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At least 55 records · Page 3Linked to original sources

PubMed1992

Folding protein alpha-carbon chains into compact forms by Monte Carlo methods.

A method is presented for generating folded chains of specific amino acid sequences on a simple cubic lattice. Monte Carlo simulations are used to transform extended geometries of simplified alpha-carbon chains for eight small monomeric globular proteins into folded states. Permitted chain transitions are limited to a few types of moves, all restricted to occur on the lattice. Crude residue-residue potentials derived from statistical structure data are used to describe the energies for each conformer. The low resolution structures obtained by this procedure contain many of the correct gross features of the native folded architectures with respect to average residue energy per nonbonded contact, segment density, and location of surface loops and disulfide pairs. Rms deviations between these and the native X-ray structures and percentage of native long-range contacts found in these final folded structures are 7.6 +/- 0.7 A and 48 +/- 3%, respectively. This procedure can be useful for predicting approximate tertiary interactions from amino acid sequence.

Models, Molecular↗

PubMed1990

Cyclic fatigue-crack propagation, stress-corrosion, and fracture-toughness behavior in pyrolytic carbon-coated graphite for prosthetic heart valve applications.

Fracture-mechanics tests were performed to characterize the cyclic fatigue, stress-corrosion cracking, and fracture-toughness behavior of a pyrolytic carbon-coated graphite composite material used in the manufacture of cardiac valve prostheses. Testing was carried out using compact tension C(T) samples containing "atomically" sharp precracks, both in room-temperature air and principally in a simulated physiological environment of 37 degrees C Ringer's lactate solution. Under sustained (monotonic) loads, the composite exhibited resistance-curve behavior, with a fracture toughness (KIc) between 1.1 and 1.9 MPa square root of m, and subcritical stress-corrosion crack velocities (da/dt) which were a function of the stress intensity K raised to the 74th power (over the range approximately 10(-9) to over 10(-5) m/s). More importantly, contrary to common perception, under cyclic loading conditions the composite was found to display true (cyclic) fatigue failure in both environments; fatigue-crack growth rates (da/dN) were seen to be a function of the 19th power of the stress-intensity range delta K (over the range approximately 10(-11) to over 10(-8) m/cycle). As subcritical crack velocities under cyclic loading were found to be many orders of magnitude faster than those measured under equivalent monotonic loads and to occur at typically 45% lower stress-intensity levels, cyclic fatigue in pyrolytic carbon-coated graphite is reasoned to be a vital consideration in the design and life-prediction procedures of prosthetic devices manufactured from this material.

Biocompatible Materials↗

PubMed1985

The occurrence of copper, iron, zinc and other elements and the nature of some copper and iron complexes in humic substances from municipal refuse disposed of in a landfill.

Municipal refuse was allowed to decompose in a simulated landfill for 20 months. Three different models were studied in which the refuse, in 40 m3 lots, was either compacted or mixed 2:1 with sewage sludge, the latter being studied in both uncompacted and compacted states. At 2, 6, 12 and 20 months, humic substances were extracted from samples with 0.1 M Na2P4O7 and 0.1 M NaOH, and humic acids isolated by precipitation after acidification with HCl. The humic substances were examined by electron paramagnetic resonance (EPR) to determine the free radical content and the nature of some of the metal complexes present. The principal form of copper was present in either a square planar or a tetragonally-distorted octahedral environment, probably coordinated to two nitrogen and two oxygen atoms. Fe3+ was present in at least three different environments. In one, it was probably in a complex with rhombic symmetry; another showed Fe3+ in an axially-symmetric environment, most likely as a ferric porphyrin. No distinctions could be made between the concentrations or forms of metals present in the refuse humic substances as a result of adding sewage sludge, but the additions increased the yield of humic substances, particularly in the uncompacted landfill. Humic substances in the refuse retain metal elements in complexed forms which will restrict their release from the landfill.

Carbon↗

PubMed1989

Formulation studies of tableted oral rehydration salt mixtures.

Dehydration following non-specific diarrhoea may be prevented by oral administration of a simple glucose/salt mixture. A solution tablet of this mixture would have advantages of stability under environmental exposure and transport if the costs could be held within reasonable limits. The moisture adsorption and compression characteristics of Oral Rehydration Salts (ORS) ingredients have been studied. Combinations of ingredients resulted in a moisture adsorption higher than that of the individual components. This may be explained in terms of critical relative humidity, RHo, and environmental relative humidity RHi. Preparation of a stable ORS solution tablet therefore requires protection of moisture adsorbing components from the environment. The present UNICEF ORS mixture compacted easily by direct compression but gave fragile tablets, which were hygroscopic. This can be reduced by film coating the electrolyte component as granules with a resin (Eudragit L), or by simulating direct compression of the glucose as a compression-coating around the precompressed electrolytes. The packaging of compression-coated solution tablets in inexpensive polyethylene bags may lengthen the shelf-life and make the preparation less costly than the currently supplied ORS powders packed in laminated aluminium sachets. The increased dissolution lag time for the compacted tablet is a disadvantage that can be overcome by instructions to crush the product immediately before use.

Absorption↗

PubMedDate not supplied

[Dynamics of O2 and CO2 tensions in the brain (mathematical modeling)].

The mathematical model for description of the circulation and gas exchange dynamics in the brain is suggested. The model is based on a cell of two compact parallel capillary network with a brain tissue within. The equation system describing the model was calculated on a computer. The simulation showed that steady state pO2 in the cell during blood flow changes from 0.5 mm/sec to 0.25 or 1 mm/sec is reached within 2--5 sec. The dynamics of pCO2 is more inert. It was shown that the main factor in the dynamics of pO2 in the brain is the velocity of blood flow in capillaries. The dynamic pattern of pCO2 depends on haemodynamical condition, the structure of capillary network and physical properties of CO2.

Brain↗

PubMed2026

Molecular docking, molecular dynamics simulation, and enzyme inhibitory studies of vitamin K family members on aldose reductase.

Aldose reductase (AR) is a key enzyme in the polyol pathway and plays a major role in the progression of secondary complications of diabetes. Despite extensive efforts to develop natural and synthetic aldose reductase inhibitors (ARIs), most candidates have shown limited clinical efficacy, highlighting the need for more potent and selective inhibitors. In this study, we have systematically evaluated the inhibitory potential of vitamin K family members (vitamin K1, vitamin K2, and vitamin K3) using molecular docking, protein-ligand interaction analysis, molecular dynamics simulations, and enzyme kinetics. Docking analysis predicted that vitamin K2 has the highest binding affinity for AR. Subsequent molecular dynamics simulations revealed that both vitamin K1 and vitamin K2 formed stable complexes with the protein, exhibiting comparable RMSD (∼0.5 Å difference), similar RMSF profiles, and reduced radius of gyration, indicating compact and stable binding. Interaction analysis demonstrated that ligand binding is predominantly driven by hydrophobic interactions, with vitamin K2 forming a higher number of hydrophobic contacts, while vitamin K1 exhibited slightly more hydrogen bonding. Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) results further supports stronger binding of vitamin K2 (-56 kcal/mol) compared to vitaminK1 (-51 kcal/mol). Consistent with these findings, enzyme kinetics showed a slightly lower Ki value for vitamin K2 than vitamin K1. In contrast, vitamin K3 failed to maintain stable binding and moved out of the active site during simulation. Overall, the study highlights that hydrophobic interaction-driven stabilization plays a key role in ligand binding, and identifies vitamin K1 and vitamin K2 as promising inhibitors against AR, with vitamin K2 exhibiting more favourable hydrophobic interactions and binding stability.

Aldose Reductase↗

PubMed1978

On the formation of protein tertiary structure on a computer.

In this paper we carry out computer simulation studies of some of the factors responsible for protein tertiary structure. We show that it is possible to obtain (fold) a compact globular conformation from a sequence of amino acids consisting of only glycines and alanines. Our results indicate that glycines play a central role in stabilizing globular structures by facilitating the formation of turns and by destabilizing helical structures. Using this simple two-amino-acid representation, which serves as a control experiment, we are able to obtain a conformation that resembles the native structure of pancreatic trypsin inhibitor, as closely as any obtained previously in folding studies. However, careful examination reveals that the true chain topology has not been reproduced here or in previous studies. We suggest that the discrepancies between calculated and observed structures are more significant than the similarities. The implications of these results for the validity of models for protein folding, the use of pancreatic trypsin inhibitor in folding studies, and the possible role of glycine in the evolution of protein structure are discussed.

Alanine↗

PubMed1990

Density of trunk tissues of young and medium age people.

In this study the investigations made on about 50 trunk tissue densities are described. They were performed on ten cadavers of both sexes within 24 h of the moment of death. They were 20-40 yr old. The weight of each tissue was measured on a laboratory scale and the volume by placing the tissue in a pycnometer filled with water. The density of 2/3 solid trunk tissues ranged from 1.11 to 1.20 g cm-3. The lowest mean data was obtained for a lung tissue (0.563 g cm-3). The highest density datum known from the literature was that for a compact bone: 1.892 g cm-3. The application of obtained data can be for building dummies (e.g. in experiments of car-crash simulations), as well as in the calculation of inertia values using computerized tomography images.

Adult↗

PubMed1992

Trefoil knotting revealed by molecular dynamics simulations of supercoiled DNA.

Computer simulations of the supercoiling of DNA, largely limited to stochastic search techniques, can offer important information to complement analytical models and experimental data. Through association of an energy function, minimum-energy supercoiled conformations, fluctuations about these states, and interconversions among forms may be sought. In theory, the observation of such large-scale conformational changes is possible, but modeling and numerical considerations limit the picture obtained in practice. A new computational approach is reported that combines an idealized elastic energy model, a compact B-spline representation of circular duplex DNA, and deterministic minimization and molecular dynamics algorithms. A trefoil knotting result, made possible by a large time-step dynamics scheme, is described. The simulated strand passage supports and details a supercoiled-directed knotting mechanism. This process may be associated with collective bending and twisting motions involved in supercoiling propagation and interwound branching. The results also demonstrate the potential effectiveness of the Langevin/implicit-Euler dynamics scheme for studying biomolecular folding and reactions over biologically interesting time scales.

Chemical Phenomena↗

PubMed1991

A self-organizing multiple-view representation of 3D objects.

We explore representation of 3D objects in which several distinct 2D views are stored for each object. We demonstrate the ability of a two-layer network of thresholded summation units to support such representations. Using unsupervised Hebbian relaxation, the network learned to recognize ten objects from different viewpoints. The training process led to the emergence of compact representations of the specific input views. When tested on novel views of the same objects, the network exhibited a substantial generalization capability. In simulated psychophysical experiments, the network's behavior was qualitatively similar to that of human subjects.

Cybernetics↗

PubMed1991

A practical method to integrate some stiff systems.

A compact, absolutely stable numerical method is presented to integrate stiff systems of pseudo-linear, ordinary, first-order differential equations, commonly found in the simulation of biological models. Solutions are stepwise approximated by a complete set of first order rational polynomials. Mass balance is preserved by the approximations. No matrix inversions are required. Besides being stable, the method is also convergent and can be used with deferred approximation to the limit h = 0. Comparisons between this method and the Stoer-Bullirsch algorithm and fourth-order Runge-Kutta method are presented.

Algorithms↗

PubMed1987

Comparative morphology, histology and growth of the dental plates of the Devonian dipnoan Chirodipterus.

The dental plates of the Devonian lungfish Chirodipterus australis Miles (Osteichthyes; Dipnoi) are shown to have achieved their characteristic morphology by a growth process different from that assumed for the plates of genera such as Dipterus. Each plate was thickened by the addition of layers of bone that also extended the plate labially, thus providing the base on which and into which dentine grew. Distinctive features of the dentition are: (a) labial increase of the dentine mass by the addition of blister-like denticles of simple enamel-covered dentine, which is initially ingrown by pleromic dentine and subsequently resorbed and replaced by petrodentine; (b) increase in the midline by a similar process that results in the addition of one (or possibly two) new ridges; (c) resorption of the posterior edge of the pterygoid plates and the posterior and posteromedial edges of the prearticular plates, with subsequent development over the resorbed surfaces of several generations of simple regenerative dentine; (d) resorption and redeposition of pleromic dentine and bone in a triangular region posteromedially on the pterygoid plates; (e) the formation of tuberosities that simulate teeth at a short distance in from the labial edge, by four processes: formation of an undulating plate margin, differential growth of petrodentine (hard compact dentine) within the pulp cavity, differential wear of the petrodentine and the adjacent bone plus pleromic dentine, and slightly greater growth of the petrodentine towards the occlusal surface relative to the adjacent bone and dentine; (f) expansion of the large flat surfaces of the plates by gradual replacement of the bone and dentine at the proximal ends of the furrows and also by the development of linkages of petrodentine across the furrows; (g) development of isolated tuberosities on the flat posterolateral parts of the plates. The petrodentine of the ridges, tuberosities and plateaus of the plates is indistinguishable structurally and in its mode of growth from the petrodentine in extant species of dipnoans. Plates similar to those of C. australis have been observed in Stomiahykus, Archaeonectes, Conchodus, Palaedaphus and Sunwapta, as well as several species usually referred to as Dipterus. Sunwapta may be congeneric with C. australis.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

PubMed1992

Effects of compact volume and chain stiffness on the conformations of native proteins.

An investigation of the statistical properties of the native conformations of proteins, observed from crystal structures, is reported. Protein conformations were analyzed in terms of a bond vector correlation function and molecular volume. It was observed that, while the volume of a protein structure varies nearly linearly with the number of residues, the bond vector correlation function exhibits a universal feature for all sizes of proteins. To interpret the nature of the bond vector correlation function of native protein structures quantitatively, Monte Carlo simulations of realistic polypeptide chains of specific but arbitrary amino acid sequence were carried out. The molecule was constrained in an ellipsoidal volume determined by its chain length, and conformations with unacceptable nonbonded contacts between different amino acid residues were excluded. The interactions within a terminally blocked single residue, which correlate two nearest-neighbor peptide groups in a chain, were taken into account by an energetically biased sampling of its phi-psi space. The simulated chain correlation functions were found to be in good agreement with those of the crystal structures of beta-sheet-type and mixed-type (alpha+beta) proteins of similar length. On the basis of these calculations, it is concluded that the observed conformations of these native proteins may arise from two basic factors: the compactness of structures under hydrophobic interactions and the intrinsic stiffness of polypeptide chains due to the interactions within each terminally blocked residue.

Biophysical Phenomena↗

PubMed1992

Optimal protocol and trajectory visualization for conformational searches of peptides and proteins.

Conformational searches by molecular dynamics and different types of Monte Carlo or build-up methods usually aim to find the lowest-energy conformation. However, this is often misleading, as the energy functions used in conformational calculations are imprecise. For instance, though positions of local minima defined by the repulsive part of the Lennard-Jones potential are usually altered only slightly by functional modification, the relative depths of the minima could change significantly. Thus, the purpose of conformational searches and, correspondingly, performance criteria should be reformulated and appropriate methods found to extract different local minima from the search trajectory and allow visualization in the search space. Attempts at convergence to the lowest-energy structure should be replaced with efforts to visit a maximum number of different local energy minima with energies within a certain range. We use this quantitative criterion consistently to evaluate performances of different search procedures. To utilize information generated in the course of simulation, a "stack" of low energy conformations is created and stored. It keeps track of variables and visit numbers for the best representatives of different conformational families. To visualize the search, projection of multidimensional walks onto a principal plane defined by a set of reference structures is used. With Met-enkephalin as a structural example and a Monte Carlo procedure combined with energy minimization (MCM) as a basic search method, we analyzed the influence on search efficiency of different characteristics as temperature schedules, the step size for variable modification, constrained random step and response mechanisms to search difficulties. Simulated annealing MCM had comparable efficiency with MCM at constant and elevated temperature (about 600 K). Constraining the randomized choice of side-chain chi angles to optimal values (rotamers) on every MCM step did not improve, but rather worsened, the search efficiency. Two low-energy Met-enkephalin conformations with parallel Tyr1 and Phe4 rings, a gamma-turn around the Gly2 residue, and Phe4 and Met5 side-chains forming together a compact hydrophobic cluster were found and are suggested as possible structural candidates for interaction with a receptor or a membrane.

Amino Acid Sequence↗

PubMed1988

A numerical method for simulating the dynamics of human walking.

This paper presents a general method for simulating the movement of the lower extremity during human walking. It is based upon two separate algorithms: one for single support (an open kinematic chain), and the other for the double support phase (a closed-loop linkage). Central to each of these is the recursive Newton-Euler inverse dynamics algorithm, applicable, as given, to any serial, spatial linkage. For the unconstrained single support model, the Newton-Euler scheme is applied directly to numerically generate the equations of motion. In the case of double support, however, the kinematic constraint equations are used to first eliminate the redundant degrees of freedom, and then solve for the unknown ground reactions under the constrained limb. The attractiveness of the method is that it offers a compact alternative to manually deriving the equations defining a mathematical model for human gait.

Algorithms↗

PubMedDate not supplied

Chemical control of growth and morphological characteristics of anaplastic glioma cells.

Nerve growth factor (NGF) and glia maturation factor (GMF) reverse some of the transformed characteristics of T9 glioma cells (Marushige et al., Cancer Res 47: 4109-4115, 1987). As an attempt to define the mechanisms of such actions, various chemical agents which modulate second messenger systems were examined for their effects on growth and morphological characteristics of these cells. Administration of bromo-cAMP, forskolin and methylisobutylxanthine retarded cell growth and induced formation of long, branching processes which were similar to those induced by GMF. Perturbation of Ca2(+)-mediated processes by a Ca2+ ionophore, ionomycin, and by calmodulin antagonists, chlorpromazine and W-7, on the other hand, arrested cell growth, and caused clustering of cells, spreading of the cytoplasm and development of lamellipodium-like protrusions which were reminiscent of the effects of NGF. Administration of bromo-cAMP in combination with chlorpromazine, W-7 or ionomycin prevented spreading of the cytoplasm and produced compact cell bodies with well-developed processes. The results of this study demonstrate that modulation of specific second messenger systems by chemical agents are capable of simulating selective morphological changes inducible by NGF and GMF.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗

PubMed1992

Computer simulation of occupant neck response to airbag deployment in frontal impacts.

A mathematical simulation was performed to study the potential of head and neck injury to an unbelted driver restrained by an airbag. The baseline study represented a 50th percentile male dummy driving in a compact car with the steering wheel perpendicular to the floor. The vehicle was moving at 48 km/hour at the time of impact. Model predictions were compared with sled test results. The data agreed reasonably well. A parametric study was performed to study the effect of changing the steering wheel angle and the size of the airbag. It was found that when the standard 20 degrees angle steering wheel was used, neck joint torques were decreased by 22 percent while the resultant head acceleration increased 41 percent from the base line study. When the vertical dimension of the airbag was reduced by 10 percent, neck joint torques were increased by 14 percent, while head acceleration showed a slight decrease of 9 percent.

Acceleration↗

PubMed1978

Analysis of the penetrable space within the nucleus.

Radioactive glycogen molecules have been used as passive probes to compare cavity systems within nuclei and isolated chromatin. Isolated chromatin was found to possess a narrow range of microspaces with mean effective diameters between 4.0 and 4.5 nm (40 and 45 A) depending on shape assumptions. Intact nuclei contained a far larger class of free spaces with average diameters in the order of 11.0-15.0 nm. This clearly shows that DNase-I (diam. 4.1 nm) can penetrate and occupy a large proportion of nuclear space even though this enzyme does not readily attack the undisturbed nuclear structure. A structure which simulated the pattern of penetrability and incorporated other known properties of chromatin was used to explain this DNase-I resistance of intact nuclei in terms of an ordered, compact, local structure interspersed by much larger spaces. A system for this local packing is suggested and the functional implications of this type of organization considered.

Animals↗