculated activation barriers are in all cases in good agreement with experimental reaction rates. The present results together with earlier computational and experimental work now provide a detailed picture of the complete reaction mechanism in many PTPs. The key role played by the structurally invariant signature motif in stabilizing a double negative charge is reflected by its control of the energetics of both transition states and the reaction intermediate.

Animals↗
PubMed2006

Hyaluronan: the local solution conformation determined by NMR and computer modeling is close to a contracted left-handed 4-fold helix.

The polysaccharide hyaluronan (HA) is a ubiquitous component of the vertebrate extracellular matrix with diverse physiological roles from space-filling to acting as a scaffold for other macromolecules. The molecular interactions responsible for these solution properties have been the subject of much debate and, primarily due to the lack of residue-specific experimental data, no consensus model for the three-dimensional conformation nor dynamics of HA in solution has emerged. Here, the solution conformation of HA is investigated using molecular dynamics (MD) simulations and high-field nuclear magnetic resonance (NMR). In contrast to previous studies, MD simulations incorporated explicit water molecules and sodium ions, while NMR experiments utilized (15)N-enriched oligosaccharides to allow residue-specific information to be obtained. The resultant average conformation is predicted to be almost a contracted left-handed 4-fold helix; i.e. similar to that observed for sodium hyaluronate fibers by X-ray diffraction, but with the acetamido side-chain trans to H(2). The glycosidic linkages and acetamido side-chains are predicted to have standard deviation rotations of 13 degrees and 18 degrees around their mean conformations in free solution, respectively, and are not observed to be stabilized by strong intramolecular hydrogen bonds as X-ray fiber diffraction refinements describe for the solid-state. Rather, weak and transient hydrogen bonds that are in rapid interchange with solvent molecules are predicted. These predictions are quantitatively consistent with demanding residue-specific NMR data and correspond to an HA molecule that is rod-like as an oligosaccharide and behaves as a stiffened random coil at large molecular mass, in close agreement with previous hydrodynamic observations. This new description of the solution conformation of HA is consistent with all available experimental data and accounts for its viscoelastic space-filling properties. This representation can be used as a basis for modeling the association between HA and proteins, which will elucidate important aspects of extracellular matrix assembly.

Animals↗
PubMedDate not supplied

A computational model for heat generation in a radially layered tissue inside a 'coaxial TEM' applicator.

The electromagnetic heat dissipation in a radially layered biological tissue inside a circular cylinder has been investigated theoretically. The theory is based on a three-dimensional model and the electromagnetic field is assumed to be generated by a prescribed electric field along a ring-shaped aperture. The method of computation employs the spatial Fourier transform of all field quantities with respect to the axial coordinate, after which the field equations are solved in the spectral domain. Subsequently, an inverse Fourier transform is carried out to compute the quantities that are of interest to the clinical deep-body hyperthermia system at hand. For a number of representative configurations numerical results at 70 MHz are given.

Body Temperature↗
PubMed2002

Latent learning, shortcuts and detours: a computational model.

Voicu and Schmajuk (Rob. Auto. Syst. 35 (2001a) 23) described a model of spatial navigation and exploration that includes an action system capable of guiding, with the help of a cognitive system, the search for specific goals as determined by a motivation system. Whereas in the original model the cognitive map stores information about the connectivity between places in the environment, in the present version the cognitive map also stores information about the paths traversed by the agent. Computer simulations show that the network correctly describes experimental results including latent learning in a maze, detours in a maze, and shortcuts in an open field. In addition, the model generates novel predictions about detours and shortcuts in an open field.

Journal Article↗