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PubMed1989

A computer model to dynamically simulate protein folding: studies with crambin.

The current work describes a simplified representation of protein structure with uses in the simulation of protein folding. The model assumes that a protein can be represented by a freely rotating rigid chain with a single atom approximating the effect of each side chain. Potentials describing the attraction or repulsion between different types of amino acids are determined directly from the distribution of amino acids in the database of known protein structures. The optimization technique of simulated annealing has been used to dynamically sample the conformations available to this simple model, allowing the protein to evolve from an extended, random coil into a compact globular structure. Many characteristics expected of true proteins, such as the sequence-dependent formation of secondary structure, the partitioning of hydrophobic residues, and specific disulfide pairing, are reproduced by the simulation, suggesting the model may accurately simulate the folding process.

Computer Simulation↗

PubMed1998

Calculations on folding of segment B1 of streptococcal protein G.

We present an investigation of the folding thermodynamics and mechanism of segment B1 of streptococcal protein G. Molecular dynamics simulations of the fully solvated protein are used to probe thermodynamically significant states at different stages of folding. We performed several unfolding simulations to generate a database of initial conditions. The database is analyzed and clustered. The cluster centers extracted from this database were then used as starting points for umbrella sampling of the folding free energy landscape under folding conditions. The resulting sampling was combined with the weighted histogram analysis method. One and two-dimensional free energy surfaces were constructed along several order parameters and used to analyze the folding process. Our findings indicate that an initial collapse precedes the formation of significant native structure. Elements of local structure originate in the regions of the protein shown to have higher H/2H exchange protection factors in early stages of folding. A non-native contact, observed experimentally at the N terminus of the alpha-helix in a peptide excised from the protein, is seen to pre-organize the chain in early stages of folding. Collapse and early structure formation yields a compact globule with a significant number of water molecules present. Desolvation of the protein core is coincident with the final stages of folding from the compact state.

Bacterial Proteins↗

PubMed1999

Additional studies on the distribution of stresses during vertical compaction of gutta-percha in the root canal.

OBJECTIVE: This study was designed to investigate the effect of certain pathological alterations of the dental structures (diminishing bone support, internal resorption, root perforation, periapical lesion) on stress distribution during root canal filling procedures by the warm vertical compaction technique. DESIGN: The computer stress analyses were done for a maxillary canine tooth model which was based on dimensions recovered from a human cadaveric maxilla scanned by CT. METHODS: The finite element method was used to calculate the stresses generated during root canal filling procedures by warm vertical compaction technique. Patterns of stress distribution associated with various alterations in dental structures were investigated. For this purpose 60 cases were simulated. The hypothetical force of 10 N is taken as a unit representation. For other magnitudes of applied force, the corresponding stresses would be scaled directly because the calculations were made for linear materials. RESULTS AND CONCLUSION: It is found that, when diminishing bone support and internal resorption are concurrently simulated, a marked increase in stress magnitudes occur (maximum von Mises stress 5.37 N/mm2). However, these values still remain much below the most frequently reported tensile strength of dentine (50-100 N/mm2). If dentist's handwork is transformed into equivalent edge tractions on gutta-percha, then stresses in dentine, even when they are corrected for 3-kg applied force, appear to remain below fracture strengths of this material. This result leads us to conclude that when warm vertical compaction technique is skillfully performed and inadvertent undue force is not applied, a premature root fracture in a large rooted maxillary anterior tooth with straight root canal anatomy is not likely to occur, even for the unfavourable conditions simulated in our model. This result, like all results derived from modelling applications, is of course contingent upon agreement between the way in which the clinical operations are performed and the way in which they are mirrored for computer representation. We believe that the approach described here avoids the spurious stresses that have been reported in similar investigations.

Computer Simulation↗

PubMed2000

Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human.

BACKGROUND: Knowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrate Fugu rubripes (pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human and Fugu were studied using data from public databases. METHODS: Intron length and map positions of human and Fugu orthologues were compared to analyse relative genome compaction and synteny conservation respectively. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data. RESULTS: Analysis of 199 introns in 22 orthologous genes showed an eight-fold average size reduction in Fugu, consistent with the ratio of total genome sizes. There was no consistent pattern relating the size reduction in individual introns or genes to gene base composition in either species. For genes that are neighbours in Fugu (genes from the same cosmid or GenBank entry), 40-50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incomplete human genome sequence data and the existence of dispersed gene families. Some genes that are neighbours in Fugu have human orthologues that are several megabases and tens of genes apart. This is probably caused by small inversions or other intrachromosomal rearrangements. CONCLUSIONS: Comparison of observed data to computer simulations suggests that 4000-16 000 chromosomal rearrangements have occurred since Fugu and human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons.

Animals↗

PubMed2026

Marine air promotes structural compaction and coating growth of soot aerosols after long-range transport from East Asia.

Soot aerosol, a key global warming contributor, undergoes morphological and chemical transformations during atmospheric transport, particularly in humidified marine environments. This study investigates morphology, mixing state, and aging mechanisms of soot particles collected in the Bohai Sea and Yellow Sea. Transmission electron microscopy analyses reveal that coated soot particles dominate the marine atmosphere, accounting for over 98 % of soot-containing particles, with a mean mixing state index (χ) of 0.83. The fractal dimension (Df) of soot particles is 1.84 ± 0.05 in the Northern Yellow Sea, 1.90 ± 0.08 in the Bohai Sea, and 1.96 ± 0.07 in the Southern Yellow Sea, indicating structural compaction during long-range transport. Correspondingly, the average Dp/Dcore ratios (particle to core size ratio) are 5.3 in the Bohai Sea, 4.2 in the Northern Yellow Sea, and 3.9 in the Southern Yellow Sea. Notably, those ratios are higher in marine environments compared to those observed during continental regional transport from northern to southern China (3.54), suggesting enhanced coating growth in humid marine air. The results highlight the important role of marine atmospheres in accelerating soot aging, which in turn leads to significantly stronger light absorption compared to soot in continental air. Our results highlight the necessity of incorporating compact morphologies, uniform mixing states, and thick coatings into optical models for accurate radiative forcing simulations.

Aerosols↗

PubMed2002

Hydraulic properties and leachate level analysis of Kimpo metropolitan landfill, Korea.

Hydraulic properties of waste and cover soil from Kimpo Metropolitan Landfill were experimentally measured by laboratory tests. The degree of compaction was changed to identify the effect on hydraulic conductivity, field capacity, and permanent wilting point. Properties were utilized in developing a reliable numerical tool for leachate analysis. HELP, a simulation model for hydrologic evaluation of landfill performance, was adopted for that purpose. For calibration, results from simulation using the parameter values measured by laboratory tests were compared against the field data. The model was applied to predict the leachate level change according to the degree of compaction and cover soil thickness variation. It was found that the increase in the degree of compaction for intermediate cover soil and waste results in the decrease of field capacity and hydraulic conductivity, hence, the increase of leachate level. The effect of cover layer thickness on the leachate level was minor. Based on the findings from laboratory and numerical experiments, a guideline for reclamation practice was recommended.

Calibration↗

PubMed2000

Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering.

The shape of free Thermus flavus 5 S rRNA in solution at 1.3 nm resolution is restored from synchrotron x-ray scattering data using an ab initio simulated annealing algorithm. The free 5 S rRNA is a bent elongated molecule displaying a compact central region and two projecting arms, similar to those of the tRNA. The atomic models of the 5 S rRNA domains A-D-E and B-C in the form of elongated helices can be well accommodated within the shape, yielding a tentative model of the structure of the free 5 S rRNA in solution. Its comparison with the recent protein-RNA map in the ribosome (Svergun, D. I., and Nierhaus, K. H. (2000) J. Biol. Chem. 275, 14432-14439) indicates that the 5 S rRNA becomes essentially more compact upon complex formation with specific ribosomal proteins. A conceivable conformational change involves rotation of the B-C domain toward the A-D-E domain. The model of free 5 S rRNA displays no interactions between domains E and C, but such interactions are possible in the bound molecule.

Algorithms↗

PubMed2002

Phosphorylation-induced conformational changes in a mitogen-activated protein kinase substrate. Implications for tyrosine hydroxylase activation.

Mitogen-activated protein (MAP) kinase-mediated phosphorylation of specific residues in tyrosine hydroxylase leads to an increase in enzyme activity. However, the mechanism whereby phosphorylation affects enzyme turnover is not well understood. We used a combination of fluorescence resonance energy transfer (FRET) measurements and molecular dynamics simulations to explore the conformational free energy landscape of a 10-residue MAP kinase substrate found near the N terminus of the enzyme. This region is believed to be part of an autoregulatory sequence that overlies the active site of the enzyme. FRET was used to measure the effect of phosphorylation on the ensemble of peptide conformations, and molecular dynamics simulations generated free energy profiles for both the unphosphorylated and phosphorylated peptides. We demonstrate how FRET transfer efficiencies can be calculated from molecular dynamics simulations. For both the unphosphorylated and phosphorylated peptides, the calculated FRET efficiencies are in excellent agreement with the experimentally determined values. Moreover, the FRET measurements and molecular simulations suggest that phosphorylation causes the peptide backbone to change direction and fold into a compact structure relative to the unphosphorylated state. These results are consistent with a model of enzyme activation where phosphorylation of the MAP kinase substrate causes the N-terminal region to adopt a compact structure away from the active site. The methods we employ provide a general framework for analyzing the accessible conformational states of peptides and small molecules. Therefore, they are expected to be applicable to a variety of different systems.

Animals↗

PubMed1990

In vitro comparison of the cytotoxicity of twelve endodontic materials using a new technique.

An in vitro method for the cytotoxicity testing of endodontic materials is described which aims to simulate the clinical situation. Materials can be tested in the presence or absence of a compacted layer of dentine chips mimicking the periapical dentine plug. A total of twelve materials were tested. In the absence of dentine, Kloroperka, Biocalex, Diaket and Endomethasone were slightly cytotoxic; AH26 with and without silver, Sealapex, Tubliseal and Kerr's pulp canal sealer were moderately cytotoxic, while Forfenan, Spad and Kri paste were strongly cytotoxic. In the presence of dentine the cytotoxicity of these materials was considerably reduced, with the exception of Endomethasone, Forfenan, Spad and Kri paste. The method provides a satisfactory alternative to implantation testing and is an inexpensive and reproducible test system in which dentine can be incorporated.

Administration, Topical↗

PubMed2003

Neural network training with global optimization techniques.

This paper presents an approach of using Simulated Annealing and Tabu Search for the simultaneous optimization of neural network architectures and weights. The problem considered is the odor recognition in an artificial nose. Both methods have produced networks with high classification performance and low complexity. Generalization has been improved by using the backpropagation algorithm for fine tuning. The combination of simple and traditional search methods has shown to be very suitable for generating compact and efficient networks.

Algorithms↗

PubMed2002

Large clusters in supercritical percolation.

The statistical behavior of the size of large finite clusters in supercritical percolation on a finite lattice is investigated (below the critical dimension of the space d(c)=6). For this purpose, an approximate system of ordinary differential equations for a number of finite clusters is obtained. The correlation between the critical exponents zeta that determine the cluster decay law (ln n(s) approximately -s(zeta)) and the surface of clusters is shown. It is found that for clusters without self-intersections having a maximal surface zeta=1. For clusters with a small number of self-intersections zeta=1-eta. Here eta is a function depending on the ratio of the surface area of a cluster to its size, which tends to zero, when the surface tends to a maximum. For compact clusters with a minimum or near-minimum surface area, the first correction to the cluster decay law above percolation threshold (ln n(s) approximately -s((d-1)/d)) has been found on the basis of the drop model and the derived system of equations. The predictions are tested numerically on two- and three-dimensional lattices by Monte Carlo simulations. The results of the work allow one to conclude that above the percolation threshold majority of large clusters are compact and that the cluster surface is the main factor affecting its behavior in supercritical percolation.

Journal Article↗

PubMed1999

Simulation of the packing of idealized transmembrane alpha-helix bundles.

The aim of this study is to investigate if the packing motifs of native transmembrane helices can be produced by simulations with simple potentials and to develop a method for the rapid generation of initial candidate models for integral membrane proteins composed of bundles of transmembrane helices. Constituent residues are mapped along the helix axis in order to maintain the amino acid sequence-dependent properties of the helix. Helix packing is optimized according to a semi-empirical potential mainly composed of four components: a bilayer potential, a crossing angle potential, a helix dipole potential and a helix-helix distance potential. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. Preliminary testing of the method has been conducted with idealized seven Ala(20) helix bundles. The structures generated show a high degree of compactness. It was observed that both bacteriorhodopsin-like and delta-endotoxin-like structures are generated in seven-helix bundle simulations, within which the composition varies dependent upon the cooling rate. The simulation method has also been employed to explore the packing of N = 4 and N = 12 transmembrane helix bundles. The results suggest that seven and 12 transmembrane helix bundles resembling those observed experimentally (e.g., bacteriorhodopsin, rhodopsin and cytochrome c oxidase subunit I) may be generated by simulations using simple potentials.

Bacteriorhodopsins↗

PubMed2025

RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.

RNA G-quadruplexes (rG4s) are emerging as vital structural elements involved in processes like gene regulation, translation, and genome stability. Found in untranslated regions of messenger RNAs (mRNAs), they influence translation efficiency and mRNA localization. Additionally, rG4s of long noncoding RNAs and telomeric RNA play roles in RNA processing and cellular aging. Despite their significance, the atomic-level folding mechanisms of rG4s remain poorly understood due to their complexity. We studied the folding of the r(GGGA)3GGG and r(GGGUUA)3GGG (TERRA) sequences into parallel-stranded rG4 using all-atom enhanced-sampling molecular dynamics simulations, applying well-tempered metadynamics coupled with solute tempering. The obtained folding pathways suggest that RNA initially adopts a compacted coil-like ensemble characterized by dynamic guanine stacking and pairing. The three-quartet rG4 gradually forms from this compacted coil ensemble via diverse routes involving strand rearrangements and guanine incorporations. While the folding mechanism is multipathway, various two-quartet rG4 structures appear to be a common transitory ensemble along most routes. Thus, the process seems more complex than previously predicted, as G-hairpins or G-triplexes do not act as distinct intermediates, even though some are occasionally sampled. We also discuss the challenges of applying enhanced sampling methodologies to such a multidimensional free-energy surface and address the force-field limitations.

G-Quadruplexes↗

PubMed1999

Fatigue-crack propagation in Nitinol, a shape-memory and superelastic endovascular stent material.

Improving the design and performance of medical stents for implantation in the human body is of current interest. This paper describes a study of fatigue-crack propagation behavior in the superelastic alloy Nitinol. Specifically, the objective of this work was to study the effect of environment on cyclic crack-growth resistance in an approximately 50Ni-50Ti (atom %) alloy and to provide the necessary data for the safe life prediction of Nitinol endovascular stents. The material selected for this study was heat treated such that it was superelastic at human body temperature; this was confirmed with monotonic uniaxial tensile tests. Characterization of fatigue-crack growth rates was performed at 37 degrees C on disk-shaped compact-tension samples in environments of air, aerated deionized water, and aerated Hank's solution (a simulated body fluid). The effect of cyclic loading on the uniaxial constitutive behavior was investigated at a strain range of 6.4%, and results indicate that the magnitude of available superelastic strain ( approximately 5.0%) is maintained even after cyclic softening. However, despite the persistence of nucleating the stress-induced martensitic phase after cycling with a maximum strain slightly below the plastic yield point, Nitinol was found to have the lowest fatigue-crack growth resistance of the principal metallic alloys currently used for implant applications.

Alloys↗

PubMedDate not supplied

Crystal structure of chicken liver basic fatty acid-binding protein at 2.7 A resolution.

The three-dimensional structure of chicken liver basic fatty acid-binding protein has been determined at 2.7 A resolution by X-ray crystallography. Phases were calculated using the multiple isomorphous replacement procedure and a preliminary model was built. This model, with an initial R-factor of 0.57, was then improved by a cycle of refinement by simulated annealing which brought the R factor down to 0.32. The protein is structured as a compact 10-stranded-beta-barrel which encapsulates a residual electron density that can be interpreted as a fatty acid molecule. The NH2-terminus portion of the molecule contains two short alpha-helices. The structure of this liver protein appears very similar to that of the Escherichia coli derived rat intestinal FABP recently determined by X-ray diffraction methods.

Animals↗

PubMed1999

Bioactive ceramics prepared by sintering and crystallization of calcium phosphate invert glasses.

Novel glass-ceramics were synthesized via sintering and crystallization by heating powder compacts of SiO2-free calcium phosphate invert glasses of 60CaO x 30P2O5 x 7Na2O x 3TiO2 or 60CaO x 30P2O5 x 7Na2O x 3MgO at 800-850 degrees C in air. The glass-ceramics were relatively dense materials consisting of crystalline phases such as beta-Ca3(PO4)2 and beta-Ca2P2O7 with glassy phases. The compacts were densified by the viscous flow of the glassy phases while heating. By soaking in simulated body fluid at 37 degrees C, a calcium phosphate phase was formed newly on the surface of the glass-ceramic derived from 60CaO x 30P2O5 x 7Na2O x 3TiO2 glass, while the phase was not formed on that derived from 60CaO x 30P2O5 x 7Na2O x 3MgO glass: the former was implied to show bioactivity. Composition of the glassy phase as the matrix varies with the additives such as TiO2 and MgO, and the chemical properties of the phase influence the bioactivity of the glass-ceramics. The glass-ceramic derived from 60CaO x 30P2O5 x 7Na2O x 3TiO2 glass has relatively high fracture toughness of K(IC) approximately 2 MPa m(0.5) and bending strength of 100-120 MPa.

Calcium Compounds↗

PubMed1995

Solution structure of the MutT enzyme, a nucleoside triphosphate pyrophosphohydrolase.

The MutT enzyme (129 residues) catalyzes the hydrolysis of normal and mutagenic nucleoside triphosphates, such as 8-oxo-dGTP, by substitution at the rarely attacked beta-P, to yield NMP and pyrophosphate. Previous heteronuclear NMR studies of MutT have shown the secondary structure to consist of a five-stranded mixed beta-sheet connected by the loop I-alpha-helix I--loop II motif, by two tight turns, and by loop III, and terminated by loop IV--alpha-helix II [Abeygunawardana et al. (1993) Biochemistry 32, 13071-13080; Weber et al. (1993) Biochemistry 32, 13081-13087). Complete side-chain assignments of 1H and 13C resonances have now been made by 3D C(CO)NH and HCCH-TOCSY experiments. A total of 1461 interproton proximities (11 per residue), obtained by 3D 15N-resolved NOESY-HSQC and 3D 13C-resolved NOESY-HSQC spectra, including 372 long-range NOEs, as well as 65 dihedral angle (phi) restraints and 34 backbone hydrogen bond restraints were used to determine the tertiary structure of MutT by distance geometry, simulated annealing, and energy minimization with the program X-PLOR. The structure is globular and compact with the parallel portion of the beta-sheet sandwiched between the two alpha-helices, forming an alpha+beta fold. The essential divalent cation has previously been shown to bind near residues Gly-37, Gly-38, Lys-39, and Glu-57, and nucleotides have been shown to bind near residues Leu-54 and Val-58 by NMR relaxation methods [Frick et al. (1995) Biochemistry 34, 5577-5586].(ABSTRACT TRUNCATED AT 250 WORDS)

Bacterial Proteins↗

PubMed1991

Mathematical model of geometry and fibrous structure of the heart.

We developed a mathematical representation of ventricular geometry and muscle fiber organization using three-dimensional finite elements referred to a prolate spheroid coordinate system. Within elements, fields are approximated using basis functions with associated parameters defined at the element nodes. Four parameters per node are used to describe ventricular geometry. The radial coordinate is interpolated using cubic Hermite basis functions that preserve slope continuity, while the angular coordinates are interpolated linearly. Two further nodal parameters describe the orientation of myocardial fibers. The orientation of fibers within coordinate planes bounded by epicardial and endocardial surfaces is interpolated linearly, with transmural variation given by cubic Hermite basis functions. Left and right ventricular geometry and myocardial fiber orientations were characterized for a canine heart arrested in diastole and fixed at zero transmural pressure. The geometry was represented by a 24-element ensemble with 41 nodes. Nodal parameters fitted using least squares provided a realistic description of ventricular epicardial [root mean square (RMS) error less than 0.9 mm] and endocardial (RMS error less than 2.6 mm) surfaces. Measured fiber fields were also fitted (RMS error less than 17 degrees) with a 60-element, 99-node mesh obtained by subdividing the 24-element mesh. These methods provide a compact and accurate anatomic description of the ventricles suitable for use in finite element stress analysis, simulation of cardiac electrical activation, and other cardiac field modeling problems.

Animals↗