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At least 1,117 records · Page 62Linked to original sources
PubMed1990

Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis.

Alignment of the 87 available sequences of group I self-splicing introns reveals numerous instances of covariation between distant sites. Some of these covariations cannot be ascribed to historical coincidences or the known secondary structure of group I introns, and are, therefore, best explained as reflecting tertiary contacts. With the help of stereochemical modelling, we have taken advantage of these novel interactions to derive a three-dimensional model of the conserved core of group I introns. Two noteworthy features of that model are its extreme compactness and the fact that all of the most evolutionarily conserved residues happen to converge around the two helices that constitute the substrate of the core ribozyme and the site that binds the guanosine cofactor necessary for self-splicing. Specific functional implications are discussed, both with regard to the way the substrate helices are recognized by the core and possible rearrangements of the introns during the self-splicing process. Concerning potential long-range interactions, emphasis is put on the possible recognition of two consecutive purines in the minor groove of a helix by a GAAA or related terminal loop.

Animals↗
PubMed2002

J-integral fracture toughness and tearing modulus measurement of radiation cross-linked UHMWPE.

Radiation and chemical cross-linking of medical grade ultrahigh molecular weight polyethylene (UHMWPE) has recently been utilized in an effort to improve wear performance of total joint replacement components. However, reductions in mechanical properties with cross-linking are cause for concern regarding the use of cross-linked UHMWPE for high-stress applications such as in total knee replacement prostheses. In this study, the fracture behavior of radiation cross-linked UHMWPE was compared to that of uncross-linked UHMWPE. The Rice and Sorensen model that utilizes mechanical parameters obtained from uniaxial tensile and compact tension tests was used to calculate the steady state J-integral fracture toughness, Jss, for radiation cross-linked UHMWPE. Jss decreased monotonically with increase in radiation dose. UHMWPE exhibited tough, ductile tearing behavior with stable crack growth when it was cross-linked using a gamma radiation dose of 0-50 kGy. However, in cross-linked UHMWPE irradiated to a dose of 100 and 200 kGy, unstable fracture occurred spontaneously upon attaining the initial crack driving force, J1c. This indicates that a high degree of cross-linking is less desirable for high-stress applications in orthopaedic implants. However, a substantial increase in J1c, even at a low degree of cross-linking, suggests that a low degree of cross-linking may be beneficial for resistance to delamination and catastrophic failure, both of which require an initiation step for the fracture to propagate in the material. This mechanical test should, however, be considered along with fatigue tests and joint simulator testing before determination of an appropriate amount of cross-linking for total joint replacement prostheses that experience high stresses.

Arthroplasty, Replacement, Knee↗
PubMed1991

Molecular mechanics studies of dinucleoside methylphosphonates: influence of methylphosphonate and its chirality on the phosphodiester conformation.

Molecular mechanics studies are performed on single stranded as well as base paired forms of dinucleoside methylphosphonates comprising different base sequences for both the S- and R-isomers of methylphosphonate (MP). S-MP produces noticeable distortions in the geometry, locally at the phosphate center, and this enables the stereochemical feasibility of compact g- g- phosphodiester. Besides, it tends to perturb the conformations around the P-O3' and glycosyl bonds, causing minor variations in stacking interactions. In single stranded dinucleosides, the gain in adjacent base stacking interaction energies seems to be sufficient to overcome the barrier to P-O3' bond rotation arising due to S-MP...sugar interaction, and this results in transition to a compact phosphodiester (BI-type) from an initial extended phosphodiester (BII-type) conformation. Such a thing seems rather difficult in base pair constrained duplexes. Dinucleosides with R-MP behave analogous to normal phosphate duplexes as the methyl group is away from the sugar. It is found that dinucleoside methylphosphonates are energetically less favoured than the corresponding dinucleoside phosphates mainly due to the depletion of contributions from electrostatic attractive interactions involving the base and sugar with the methylphosphonate consequent to the nonionic nature of the latter. Neither S-MP nor R-MP seem to significantly alter the stereochemistry of duplex structure.

Computer Simulation↗
PubMed2006

Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers.

When mixed together, DNA and polyaminoamide dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension curves (FECs). A characteristic force plateau (around 10 pN) and hysteresis between the pulling and relaxation cycles are observed for different dendrimer sizes, indicating the existence of a first-order transition between two phases (condensed and extended) of the fiber. Upon salt variation FECs change noticeably confirming that electrostatic forces drive the condensation transition. We propose a simple model for the decondensing transition that qualitatively reproduces the FECs and which is confirmed by atomic force microscopy images.

Bacteriophage lambda↗
PubMed2001

Reconstructing hierarchical tetrahedral mesh density models of bony anatomy.

We proposed an efficient and automatic method to reconstruct hierarchical tetrahedral meshes and build density models for bony anatomy from CT data sets. The mesh is reconstructed from contours extracted in CT images corresponding to the outer bone surfaces and the boundaries between compact bone, spongy bone and medullary cavity. Key problems, such as tiling problem, branching problem, correspondence problem, and constraint problem, have been solved. We then approximated bone density variations by means of continuous density functions in each tetrahedron. The density functions are written as smooth Bernstein polynomial spline expressed in terms of barycentric coordinates associated with each tetrahedron. We further performed the tetrahedral mesh simplification by edge collapsing and built hierarchical structure of multiple resolution meshes. We applied our density model to efficiently generate Digitally Reconstructed Radiographs. This research is part of our effort to build a bone density atlas.

Algorithms↗
PubMed2004

Stress intensity variations in bone microcracks during the repair process.

Microscopic cracks form and grow in compact bone in vivo due to cyclic loading. Their growth can cause stress fractures and has been implicated in the processes of remodelling and adaptation. These cracks are repaired by the actions of BMUs which are mobile resorption cavities. In this work, we studied the interaction between cracks and BMUs by making finite element models representing different stages in the repair process. The tendency of the crack to grow was measured by its stress intensity factor, K. We found that K changes in a complex manner during the repair process, both decreasing and increasing depending on the size of the crack and the type of loading applied. For loading conditions similar to those that exist in vivo, the presence of the BMU can cause K to rise significantly, in some cases by more than 20%, implying a substantial increase in crack growth rate. This information is important for our general understanding of the complexities of the repair process, and especially for the development of theoretical models to simulate damage and repair in bone.

Animals↗
PubMed2005

How the chromatin fiber deals with topological constraints.

In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of the so-called 30-nm chromatin fiber and accordingly imposes strong topological constraints. We present a general method for computing both the twist and the writhe of any winding pattern. An explicit derivation is implemented for the chromatin fiber which provides the linking number of DNA in eukaryotic chromosomes. We show that there exists one and only one unwinding path which satisfies both topological and mechanical constraints that DNA has to deal with during condensation/decondensation processes.

Animals↗
PubMed2005

Fast method for estimating the energy distribution of globular states of proteins.

By an enumeration study, we show that the energy distributions of a lattice protein sequence on all possible compact lattice configurations can be approximated by the energy distribution of shuffled sequences on a given lattice structure. We also show that the random energy model (REM) gives a good analytical approximation for the energy distribution of shuffled sequences on lattice structures. For real proteins, when a gapped threading method is used, REM calculations systematically underestimate the mean value of the energy distributions. We found that this discrepancy can be roughly compensated by a linear correction obtained from empirical fits. This result can be used to greatly reduce the computational effort in protein threading calculations.

Algorithms↗
PubMed2002

A compact view of isochores in the draft human genome sequence.

Prior to genome sequencing, information on base composition (GC level) and its variation in mammalian genomes could be obtained using density gradient ultracentrifugation. Analyses using this approach led to the conclusion that mammalian genomes are organized into mosaics of fairly homogeneous regions, called isochores. We present an initial compositional overview of the chromosomes of the recently available draft human genome sequence, in the form of color-coded moving window plots and corresponding GC level histograms. Results obtained from the draft human genome sequence agree well with those obtained or deduced earlier from CsCl experiments. The draft sequence now permits the visualization of the mosaic organization of the human genome at the DNA sequence level.

Base Composition↗
PubMed1992

Molecular conformation of ubiquitinated structures and the implications for regulatory function.

The molecular conformation of ubiquitinated structures and the validity of the N-end rule were examined by simulating the molecular mechanics to ascertain the global energy-minimized structure. We examined the chemical linkage involved in attaching the ubiquitin carboxyl terminus to the N-terminus of three different x-hexapeptides, where x is the amino group of the acceptor peptide--either valine, arginine or glutamic acid--(x-K linkage) and to the epsilon-amino group of lysine of the acceptor hexapeptide x-glu1-his2-lys3-gly4-lys5-val6 (K-K linkage) through the formation of an isopeptide bond. Changes in conformation and molecular stability of the multi-ubiquitinated structures were determined by energy-minimization procedures using the SYBYL program developed by Tripos Associates. In the x-K linkage, the ubiquitin molecule is stretched in the beta-pleated sheets and beta-turns while the alpha-helices expand, as the molecule continues to unfold linearly. In the K-K linkage, the ubiquitin molecules have turned into a u-shaped, semi-circular alignment, contracting into a compact, folded structure.

Amino Acid Sequence↗
PubMed2006

Gaseous bradykinin and its singly, doubly, and triply protonated forms: a first-principles study.

The conformers of gaseous bradykinin, BK, (Arg(1)-Pro(2)-Pro(3)-Gly(4)-Phe(5)-Ser(6)-Pro(7)-Phe(8)-Arg(9)) and its protonated forms, [BK + H](+), [BK + 2H](2+), and [BK + 3H](3+), were examined theoretically using a combination of the Merck molecular force field, Hartree-Fock, and density functional theory. Neutral BK, [BK + H](+), and [BK + 2H](2+) exist in zwitterionic forms that are stabilized by internal solvation and have compact structures; [BK + 3H](3+) differs by the absence of a salt bridge and adopts an elongated form. The common structural feature in all four BK species is a beta-turn in the Ser(6)-Pro(7)-Phe(8)-Arg(9) sequence. The gas-phase basicity of [BK + H](+) estimated from the calculated protonation energy is in accord with published experimental basicity; population-weighted collision cross-sections of the three ionic forms are in agreement with experimental cross-sections in the literature.

Arginine↗
PubMed2003

Electromagnetic radiation from ingested sources in the human intestine between 150 MHz and 1.2 GHz.

The conventional method of diagnosing disorders of the human gastro-intestinal (GI) tract is by sensors embedded in cannulae that are inserted through the anus, mouth, or nose. However, these cannulae cause significant patient discomfort and cannot be used in the small intestine. As a result, there is considerable ongoing work in developing wireless sensors that can be used in the small intestine. The radiation characteristics of sources in the GI tract cannot be readily calculated due to the complexity of the human body and its composite tissues, each with different electrical characteristics. In addition, the compact antennas used are electrically small, making them inefficient radiators. This paper presents radiation characteristics for sources in the GI tract that should allow for the optimum design of more efficient telemetry systems. The characteristics are determined using the finite-difference time-domain method with a realistic antenna model on an established fully segmented human body model. Radiation intensity outside the body was found to have a Gaussian-form relationship with frequency. Maximum radiation occurs between 450 and 900 MHz. The gut region was found generally to inhibit vertically polarized electric fields more than horizontally polarized fields.

Adult↗
PubMed1994

Visualization of protein-nucleic acid interactions involved in the in vitro assembly of the Escherichia coli 50 S ribosomal subunit.

Protein-nucleic acid interactions which occur during Escherichia coli 50 S ribosomal subunit assembly between 23 S rRNA, 5 S rRNA and a complete set of 34 L-proteins were monitored by high resolution scanning transmission electron microscopy (STEM). This approach made it possible to visualize and quantitatively analyze conformational changes induced in the rRNAs during E. coli 50 S ribosomal subunit assembly. The reconstituted RNA-protein complexes, the control 23 S rRNA and native 50 S subunits were characterized by their mass and morphology. Association of 23 S rRNA with the first assembly protein, L24, led to the formation of a distinct nucleus of mass ("cluster") on the filamentous and loosely coiled molecule of the 23 S rRNA. This structural feature was preserved and enhanced in 23 S rRNA after its association with the rest of the early assembly proteins, namely L3, L20, L13, L4 and L22. Since the above proteins, with the exception of L3, bind to the 5' end of the 23 S rRNA, the cluster seems to be formed predominantly by interactions of L24, L13, L20, L22 and L4 with this segment of the 23 S rRNA molecule. Association with the rest of the primary binding proteins (L2, L23, L9, L1), which interact with the 3' end of the 23 S rRNA, appears to result in the formation of a second mass center. Binding of additional proteins led to the formation of compact particles with an apparent similarity to the 50 S subunit. However, particles with defined structural features characteristic of the native 50 S subunit requires the interaction of both 23 S rRNA and 5 S rRNA with all of the L-proteins. STEM image analysis demonstrated that 50 S subunit reconstitution proceeds by the immediate folding of the 23 S rRNA into a single mass center followed by the formation of a second mass center. These mass centers merge into one central body, which is gradually enhanced and decorated with structural elements characteristic of the 50 S subunit in the latter stages of assembly.

Computer Simulation↗
PubMed2006

Experimental and theoretical analysis of neuron-transistor hybrid electrical coupling: the relationships between the electro-anatomy of cultured Aplysia neurons and the recorded field potentials.

Understanding the mechanisms that generate field potentials (FPs) by neurons grown on semiconductor chips is essential for implementing neuro-electronic devices. Earlier studies emphasized that FPs are generated by current flow between differentially expressed ion channels on the membranes facing the chip surface, and those facing the culture medium in electrically compact cells. Less is known, however, about the mechanisms that generate FPs by action potentials (APs) that propagate along typical non-isopotential neurons. Using Aplysia neurons cultured on floating gate-transistors, we found that the FPs generated by APs in cultured neurons are produced by current flow along neuronal compartments comprising the axon, cell body, and neurites, rather than by flow between the membrane facing the chip substrate and that facing the culture medium. We demonstrate that the FPs waveform generated by non-isopotential neurons largely depends on the morphology of the neuron.

Action Potentials↗
PubMed2005

High-salt stabilization of Laponite clay particles.

Colloidal radioactive transuranic wastes are currently buried in large tanks in the form of dense colloids in high salt, high pH aqueous media. These facilities are beginning to fail, so it is necessary to transport and "package" them for more permanent disposal, processes requiring understanding of the microstructure that develops under such conditions. Laponite RD clay is believed to be a good simulant for the colloids in the waste tanks, and the present study addresses their behavior under high salt conditions, where previous studies have frequently observed the phenomenon of "restabilization," i.e., the attainment of aggregation stability at high electrolyte conditions. Specifically, the aggregation kinetics and the resulting cluster structure (fractal dimension) of Laponite RD clay colloids at high concentrations of BaCl2 (an electrolyte previously shown to lead to restabilization) are investigated. At low-to-intermediate electrolyte concentrations, the clay is found to behave in accord with DLVO theory, i.e., low salt conditions yield slow aggregation into densely-packed aggregates, whereas intermediate salt concentrations, sufficient to cause double layer collapse, produce rapid aggregation into open aggregates. High salt concentrations, however, show slow rates of aggregation. The aggregate structure under these conditions is found to mimic that found for very low electrolyte concentrations, i.e., high fractal dimension. Further experiments show that a sudden increase in salt concentration in a system containing young open aggregates produced under intermediate salt concentrations causes them to reform into more compact structures.

Journal Article↗
PubMed2004

Online adaptive decision trees.

Decision trees and neural networks are widely used tools for pattern classification. Decision trees provide highly localized representation, whereas neural networks provide a distributed but compact representation of the decision space. Decision trees cannot be induced in the online mode, and they are not adaptive to changing environment, whereas neural networks are inherently capable of online learning and adpativity. Here we provide a classification scheme called online adaptive decision trees (OADT), which is a tree-structured network like the decision trees and capable of online learning like neural networks. A new objective measure is derived for supervised learning with OADT. Experimental results validate the effectiveness of the proposed classification scheme. Also, with certain real-life data sets, we find that OADT performs better than two widely used models: the hierarchical mixture of experts and multilayer perceptron.

Computer Simulation↗
PubMed1996

A designer's polymer as an oral drug carrier (tablet) with pseudo-zero-order release kinetics.

A new synthetic polymeric material has been investigated as an oral controlled-release system. The water soluble polymer consists of a non-cross-linked, ionic polymer possessing sulfonate functional groups: poly(sulfopropyl methacrylate potassium-co- methyl methacrylate) (PSPMK/MMA). Drug-resin complexes were obtained by preparing an aqueous solution of the polymer to which propranolol HCl as a model drug was added. Using either dextrose or microcrystalline cellulose as a tablet binder did not cause any problems in fabricating a compact drug-resinate tablet. The release of propranolol HCl from drug-resinate tablets (2.5 mm x 9.0 mm, 10% dextrose) was pseudo-zero-order kinetics from the beginning to the end for over 21 h. This was due to the greater contribution of drug release from the edge of the tablets. However, zero-order release tablets were obtained by increasing the radius to thickness ratio of the tablet to greater than 3.13. A mathematical model describing release kinetics from drug-resinate tablets predicted the effects of drug loading and the physical dimensions of the tablets by a heterogeneous dissociation/erosion-controlled mechanism. As the content of dextrose in the tablets increased, the dissociation/erosion rate constant (K0) increased due to the greater influx of water into the tablets along with counterions. As expected, the release rate was decreased as the stirring rate decreased from 100 to 50 rpm, resulting in the dissociation/erosion rate constant of 2.62-2.04 mg/cm2h, respectively. Therefore, this system has been proven to release drugs independent of the pH of simulated gastric/intestinal fluids (1.2 and 7.5) as well as the compression force of the tablet, which ranged from 1500 to 4400 lbs.

Cellulose↗
PubMed2005

A mutation designed to alter crystal packing permits structural analysis of a tight-binding fluorescein-scFv complex.

The structure of the scFv fragment FITC-E2, obtained from a naive phage antibody scFv library derived from human donors, was determined at 2.1 A resolution in the free form and at 3.0 A in the complexed form. The wild-type (wt) scFv binds fluorescein with a K(D) of 0.75 nM. The free scFv readily crystallizes by compacting its 18 amino acid-long CDR-H3, partially occluding the binding site and further blocking access by binding to the "bottom" of a neighboring scFv molecule with a cluster of exposed aromatic residues within CDR-H3. Only upon mutating one of the residues involved in this dominant crystal contact, an exposed tryptophan in the middle of CDR-H3, crystals of the complex could be obtained. A series of alanine mutants within the putative antigen binding site, covering a range of binding affinities, were used to relate macroscopic thermodynamic and kinetic binding parameters to single-molecule disruption forces measured by AFM. The effects of the mutations on the binding properties, particularly on the fraction of binding-competent molecules within the population, cannot be fully explained by changes in the strength of local interactions. The significant conformational change of CDR-H3 between the free and the liganded form illustrates the plasticity of the binding site. An accompanying study in this issue by Curcio and colleagues presents the molecular dynamics simulation of the forced unbinding experiments and explores possible effects of the mutations on the unbinding pathway of the hapten.

Antibodies, Monoclonal↗