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Results for “Models, Structural”

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At least 19 recordsLinked to original sources

PubMed1995

Clarifying body-image disturbance: analysis of a multidimensional model using structural modeling.

A multidimensional model of body-image disturbance was tested. The model incorporated the concepts of body-size distortion, preference for thinness, body dissatisfaction, and fear of fatness as predictors of restrictive eating. The LISREL 7 program was used to perform a structural modeling analysis of the theoretical model. A total of 175 women participated in the study (54 eating-disordered patients and 121 undergraduate students). The results supported the hypothesized four-dimensional model relative to alternative one-, two-, and three-dimensional models. Body dissatisfaction appeared to be directly affected by both body-size distortion and preference for thinness. Fear of fatness was found to be the best predictor of restrictive eating. The results appeared consistent across the clinical and nonclinical samples. These data may help resolve many of the current controversies in the body-image literature. The results also suggested the need to develop more sound assessment instruments for fear of fatness.

Journal Article↗

PubMed2000

Protein structure modeling for structural genomics.

The shapes of most protein sequences will be modeled based on their similarity to experimentally determined protein structures. The current role, limitations, challenges and prospects for protein structure modeling (using information about genes and genomes) are discussed in the context of structural genomics.

Computer Simulation↗

PubMed1990

Tertiary structure of RNase Pch1 predicted from the model structure of RNase Ms and the crystal structure of RNase T1. Comparison among the model structures--testing the limits of modelling by homology.

In this paper we predict the structure of RNase Pch1 as modelled from the previously predicted structure of RNase Ms and the crystal structure of RNase T1 in the complex with 2'GMP. The predicted structures and their initial energy minimized structural RNase T1 template are compared. The predicted structures of RNase Pch1 show, independent of their prediction form RNase Ms or T1, a higher structural similarity to RNase T1 than to RNase Ms, in agreement with higher sequence similarity and specificity - RNases T1 and Pch1 are specific for guanine whereas RNase Ms is base-unspecific with preference for guanine.

Amino Acid Sequence↗

PubMed2000

17Beta-hydroxysteroid dehydrogenase from Cochliobolus lunatus: model structure and substrate specificity.

A homology-built structural model of 17beta-hydroxysteroid dehydrogenase from the fungus Cochliobolus lunatus, a member of the short-chain dehydrogenase/reductase family, was worked out using the known three-dimensional structure of trihydroxynaphthalene reductase (EC 1.3.1.50) from Magnaporthe grisea as a template. Due to 61% sequence identity, the model also revealed a similar backbone trace. On the basis of qualitative thin-layer chromatography and comparative kinetic tests of the activity toward various potential steroid substrates, we conclude that androgens are more efficiently converted than estrogens. Their specific oxidoreduction predominantly occurs at the C17 position while no significant conversion at C3 and C20 was determined. Additionally, a thousand times effective inhibition by 5-methyl-(1,2,4)-triazolo[3,4-b]benzothiazole and no activity toward 2,3-dihydro-2,5-dihydroxy-4H-benzopyran-4-one indicate distinct specificies of 17beta-hydroxysteroid dehydrogenase from the fungus C. lunatus and trihydroxynaphthalene reductase. The results of the analysis of progress curve measurements for the forward and backward reactions are consistent with the Theorell-Chance reaction mechanism also predicted from the structural model. In accordance with these results, 4-androstene-3,17-dione was docked into the enzyme active site using molecular modeling and dynamics calculations.

17-Hydroxysteroid Dehydrogenases↗

PubMed1995

A proposed structural model of domain 1 of fasciclin III neural cell adhesion protein based on an inverse folding algorithm.

Fasciclin III is an integral membrane protein expressed on a subset of axons in the developing Drosophila nervous system. It consists of an intracellular domain, a transmembrane region, and an extracellular region composed of three domains, each predicted to form an immunoglobulin-like fold. The most N-terminal of these domains is expected to be important in mediating cell-cell recognition events during nervous system development. To learn more about the structure/function relationships in this cellular recognition molecule, a model structure of this domain was built. A sequence-to-structure alignment algorithm was used to align the protein sequence of the fasciclin III first domain to the immunoglobulin McPC603 structure. Based on this alignment, a model of the domain was built using standard homology modeling techniques. Side-chain conformations were automatically modeled using a rotamer search algorithm and the model was minimized to relax atomic overlaps. The resulting model is compact and has chemical characteristics consistent with related globular protein structures. This model is a de novo test of the sequence-to-structure alignment algorithm and is currently being used as the basis for mutagenesis experiments to discern the parts of the fasciclin III protein that are necessary for homophilic molecular recognition in the developing Drosophila nervous system.

Algorithms↗

PubMed2005

Model structures of alpha-2 adrenoceptors in complex with automatically docked antagonist ligands raise the possibility of interactions dissimilar from agonist ligands.

Antagonist binding to alpha-2 adrenoceptors (alpha2-ARs) is not well understood. Structural models were constructed for the three human alpha2-AR subtypes based on the bovine rhodopsin X-ray structure. Twelve antagonist ligands (including covalently binding phenoxybenzamine) were automatically docked to the models. A hallmark of agonist binding is the electrostatic interaction between a positive charge on the agonist and the negatively charged side chain of D3.32. For antagonist binding, ion-pair formation would require deviations of the models from the rhodopsin structural template, e.g., a rotation of TM3 to relocate D3.32 more centrally within the binding cavity, and/or creation of new space near TM2/TM7 such that antagonists would be shifted away from TM5. Thus, except for the quinazolines, antagonist ligands automatically docked to the model structures did not form ion-pairs with D3.32. This binding mode represents a valid alternative, whereby the positive charge on the antagonists is stabilized by cation-pi interactions with aromatic residues (e.g., F6.51) and antagonists interact with D3.32 via carboxylate-aromatic interactions. This binding mode is in good agreement with maps derived from a molecular interaction library that predicts favorable atomic contacts; similar interaction environments are seen for unrelated proteins in complex with ligands sharing similarities with the alpha2-AR antagonists.

Adrenergic alpha-2 Receptor Agonists↗

PubMed1991

Modeling RNA secondary structures. I. Mathematical structural model for predicting RNA secondary structures.

A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure. All admissible solutions belong to the configuration space and can be obtained directly from its basis.

Algorithms↗

PubMed1995

The interactionist nature of drinking and driving: a structural model.

A structural model is described that examines the contributions of personal and situational determinants (interactionist theory) for the elicitation of previous self-reported drink-driving offending. Responses of 1011 UK driver's licence holders to 57 questions concerning demographics, driving experience/exposure, deterrence issues, attitudinal factors and situation specific drink-driving behaviour were subjected to a series of multiple regression analyses. Seven variables (five personal and two situational) accounting for 46% of the sample variance were shown to be significantly predictive of undetected offending behaviour. Of these age and safe driving consumption estimates were found to be best described in terms of their direct effects on offending behaviour. The relationships between general alcohol consumption and exposure to secondary level enforcement (breath test) with drink-driving behaviour have both direct and indirect effects. Two attitudinal factors referring to a belief of deterrence if random breath testing were introduced into the UK, and arranging alternative transport on a drinking occasion, as well as exposure to a drink-driving charge, show approximately proportional direct and spurious links with offending. Findings are discussed i n terms of the utility of an interactionist approach for the study of drink-driving behaviour, previous attempts at modelling drink-driving behaviour, and the implications that such results have for counter-measure development.

Adolescent↗

PubMed1984

Biological activities of analogues of lipid A based chemically on the revised structural model. Comparison of mediator-inducing, immunomodulating and endotoxic activities.

Lipid A analogues were chemically synthesized based on the model structure recently revised, and biological activities of the analogues were tested. The analogue, (beta-1,6)-linked glucosamine disaccharide carrying ester-bound 3-hydroxytetradecanoic acids at 3 and 3' position of reducing and nonreducing glucosamine in addition to amide-bound 3-hydroxytetradecanoic acids and glycosidic-linked and ester-linked phosphate groups, showed much stronger activities for mediator inducing and immunomodulating as well as endotoxic activities than those exhibited by the previously synthesized analogues based on the old model. Among the activities tested, induction of interferon and tumor necrosis factor as well as mitogenicity, adjuvanticity and pyrogenicity were, however, not expressed so strongly as natural lipid A used as controls. In contrast, the analogue exhibited comparable activities to those of control lipid A in the test of lethal toxicity to mice and gelating activity of Limulus amebocyte lysate. Other synthetic analogues carrying a phosphate group showed comparable, slightly stronger or weaker activities depending on the test, but nonphosphorylated analogue exhibited no apparent or only very weak activities.

Adjuvants, Immunologic↗

PubMed1991

Predicting postpartum depressive symptoms: a structural modelling analysis.

In this prospective, longitudinal study, 42 first-time mothers, recruited through prenatal classes, were assessed on variables predictive of postpartum depressive symptoms. Using a causal modelling structural analysis, it was found that prenatal depression, partners' support, and infant-related factors all contributed to the development of depression following childbirth.

Adult↗

PubMed1984

Testing of a potential mechanism for E. coli temporal cycle imprecision with a structural model.

A structured model for E. coli B/r-A was used to test a potential mechanism for cell cycle temporal imprecision. The mechanism assumes that variations in the activity of septation enzymes can occur. Such variations result in D period imprecision while the chromosome replication schedule is not directly affected. The main results of inserting the mechanism were the predicted ratio of cell doubling time to fission size coefficient of variations agreed with reported data as did the predicted negative correlation between parent-offspring cycle times. Consequently, the proposed mechanism, which suggests that D period fluctuations are the primary source of cell cycle variations, appears consistent with observed cell behavior.

Cell Cycle↗

PubMed1997

The transmission of parent/adult-child drinking patterns: testing a gender-specific structural model.

A structural model on parent/adult-child alcohol use patterns was examined. Three analytical blocks were specified: adult-children's alcohol use onset by types of alcoholic beverage, their current use of these alcoholic beverages, and parents' drinking patterns. The model was examined with data collected from drunken driving offenders in California and Maryland treatment programs. The findings indicate that parent/child alcohol use transmission is more gender specific than race specific; fathers' drinking tends to affect sons' drinking and mothers' drinking tends to affect daughters' drinking. Beer use onset is the earliest and more effective in influencing future alcohol use than the onset of wine or liquor.

Accidents, Traffic↗

PubMed2005

An application of model-fitting procedures for marginal structural models.

Marginal structural models (MSMs) are being used more frequently to obtain causal effect estimates in observational studies. Although the principal estimator of MSM coefficients has been the inverse probability of treatment weight (IPTW) estimator, there are few published examples that illustrate how to apply IPTW or discuss the impact of model selection on effect estimates. The authors applied IPTW estimation of an MSM to observational data from the Fresno Asthmatic Children's Environment Study (2000-2002) to evaluate the effect of asthma rescue medication use on pulmonary function and compared their results with those obtained through traditional regression methods. Akaike's Information Criterion and cross-validation methods were used to fit the MSM. In this paper, the influence of model selection and evaluation of key assumptions such as the experimental treatment assignment assumption are discussed in detail. Traditional analyses suggested that medication use was not associated with an improvement in pulmonary function--a finding that is counterintuitive and probably due to confounding by symptoms and asthma severity. The final MSM estimated that medication use was causally related to a 7% improvement in pulmonary function. The authors present examples that should encourage investigators who use IPTW estimation to undertake and discuss the impact of model-fitting procedures to justify the choice of the final weights.

Air Pollutants↗

PubMed2001

The effects of scrambling on Spanish and Korean agrammatic interpretation: why linear models fail and structural models survive.

Several models of comprehension deficits in agrammatic aphasia rely heavily on linear considerations in the assignment of thematic roles to structural positions (e.g., the Trace-Deletion Hypothesis, the Mapping Hypothesis, and the Argument-Linking Hypothesis). These accounts predict that constructions in languages with rules that affect syntactic structure but preserve relative linear order should be unimpaired. Other models [e.g., the Double-Dependency Hypothesis, (DDH)] do not resort to linearity but are purely structural in conception and therefore should be immune to word-order effects. We tested linear and nonlinear accounts with scrambling structures in Korean and topicalization structures in Spanish. The results are very clear. The (nonlinear) DDH is entirely compatible with the evidence, but the linear accounts are not.

Adult↗

PubMed1994

Identification and analysis of a template-primer (ds-DNA) binding cleft in E. coli DNA polymerase I: an electrostatic potential contour pattern of the modeled structure.

In the modeled structure of the Klenow fragment of E. coli DNA polymerase I, we have identified a distinct region that exhibits a strong electropositive potential contour. The examination of the distribution of the electropositive and negative potential across the two-dimensional slices of the modeled structure revealed that the positive potential was concentrated around the cleft. The approximate size and shape of the region appears well suited to accommodate eight base pairs of duplex DNA and is consistent with the position of the dsDNA binding cleft reported in the crystal structure [Beese et al., Science (1993) 260, 352-355].

Binding Sites↗

PubMed2006

The effect of model structure and data in modeling land conditions in disturbed complex ecosystems.

Off-road vehicles increase soil erosion by reducing vegetation cover and other types of ground cover, and by changing the structure of soil. The investigation of the relationship between disturbance from off-road vehicles and the intensity of the activities that involve use of vehicles is essential for water and soil conservation and facility management. Models have been developed in a previous study to predict disturbance caused by off-road vehicles. However, the effect of data on model quality and model performance, and the appropriate structure of models have not been previously investigated. In order to improve the quality and performance of disturbance models, this study was designed to investigate the effects of model structure and data. The experiment considered and tested: (1) two measures of disturbance based on the Vegetation Cover Factor (C Factor) of the Revised Universal Soil Loss Equation (RUSLE) and Disturbance Intensity; (2) model structure using two modeling approaches; and (3) three subsets of data. The adjusted R-square and residuals from validation data are used to represent model quality and performance, respectively. Analysis of variance (ANOVA) is used to identify factors which have significant effects on model quality and performance. The results of the ANOVA show that subsets of data have significant effects on both model quality and performance for both measures of disturbance. The ANOVA also detected that the C Factor models have higher quality and performance than the Disturbance models. Although modeling approaches are not a significant factor based on the ANOVA tests, models containing interaction terms can increase the adjusted R-squares for nearly all tested conditions and the maximum improvement can reach 31%.

Ecosystem↗

PubMedDate not supplied

Enhanced antibody production at slowed growth rates: experimental demonstration and a simple structured model.

A simple structured model for monoclonal antibody (MAb) production kinetics was formulated by combining the cell cycle theory with the estimated number of MAb-coded messenger RNA (mRNA) molecules per cell: it is assumed that the rate-controlling step is first order in this mRNA and that the growth rate variation does not alter the MAb synthesis rate within any cycle phase but only changes the relative time length of the individual phases. The model predicted "negatively growth associated" MAb production kinetics and thus an enhanced MAb production rate to be achieved by slowing the cell growth. Experiments consistent with these assumptions provided support for the model. Hybridoma cultures where growth was slowed by either a DNA synthesis inhibitor (thymidine or hydroxyurea) or by a selective inhibitor of initiation of nonantibody protein (potassium acetate) exhibited 50-130% MAb production rate enhancement for growth slowed up to 50%; however, further decreases in the growth rate also decreased the MAb production rate. Experiments inconsistent with these assumptions showed other behavior: general inhibition of protein chain elongation (by cycloheximide) or inhibition of ribosomal RNA (rRNA) synthesis (by actinomycin D) each slowed both growth and the specific MAb production rate, leading to net "positive" growth associated MAb production rates. Thus, a need for models with greater structure is also demonstrated.

Animals↗

PubMed1995

Elastic properties of human aortas in relation to age and atherosclerosis: a structural model.

A new structural model is described for the tension-radius relationship of blood vessels, taking into account their mechanically important constituents: collagen, elastin and smooth muscle. The model has four characteristic parameters: EC, the Young's modulus of the collagen fibres; ESE, the Young's modulus of the combined smooth-muscle/elastin network; epsilon mu, the amount of strain at which the high stiffness region on the tension-radius curve is reached, and eta an indicator for the degree of collagen fibre stretching. The structural stiffness of the wall constituents is reflected by EC and ESE whereas the global stiffness of the entire blood vessel is described by epsilon mu and eta. All these elasticity parameters are pressure independent, in contrast to generally quoted values for the incremental modulus or vascular compliance which are strongly pressure dependent. Hence, an objective comparison of the mechanical properties for various types of blood vessel, based on the present model parameters, has been made possible. The model was successfully fitted to tension-radius data of 65 human aortas, age range 30-88 years, with moderate or severe atherosclerosis. The structural as well as the global stiffness changes with age, e.g. collagen stiffness shows a ninefold increase over 60 years. Global stiffness depends on atherosclerosis.

Adult↗