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At least 379 records · Page 21Linked to original sources

PubMed2003

Dissecting the assembly of Abeta16-22 amyloid peptides into antiparallel beta sheets.

Multiple long molecular dynamics simulations are used to probe the oligomerization mechanism of Abeta(16-22) (KLVFFAE) peptides. The peptides, in the monomeric form, adopt either compact random-coil or extended beta strand-like structures. The assembly of the low-energy oligomers, in which the peptides form antiparallel beta sheets, occurs by multiple pathways with the formation of an obligatory alpha-helical intermediate. This observation and the experimental results on fibrillogenesis of Abeta(1-40) and Abeta(1-42) peptides suggest that the assembly mechanism (random coil --> alpha helix --> beta strand) is universal for this class of peptides. In Abeta(16-22) oligomers both interpeptide hydrophobic and electrostatic interactions are critical in the formation of the antiparallel beta sheet structure. Mutations of either hydrophobic or charged residues destabilize the oligomer, which implies that the 16-22 fragments of Arctic (E22G), Dutch (E22Q), and Italian (E22K) mutants are unlikely to form ordered fibrils.

Amyloid↗

PubMed1998

Mapping the active site of factor Xa by selective inhibitors: an NMR and MD study.

The structure of two selective inhibitors, Ac-Tyr-Ile-Arg-Ile-Pro-NH2 and Ac-(4-Amino-Phe)-(Cyclohexyl-Gly)-Arg-NH2, in the active site of the blood clotting enzyme factor Xa was determined by using transferred nuclear Overhauser effect nuclear magnetic resonance (NMR) spectroscopy. They represent a family of peptidic inhibitors obtained by the screening of a vast combinatorial library. Each structure was first calculated by using standard computational procedures (distance geometry, simulated annealing, energy minimization) and then further refined by systematic search of the conformation of the inhibitor docked in the active site and repeating the simulated annealing and energy minimization. The final structure was optimized by molecular dynamics simulations of the inhibitor-complex in water. The NMR restraints were kept throughout the refinement. The inhibitors assume a compact, very well defined conformation, embedded into the substrate binding site not in the same way as a substrate, blocking thus the catalysis. The model allows to explain the mode of action, affinity, and specificity of the peptides and to map the active site.

Amino Acid Sequence↗

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↗

PubMed2002

Completion and refinement of 3-D homology models with restricted molecular dynamics: application to targets 47, 58, and 111 in the CASP modeling competition and posterior analysis.

A method is presented to refine models built by homology by the use of restricted molecular dynamics (MD) techniques. The basic idea behind this method is the use of structure validation software to determine for each residue the likelihood that it is modeled correctly. This information is used to determine constraints and restraints in an MD simulation including explicit solvent molecules, which is used for model refinement. The procedure is based on the idea that residues that the validation software identifies as correctly positioned should be strongly constrained or restrained in the MD simulations, whereas residues that are likely to be positioned wrongly should move freely. Two different protocols are compared: one (applied to CASP3 target T58) using full structural constraints with separate optimization of each short fragment and the other (applied to T47) allowing some freedom using harmonic restraining potentials, with automatic optimization of the whole molecule. Structures along the MD trajectory that scored best in structural checks were selected for the construction of models that appeared to be successful in the CASP3 competition. Model refinement with MD in general leads to a model that is less like the experimental structure (Levitt et al. Nature Struct Biol 1999;6:108-111). Actually, refined T47 was slightly improved compared to the starting model; changes in model T58 led not to further enhancement. After the X-ray structure of the modeled proteins became known, the procedure was evaluated for two targets (T47 and the CASP4 target T111) by comparing a long simulation in water with the experimental target structures. It was found that structural improvements could be obtained on a nanosecond time scale by allowing appropriate freedom in the simulation. Structural checks applied to fast fluctuations do not appear to be informative for the correctness of the structure. However, both a simple hydrogen bond count and a simple compactness measure, if averaged over times of typically 300 ps, correlate well with structural correctness and we suggest that criteria based on these properties may be used in computational folding strategies.

Amino Acid Sequence↗

PubMed1997

The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis.

We studied the conformations of supercoiled DNA as a function of superhelicity and ionic conditions by determining its sedimentation coefficient both experimentally and by calculation. To cancel out unknown parameters from both calculations and experiments, we determined the ratio of the sedimentation coefficient, s, to that of open circular DNA, s(oc). Calculations of the sedimentation coefficient were based on direct solution of the Burgers-Oseen problem for an equilibrium set of DNA conformations generated for each condition by the Metropolis Monte Carlo procedure. There were no adjustable parameters in the Monte Carlo simulations because all three parameters of the DNA model used, bending and torsional elasticity of DNA and DNA effective diameter specifying electrostatic interactions, were known from independent data. The good agreement between measured and calculated values of s/s(oc) allowed us to interpret the sedimentation results in terms of DNA conformations, with particular emphasis on the marked effect of ionic conditions. As NaCl concentration decreases, s/s(oc) increases because the superhelix becomes less regular and more compact. In the presence of just 10 mM MgCl(2), supercoiled DNA adopts essentially the same set of conformations as in moderate to high concentrations of NaCl. Our simulations showed that s is a strong function of the superhelix branching frequency. At near physiological ionic conditions, there are about four branches in the 7 kb DNA molecule used in this work. We found no indication of superhelix collapse in any ionic conditions even remotely approaching physiological ones. For all ionic conditions studied, we conclude that the electrostatic interaction of DNA segments specified by the DNA effective diameter is the primary determinant of supercoiled DNA conformations.

Centrifugation, Density Gradient↗

PubMed2006

The simulation of the three-dimensional lattice hydrophobic-polar protein folding.

One of the most prominent problems in computational biology is to predict the natural conformation of a protein from its amino acid sequence. This paper focuses on the three-dimensional hydrophobic-polar (HP) lattice model of this problem. The modified elastic net (EN) algorithm is applied to solve this nonlinear programming hard problem. The lattice partition strategy and two local search methods (LS(1) and LS(2)) are proposed to improve the performance of the modified EN algorithm. The computation and analysis of 12 HP standard benchmark instances are also involved in this paper. The results indicate that the hybrid of modified EN algorithm, lattice partition strategy, and local search methods has a greater tendency to form a globular state than genetic algorithm does. The results of noncompact model are more natural in comparison with that of compact model.

Algorithms↗

PubMed2003

Monitoring folding transitions of synthetic, branched-chain polypeptides by capillary zone electrophoresis.

The coil/helix transition of a synthetic, branched-chain polymeric polypeptide (poly (Lys(Glu(1)-DL-Ala(3))EAK), 50-Lys residues long in the backbone, as a function of increasing molarities of methanol in solution, is here studied by both, circular dichroism (CD) and capillary zone electrophoresis. CD spectra showed that, at 75% v/v methanol, the transition from random coil to fully helical structure was obtained, in a pH 1.1 HCI solution in the presence of 20 mM NaCI. CZE studies, run in parallel, exhibited the classical unfolding to folding sigmoidal transition, with mid-point at 60% v/v methanol concentration, plateauing at ca. 80% v/v organic solvent. Surprisingly, though, such unfolding to folding transition was accompanied by an expansion, rather than a contraction, of the resulting ordered polypeptide. As the charge of the polypeptide (a pure polycation at a pH of 2.1 in CZE) was kept rigorously constant, a plot of the radius of the polymer along the sigmoidal transition clearly showed that the radius of gyration of the helical, structured polypeptide was in fact larger than that of the random coil. Such results were confirmed by molecular dynamics simulations, which indicated that the dimensions of such polypeptide, in alpha-helix configuration, were 8.5 nm (in length) and 3.2 nm (in diameter), whereas those of the corresponding random coil were 7.2 nm (in length) and 5.1 nm (length of shorter axis). It would thus appear that the randomized structure assumes the shape of a more compact object, roughly resembling a "rugby ball".

Buffers↗

PubMed2005

Study of the Villin headpiece folding dynamics by combining coarse-grained Monte Carlo evolution and all-atom molecular dynamics.

The folding mechanism of the Villin headpiece (HP36) is studied by means of a novel approach which entails an initial coarse-grained Monte Carlo (MC) scheme followed by all-atom molecular dynamics (MD) simulations in explicit solvent. The MC evolution occurs in a simplified free-energy landscape and allows an efficient selection of marginally-compact structures which are taken as viable initial conformations for the MD. The coarse-grained MC structural representation is connected to the one with atomic resolution through a "fine-graining" reconstruction algorithm. This two-stage strategy is used to select and follow the dynamics of seven different unrelated conformations of HP36. In a notable case the MD trajectory rapidly evolves towards the folded state, yielding a typical root-mean-square deviation (RMSD) of the core region of only 2.4 A from the closest NMR model (the typical RMSD over the whole structure being 4.0 A). The analysis of the various MC-MD trajectories provides valuable insight into the details of the folding and mis-folding mechanisms and particularly about the delicate influence of local and nonlocal interactions in steering the folding process.

Algorithms↗

PubMed2006

Implementation of discrete unitary transformations by multimode waveguide holograms.

Integration of holograms into multimode waveguides allows the implementation of arbitrary unitary mode transformations and unitary matrix-vector multiplication. Theoretical analysis is used to justify a design approach to implement specific functions in these devices. Based on this approach, a compact mode-order converter, a Hadamard transformer, and a spatial pattern generator-correlator are proposed and analyzed. Beam propagation simulations are used to verify the theoretical calculations and to address bandwidth, scalability, and fabrication criteria. Optical pattern generators were successfully fabricated using standard photolithographic techniques to demonstrate the feasibility of the devices.

Journal Article↗

PubMed1989

Applied potential tomography.

Applied Potential Tomography (APT) is a new method of imaging changes in the distribution of electrical resistivity within the human body. Such changes occur during respiration and, because of the movement of blood within the chest, during the cardiac cycle. Changes can also be observed due to redistribution of fluid within the body during simulated weightlessness. As very low electric currents are used to take measurements the method is safe. The equipment is simple and compact and ideal for use in space based measurement of physiological changes in the human body.

Aerospace Medicine↗

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↗

PubMed1994

Hermite expansions of compact support waveforms: applications to myoelectric signals.

Nonstationary signals with finite time support are frequently encountered in electrophysiology and other fields of biomedical research. It is often desirable to have a compact description of their shape and of their time evolution. For this purpose, Fourier analysis is not necessarily the best tool. The Hermite-Rodriguez and Associated Hermite basis functions are applied in this work. Both are based on the product of Hermite polynomials and Gaussian functions. Their general properties relevant to biomedical signal processing are reviewed. Preliminary applications are described concerning the analysis and description of: a) test signals such as a square pulse and a single cycle of a sinewave, b) electrically evoked myoelectric signals, and c) power spectra of either voluntary or evoked signals. It is shown that expansions with only five to ten terms provide an excellent description of the computer simulated and real signals. It is shown that these two families of Hermite functions are well suited for the analysis of nonstationary biological evoked potentials with compact time support. An application to the estimation of scaling factors of electrically evoked myoelectric signals is described. The Hermite functions show advantages with respect to the more traditional spectral analysis, especially in the case of signal truncation due to stimulation with interpulse intervals smaller than the duration of the evoked response. Finally, the Hermite approach is found to be suitable for classification of spectral shapes and compression of spectral information of either voluntary or evoked signals. The approach is very promising for neuromuscular diagnosis and assessment because of its capability for information compression and waveform classification.

Electrophysiology↗

PubMed2006

Numerical simulation of reactive processes in an experiment with partially saturated bentonite.

Bentonites are preferred materials for use as engineered barriers for high-level nuclear waste repositories. Simulation of geochemical processes in bentonite is therefore important for long-term safety assessment of those repositories. In this work, the porewater chemistry of a bentonite sample subject to simultaneous heating and hydration, as studied by Cuevas et al. [Cuevas, J., Villar, M., Fernández, A., Gómez, P., Martín, P., 1997. Porewaters extracted from compacted bentonite subjected to simultaneous heating and hydration. Applied Geochemistry 12, 473-481.], was assessed with a non-isothermal reactive transport model by coupling the geochemical software PHREEQC2 with the object-oriented FEM simulator GeoSys/RockFlow. Reactive transport modelling includes heat transport, two-phase flow, multicomponent transport and geochemical reactions in the liquid phase, i.e. ion exchange, mineral dissolution/precipitation and equilibrium reactions. Simulations show that the easily soluble minerals in bentonite determine the porewater chemistry. Temperature affects both two-phase flow and geochemical reactions. Porosity change due to dissolution/precipitation is low during the experiment. However, changes of the effective porosity caused by bentonite swelling can be very large. The simulated results agree well with the experimental data.

Bentonite↗

PubMed2003

CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle.

The further understanding of the mechanisms of gene regulatory networks requires comprehensive tools for both the representation of complicated signal transduction pathways and the in silico identification of genomic signals that govern the regulation of gene expression. Consequently, sophisticated notation must be developed to represent the signal transduction pathways in a form that can be readily processed by both computers and humans. We propose the regulator-reaction equations combined with detailed attributes including the associated cellular component, molecular function, and biological process and present the simulation-directed graphical notation that is derived from modification of Kohn's method. We have developed the software suite, CADLIVE (Computer-Aided Design of LIVing systEms), which features a graphical user interface (GUI) to edit large-scale maps of complicated signal transduction pathways using a conventional XML-based representation. The regulator-reaction equations represent not only mechanistic reactions, but also semantic models containing ambiguous and incomplete processes. In order to demonstrate the feasibility of CADLIVE, we constructed a detailed map of the budding yeast cell cycle, which consists of 184 molecules and 152 reactions, in a really compact space. CADLIVE enables one to look at the whole view of a large-scale map, to integrate postgenomic data into the map, and to computationally simulate the signal transduction pathways, which greatly facilitates exploring novel or unexpected interactions.

Cell Cycle↗

PubMed1999

Gradual development of protein-like global structures through functional selection.

This work focuses on streamlining the exploration of all possible sequences in an attempt to find polypeptides capable of folding into unique structures. Using a computer simulation, we have demonstrated the efficacy of constraining an 'active site' toward the correct configuration, in this case a particular conformation of a four-residue sequence, to bring about protein-like structure from a significant fraction of random sequences. The successive selections for a correct local configuration lead also to the gradual development of overall folding ability, helicity and compactness within 200 generations. The selection thus imposed alleviates an exhaustive search in sequence space.

Computer Simulation↗

PubMed2002

Shocks in vertically oscillated granular layers.

We study shock formation in vertically oscillated granular layers, using both molecular dynamics simulations and numerical solutions of continuum equations to Navier-Stokes order. A flat layer of grains is thrown up from an oscillating plate during each oscillation cycle and collides with the plate later in the cycle. The collisions produce layer compaction near the plate and a high temperature shock front that rapidly propagates upward through the layer. The shock is highly time dependent, propagating through the layer in only a quarter of the cycle. We compare numerical solutions of the continuum equations to molecular dynamics simulations that assume binary, instantaneous collisions between frictionless, inelastic hard spheres. The two simulations yield results for the shock position, shape, and speed that agree well. An investigation of the effect of inelasticity shows that the shock velocity increases continuously with decreasing inelasticity; the elastic limit is not singular.

Journal Article↗

PubMed1993

Protein three-dimensional structure generation with an empirical hydrophobic penalty function.

Given current computational environments, it is worthwhile to establish amino acid residue-level functions which approximate protein folds quite well. Such functions must be the interim steps toward protein three-dimensional structure prediction. I have shown that an empirical hydrophobic penalty function of protein, derived from the number of residues in a sphere around each residue, could be utilized to distinguish the correctly folded structure from the incorrect ones. In order to assess the predictive power of the penalty function, I have generated conformations by randomly changing main chain dihedral angles, and applied the penalty function to them. If only a local region was allowed to change its conformation, native-like structures could be generated within a reasonable computational time. In global simulations, however, a considerable number of nonnative conformations, which gave as small a penalty value as that of the native protein, were found. Although some of the conformations were compact and globular, they were quite different from the native structure in that they lacked most of the secondary structures. This result shows that the penalty function alone cannot define the native structure, and that substructure information may help the penalty function to reach the correctly folded structure.

Algorithms↗