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PubMed2005

Disulfide linkages and a three-dimensional structure model of the extracellular ligand-binding domain of guanylyl cyclase C.

Guanylyl cyclase C (GC-C) is a single-transmembrane receptor that is specifically activated by endogenous ligands, including guanylin, and the exogenous ligand, heat-stable enterotoxin. Using combined HPLC separation and MS analysis techniques the positions of the disulfide linkages in the extracellular ligand-binding domain (ECD) of GC-C were determined to be between Cys7-Cys94, Cys72-Cys77, Cys101-Cys128 and Cys179-Cys226. Furthermore, a three-dimensional structural model of the ECD was constructed by homology modeling, using the structure of the ECD of GC-A as a template (van den Akker et al., 2000, Nature, 406: 101-104) and the information of the disulfide linkages. Although the GC-C model was similar to the known structure of GC-A, importantly its ligand-binding site appears to be located on the quite different region from that in GC-A.

Amino Acid Sequence↗

PubMed1996

Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system.

The 4 A X-ray structure model of trimeric photosystem I of the cyanobacterium Synechococcus elongatus reveals 31 transmembrane, nine surface and three stromal alpha-helices per monomer, assigned to the 11 protein subunits: PsaA and PsaB are related by a pseudo two-fold axis normal to the membrane plane, along which the electron transfer pigments are arranged. 65 antenna chlorophyll a (Chl a) molecules separated by < or = 16 A form an oval, clustered net continuous with the electron transfer chain through the second and third Chl a pairs of the electron transfer system. This suggests a dual role for these Chl a both in excitation energy and electron transfer. The architecture of the protein core indicates quinone and iron-sulphur type reaction centres to have a common ancestor.

Cell Membrane↗

PubMed1998

Job characteristics, work-school conflict, and school outcomes among adolescents: testing a structural model.

A conceptual model of work-school conflict was developed and tested. This study extends prior adolescent employment research by investigating the process by which job characteristics are associated with school outcomes. Data were obtained from a sample of 319 adolescents (16 to 19 years old) who were full-time students and part-time workers. The model was tested using structural equation modeling techniques. Results supported the hypothesized path model. Job characteristics (workload, number of work hours, and job dissatisfaction) were positively related to work-school conflict. Work-school conflict was negatively related to school readiness. School readiness was positively related to school performance, which was negatively associated with school dissatisfaction. In addition, results support a feedback relation, such that school dissatisfaction is negatively related to school readiness.

Achievement↗

PubMed1994

A homology-derived structural model of the murine macrophage inflammatory protein, MIP-1 alpha.

Macrophage inflammatory protein 1 alpha (MIP-1 alpha), a monocyte cytokine, has roles postulated for it in neutrophil chemoattraction, the inflammatory response and the control of haemopoietic stem cell proliferation. The three-dimensional structure of MIP-1 alpha has been modelled structurally, based on its sequence similarity to interleukin-8 and related proteins. The predicted dimeric form of MIP-1 alpha contains two symmetry-related antiparallel alpha-helices lying at an angle across a beta-sheet. The interhelical region and the beta-sheet flooring it are discussed as the potential receptor-binding site in terms of the distribution of negatively charged amino-acid side-chains, which contrasts remarkably with the corresponding positively-charged locations for IL-8. The general topographical features of this (alpha + beta) structural family of cytokines and related proteins (including HLA-A2, PF-4) are discussed. The members of this cytokine family fall into two structural groups as the antiparallel helices (N to C directed) mounted across the beta-sheet platform can be located in a clockwise (e.g. HLA-A2) or anticlockwise (e.g. MIP-1 alpha) sense with respect to the beta-floor).

Amino Acid Sequence↗

PubMed1990

Structural models for the cell surface lipooligosaccharides of Neisseria gonorrhoeae and Haemophilus influenzae.

A structural model is proposed for the surface glycolipids, or lipooligosaccharides (LOS), of gram-negative pathogenic bacteria that colonize human mucosae, e.g. Neisseria gonorrhoeae and Haemophilus influenzae. The development of this model has involved analysis of a series of pyocin-resistant mutants with altered LOS and other recent immunochemical and structural data. A comprehensive approach to determining the necessary structural data has been constructed that utilizes liquid secondary ion mass spectrometry, tandem mass spectrometry, methylation analysis and nuclear magnetic resonance. To prepare purified oligosaccharides for these analyses, chromatographic and chemical techniques have been developed that include high-pH anion-exchange chromatography of underivatized oligosaccharides and reverse-phase chromatography after derivatization with hydrazino alkyl benzoates. The proposed LOS model has several unique features that distinguish it from models developed for the lipopolysaccharides of enteric bacteria. This information should lead to an understanding of the unique structure/function relationship of LOS and to the development of carbohydrate-based vaccines.

Chromatography, Gel↗

PubMed1985

Use and application of structural models in dental education research.

The notion of prediction implies causation. Path and structural models explore the causal links rather than mere empirical relationships between variables. This technique involves a breakdown of correlations; it differs from correlation and regression methods in that it provides relevant information in the presence of important but unobserved (latent) explanatory variables and of measurement errors in the data. It also allows for more than one regression analysis simultaneously and affords inference through tests of the model. In this study, latent abilities of dental students were analyzed as causes and professional achievements as effects, with preadmission performances as indicators of latent abilities. A model with three constructs is consistent with the observed data. The results demonstrate that whereas correlation analysis presents limitations in interpretation, structural analysis focuses clearly on the direct impact of the quality of dental school education, rather than preadmission background, on clinical performance and board success as measures of future professional performance.

Aptitude↗

PubMed2003

Molecular modeling studies on CNG channel from bovine retinal rod: a structural model of the cyclic nucleotide-binding domain.

A dimeric model of the cyclic nucleotide-binding domain of the all-alpha homomeric cyclic nucleotide-gated channel from bovine retinal rod is constructed. The model, based on the structure of the fairly homologous catabolite gene activator protein (Weber and Steitz, J Mol Biol 1987;198:311-326), is obtained by use of comparative modeling and molecular dynamics simulations. Our model provides a structural basis for the experimentally measured difference in activity between cAMP and cGMP, as well as the different solvent accessibilities of GLY597 in the complex with cGMP, with cAMP and in the protein in free state. In addition, it provides support for the rearrangement of the domain C helix on ligand binding and releasing proposed by Matulef et al. (Neuron 1999;24:443-452).

Animals↗

PubMed2002

A structural model for Alzheimer's beta -amyloid fibrils based on experimental constraints from solid state NMR.

We present a structural model for amyloid fibrils formed by the 40-residue beta-amyloid peptide associated with Alzheimer's disease (Abeta(1-40)), based on a set of experimental constraints from solid state NMR spectroscopy. The model additionally incorporates the cross-beta structural motif established by x-ray fiber diffraction and satisfies constraints on Abeta(1-40) fibril dimensions and mass-per-length determined from electron microscopy. Approximately the first 10 residues of Abeta(1-40) are structurally disordered in the fibrils. Residues 12-24 and 30-40 adopt beta-strand conformations and form parallel beta-sheets through intermolecular hydrogen bonding. Residues 25-29 contain a bend of the peptide backbone that brings the two beta-sheets in contact through sidechain-sidechain interactions. A single cross-beta unit is then a double-layered beta-sheet structure with a hydrophobic core and one hydrophobic face. The only charged sidechains in the core are those of D23 and K28, which form salt bridges. Fibrils with minimum mass-per-length and diameter consist of two cross-beta units with their hydrophobic faces juxtaposed.

Amino Acid Sequence↗

PubMed2005

Structural stability of a stage structured model of fish: the case of the anchovy (Engraulis encrasicolus L.) in the Bay of Biscay.

A study of stage structured model of fish population is presented. This model focuse on the anchovy population in the Bay of Biscay (Engraulis encrasicolus L.) is presented. The method of study is based on an intermediate complexity mathematical model, taking into account the spatialisation, the environmental conditions and the stage-structure of the fishes. First, to test the model, we show mathematical properties, such as unicity of the solution of structural stability. Then we provide numerical simulations, to validate the model and to test the dynamics according to the variations of the parameters.

Animals↗

PubMed2006

Structural models of amyloid-like fibrils.

Amyloid fibrils are elongated, insoluble protein aggregates deposited in vivo in amyloid diseases, and amyloid-like fibrils are formed in vitro from soluble proteins. Both of these groups of fibrils, despite differences in the sequence and native structure of their component proteins, share common properties, including their core structure. Multiple models have been proposed for the common core structure, but in most cases, atomic-level structural details have yet to be determined. Here we review several structural models proposed for amyloid and amyloid-like fibrils and relate features of these models to the common fibril properties. We divide models into three classes: Refolding, Gain-of-Interaction, and Natively Disordered. The Refolding models propose structurally distinct native and fibrillar states and suggest that backbone interactions drive fibril formation. In contrast, the Gain-of-Interaction models propose a largely native-like structure for the protein in the fibril and highlight the importance of specific sequences in fibril formation. The Natively Disordered models have aspects in common with both Refolding and Gain-of-Interaction models. While each class of model suggests explanations for some of the common fibril properties, and some models, such as Gain-of-Interaction models with a cross-beta spine, fit a wider range of properties than others, no one class provides a complete explanation for all amyloid fibril behavior.

Amyloid↗

PubMed1989

Alcohol advertising, consumption and abuse: a covariance-structural modelling look at Strickland's data.

Re-analysis employing covariance-structural models was conducted on Strickland's (1983) survey data on 772 drinking students from Grades 7, 9 and 11. These data bear on the relations among alcohol consumption, alcohol abuse, association with drinking peers and exposure to televised alcohol advertising. Whereas Strickland used a just-identified model which, therefore, could not be tested for goodness of fit, our re-analysis tested several alternative models, which could be contradicted by the data. One model did fit his data particularly well. Its major implications are as follows: (1) Symptomatic consumption, negative consequences and self-rated severity of alcohol-related problems apparently reflect a common underlying factor, namely alcohol abuse. (2) Use of alcohol to relieve distress and frequency of intoxication, however, appear not to reflect abuse, although frequent intoxication contributes substantially to it. (3). Alcohol advertising affects consumption directly and abuse indirectly, although peer association has far greater impact on both consumption and abuse. These findings are interpreted as lending little support to further restrictions on advertising.

Adolescent↗

PubMed1996

A structural model for 30 Rh D epitopes based on serological and DNA sequence data from partial D phenotypes.

Both cDNA RHD sequences and reactivity with monoclonal anti-D have been reported in a number of partial D phenotypes, where parts (some epitopes) of the normal D antigen are missing, and anti-D of restricted specificity may be made in response to challenge with normal D positive blood. This paper analyses these reports together and proposes a model for the structure which comprise the epitopes of the Rh D antigen. Some epitopes are proposed to be comprised of continuous peptide sequence within one extracellular loop, whereas others require interactions between two or the extracellular peptide loops.

DNA↗

PubMed1996

HOLE: a program for the analysis of the pore dimensions of ion channel structural models.

A method (HOLE) that allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented. The algorithm uses a Monte Carlo simulated annealing procedure to find the best route for a sphere with variable radius to squeeze through the channel. Results can be displayed in a graphical fashion or visualized with most common molecular graphical packages. Advances include a method to analyze the anisotropy within a pore. The method can also be used to predict the conductance of channels using a simple empirically corrected ohmic model. As an example the program is applied to the cholera toxin B-subunit pentamer. The compatibility of the crystal structure and conductance data is established.

Algorithms↗

PubMed2002

Potassium channels: structures, models, simulations.

Potassium channels have been studied intensively in terms of the relationship between molecular structure and physiological function. They provide an opportunity to integrate structural and computational studies in order to arrive at an atomic resolution description of mechanism. We review recent progress in K channel structural studies, focussing on the bacterial channel KcsA. Structural studies can be extended via use of computational (i.e. molecular simulation) approaches in order to provide a perspective on aspects of channel function such as permeation, selectivity, block and gating. Results from molecular dynamics simulations are shown to be in good agreement with recent structural studies of KcsA in terms of the interactions of K(+) ions with binding sites within the selectivity filter of the channel, and in revealing the importance of filter flexibility in channel function. We discuss how the KcsA structure may be used as a template for developing structural models of other families of K channels. Progress in this area is explored via two examples: inward rectifier (Kir) and voltage-gated (Kv) potassium channels. A brief account of structural studies of ancillary domains and subunits of K channels is provided.

Amino Acid Sequence↗

PubMed1990

A structural model for the genome of echovirus 22.

We have proposed previously that the structural model for the echovirus 22 genome is a single-stranded RNA molecule that has folded back upon itself to form a stable "hairpin" at the 5'-terminus. The vRNA of echovirus 22 has been characterized further by digestion with selective ribonucleases, electrophoresis in composite gels, hydrodynamic studies in density gradients of Cs2SO4 and sucrose, thermal denaturation and 3'-terminal ribonucleotide analysis. Based on these observations, the genome of echovirus 22 is a single-stranded RNA molecule having a region of secondary structure located at the 5'-terminus that may be characterized as a snapback hairpin with hydrogen-bonded base-pairing. In addition, a VPg-like protein is attached (presumably to the 5'-end of the RNA) and the 3'-terminus contains a polyadenylic acid tract [poly (A)].

Carrier Proteins↗

PubMed1995

Structural modeling of differential diagnosis, treatment, and results for allergic rhinitis.

This paper analyzed the relationship among the differential diagnosis, treatment, and results for allergic rhinitis using the covariance structural model. The data were collected from 274 patients with suspected allergic rhinitis who visited the Otorlaryngology Department of the Paik Hospital during 1991-1993. After each patient's characteristics was categorized and combined into several common factors, covariance structure analysis was performed to analyze the structural relationships among the differential diagnosis, treatment, and results of treatment using the significant factors obtained from discriminant analysis. The significant characteristics influenced the diagnosis were the results of skin test from mite/animal, and from mugworts, the results from laboratory tests, rhinorrhea and sneezing, and nasal polyps. The significant characteristics that influenced the method of treatment were: nasal polyps, headache/general symptom, family history/medication, and septal deviation. Headache/general symptom was the only significantly influencing factor for the treatment results.

Diagnosis, Differential↗

PubMed1986

Physician utilization of computers in medical practice: policy implications based on a structural model.

The development of policies regarding computer-based medical technology is hampered by a lack of knowledge about the process by which such applications are adopted and utilized by physicians. This study was designed to test a model of the process by which physicians change their practice behavior by utilizing a computer-based hospital information system (HIS). A structural model was developed, estimated, and tested using data from 270 members of the medical staff of a 1160 bed, private teaching hospital. The overall model consists of a measurement model which assumes that the observed variables are generated by a smaller number of unobserved variables or factors; and a structural equation model that relates exogenous and endogenous variables. The model indicates that consultation with other physicians on a hospital service leads to greater exposure to potential computer applications resulting in less concern about the potential impact of computers on medical practice. Physicians who are more knowledgeable about computers are far more likely to tailor the system to their individual practice by developing their own personal order sets for use on the HIS. All of these factors result in increased use of the HIS by physicians. A number of policy implications related to the introduction of new computer-based technology into medical practice settings are discussed.

Attitude to Computers↗

PubMed1998

Stress and low birth weight: a structural modeling approach using real life stressors.

This study presents a structural equation model describing the influence of stressful life experiences on low birth weight. Data were gathered prospectively in two waves from 5295 inner-city women as part of a city-wide preterm birth prevention project. Using interviews and the medical record, over 200 measures were gathered on each mother and her infant, where each measure was included because of its relevance documented in the risk factor literature. Seventeen of these measures reflected real life stressful experiences and through measurement modeling, eleven of these measures were chosen to represent three underlying measures of stress: economic stress, family stress, and the lack of social support. This study incorporates these psychosocial stressors into a full structural equation model to show their influence on addictive behavior and low birth weight. The full model emerged from tests of alternative causal conceptualizations of how these stressors influence each other and low birth weight--whether their influence on low birth weight in simple and direct, or whether their influence is mediated by addictive behaviors. The model was tested on the first wave, a sample of 3205, and cross-validated on the second wave, a sample of 2090. The model shows that economic stress influences both social support and family stress, but has no direct influence on low birth weight: that social support, or its absence, influences addictive behavior, but has no direct influence on low birth weight, and that family stress influences addictive behavior, and consistent with 30 years of research on humans, has no direct influence on low birth weight. Finally, the mother's history of medical risks shows an independent influence on low birth weight, while her age does not. Age, however, shows a strong influence on addictive behavior. The study demonstrates how structural equation modeling can be used to create and test alternative conceptualizations of how stress affects low birth weight. There are strong implications for planners of prenatal care programs.

Female↗