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At least 397 records · Page 22Linked to original sources
PubMed1994

Secondary structure model for an unusual SSU rRNA from the extremely thermophilic bacterium strain AZ3 B.1.

The SSU rRNA gene of the extremely thermophilic bacterium strain AZ3 B.1, encodes an rRNA containing four large inserts. A secondary structure model has been constructed which predicts that the inserts form large stem loop structures with a common sequence motif at the base of the helices. To date, these structures have only been detected in related, thermophilic organisms.

Bacteria, Anaerobic↗
PubMedDate not supplied

A structural model of stress, psychosocial resources, and symptomatic experience in chronic physical illness.

The purpose of this investigation was to test a theory-based structural model describing the relationships among psychosocial resources (strength of psychosocial attributes and basic need satisfaction), perceived stress, disease severity, and symptomatic experience in people with chronic obstructive pulmonary disease (COPD). One hundred nine subjects (58 males and 51 females) participated in the cross-sectional mail survey. Psychosocial attribute strength was a significant predictor of basic need satisfaction; basic need satisfaction was a significant predictor of perceived stress; and basic need satisfaction, perceived stress, and disease severity were significant predictors of symptomatic experience. The psychosocial attributes variable was a significant predictor of basic need satisfaction for both sexes. For males, basic need satisfaction and stress were significant predictors of symptomatic experience, while psychosocial attributes were not. For females, the psychosocial attributes variable was a significant predictor of symptomatic experience, while basic need satisfaction and stress were not. The findings suggest that psychosocial resources and perceived stress may be important factors in the symptomatic experience of adults with COPD. Males and females seem to differ in the role psychosocial attributes and basic need satisfaction play in the dynamics of the proposed model.

Adult↗
PubMed2005

Structural genomics analysis of alternative splicing and application to isoform structure modeling.

Alternative splicing is a sophisticated nuclear process that regulates gene expression. It represents an important mechanism for enhancing the functional diversity of proteins. Our current knowledge of alternatively spliced variants is derived mainly from mRNA transcripts, and very little is known about their protein tertiary structures. We carried out a large-scale analysis of known alternatively spliced variants at both protein sequence and structure levels and have shown that threading is, in general, a viable approach for modeling structures of alternatively spliced variants. An examination of alternative splicing at the protein sequence level revealed that the size of splicing events follows the power law distribution and the majority of splicing isoforms harbor only one or two alternations. We examined alternative splicing in the context of protein 3D structures and found that the boundaries of alternative splicing events generally happen in coil regions of secondary structures and exposed residues and the majority of the sequences involved in splicing are located on the surface of proteins. In light of these findings, we then proceeded to demonstrate that threading represents a useful tool for structure prediction of alternative splicing isoforms and addressed the fold stability issue of threading-based structure prediction by molecular dynamics simulation. Our analysis and the insights gained have helped to establish a viable method for structure prediction of alternatively spliced isoforms at the genome scale.

Alternative Splicing↗
PubMed1998

A structural model of the forced compression of the fingertip pulp.

The fingertip pulp modulates the force transmitted to the underlying musculoskeletal system during finger contact on external bodies. A model of the fingertip pulp is needed to represent the transmission of forces to the tendons, muscles, and bone during these contacts. In this study, a structural model of the in vivo human fingertip was developed that incorporates both the material inhomogeneity and geometry. Study objectives were to determine (1) if this fingertip model can predict the force-displacement and force contact area responses of the in vivo human fingertip during contact with a flat, rigid surface, and (2) if the stresses and strains predicted by this model are consistent with the tactile sensing functionality of the in vivo human fingertip. The in vivo fingertip pulp was modeled as an inflated, ellipsoidal membrane, containing an incompressible fluid, that is quasi-statically compressed against a flat, frictionless surface. The membrane was assigned properties of skin (Veronda and Westmann, 1970) and when inflated, possessed dimensions approximating those of a human fingertip. Finite deformation was allowed. The model was validated by the pulp force-displacement relationship obtained by Serina et al. (1997) and by measurements of the contact area when the fingertip was pressed against a rigid surface with contact forces between 0.25 and 7.0 N. Model predictions represent the experimental data sufficiently well, suggesting that geometry, inhomogeneous material structure, and initial skin tension appear to represent the nonlinear response of the in vivo human fingertip pulp under compression. The predicted response of the fingertip pulp is consistent with its functionality as a tactile sensor.

Algorithms↗
PubMed2006

Assessing the effectiveness of antiretroviral adherence interventions. Using marginal structural models to replicate the findings of randomized controlled trials.

Randomized controlled trials of interventions to improve adherence to antiretroviral medications are not always feasible. Marginal structural models (MSM) are a statistical methodology that aims to replicate the findings of randomized controlled trials using observational data. Under the assumption of no unmeasured confounders, 3 MSM estimators are available to estimate the causal effect of an intervention. Two of these estimators, G-computation and inverse probability of treatment weighted (IPTW), can be implemented using standard software. G-computation relies on fitting a multivariable regression of adherence on the intervention and confounders. Thus, it is related to the standard multivariable regression approach to estimating causal effects. In contrast, IPTW relies on fitting a multivariable logistic regression of the intervention on confounders. This article reviews the implementation of these methods, the assumptions underlying them, and interpretation of results. Findings are illustrated with a theoretic data example in which MSM are used to estimate the effect of a behavioral intervention on adherence to antiretroviral therapy.

Anti-HIV Agents↗
PubMed1989

A detailed structural model of cytotactin: protein homologies, alternative RNA splicing, and binding regions.

A combination of cDNA sequencing of the complete coding region, protein comparisons, binding site mapping, and electron microscopic imaging has permitted the formulation of a structural model of cytotactin. Cytotactin is a large extracellular matrix glycoprotein that displays a restricted tissue distribution during development. Although there appears to be a single cytotactin gene, multiple cytotactin polypeptides and mRNAs are detected in a variety of tissues. We report here the sequences and relationships of cDNAs that encode the complete amino acid sequences of two cytotactin polypeptides in chicken brain. The translated cDNA sequences agree with those obtained by direct analysis of cytotactin and fragments of the molecule. All regions of the polypeptides appear to be identical except for a 273 amino acid segment found in the larger but not in the smaller. At their amino termini, both polypeptides contain a cysteine-rich segment that probably includes those residues that link monomers into hexamers. This segment is followed by 13 epidermal growth factor-like (EGFL) repeats and then 8 consecutive segments that each resemble the type III repeats found in fibronectin. At their carboxyl termini, the polypeptides are similar to the beta and gamma chains of fibrinogen, including a calcium-binding segment. The additional sequence in the large polypeptide is inserted after the fifth type III repeat and includes three additional type III repeats. On RNA transfer blot analyses, cytotactin cDNA probes detected a 6.4-kilobase (kb) component in both brain and gizzard and larger mRNAs in both tissues, but those in gizzard were larger by about 1 kb than those in brain. A probe specific to the insert did not hybridize to the 6.4-kb mRNA in either tissue but detected the larger mRNAs in both tissues. At least a portion of the insert is thus present in both tissues, but there may be additional inserts in the gizzard mRNAs. The proposed model of cytotactin specifies the orientation of the polypeptides, the localization of interchain disulfide bonds, the structural elements constituting the thin and thick segments (EGFL repeats and type III repeats, respectively), the terminal fibrinogen-like nodular region, and the relative location of the cell-binding region.

Amino Acid Sequence↗
PubMed2005

Studying group and time invariance in maximal reliability for multiple-component measuring instruments via covariance structure modelling.

A method for examining invariance in maximal reliability for weighted combinations of congeneric measures is described. The approach is developed within the framework of covariance structure modelling and allows one to ascertain whether a multi-component instrument consisting of homogeneous measures is associated with the same minimal relative error variance in distinct populations or over time. The procedure yields as a by-product an interval measure of discrepancy in maximal reliability across independent groups or assessment occasions, and is illustrated with two examples.

Humans↗
PubMed2001

Structural modeling and characterization of a thermostable lipase from Bacillus stearothermophilus P1.

The moderate thermophilic bacterium Bacillus stearothermophilus P1 expresses a thermostable lipase that was active and stable at the high temperature. Based on secondary structure predictions and secondary structure-driven multiple sequence alignment with the homologous lipases of known three-dimensional (3-D) structure, we constructed the 3-D structure model of this enzyme and the model reveals the topological organization of the fold, corroborating our predictions. We hypothesized for this enzyme the alpha/beta-hydrolase fold typical of several lipases and identified Ser-113, Asp-317, and His-358 as the putative members of the catalytic triad that are located close to each other at hydrogen bond distances. In addition, the strongly inhibited enzyme by 10 mM PMSF and 1-hexadecanesulfonyl chloride was indicated that it contains a serine residue which plays a key role in the catalytic mechanism. It was also confirmed by site-directed mutagenesis that mutated Ser-113, Asp-317, and His-358 to Ala and the activity of the mutant enzyme was drastically reduced.

Amino Acid Sequence↗
PubMed2005

Modeled structure of a G-protein-coupled receptor: the cholecystokinin-1 receptor.

The Cholecystokinin-1 receptor (CCK1R) mediates actions of CCK in areas of the central nervous system and of the gut. It is a potential target to treat a number of diseases. As for all G-protein-coupled receptors, docking of ligands into modeled CCK1R binding site should greatly help to understand intrinsic mechanisms of activation. Here, we describe the procedure we used to progressively build a structural model for the CCK1R, to integrated, and on the basis of site-directed mutagenesis data on its binding site. Reliability of the CCK1R model was confirmed by interaction networks that involved conserved and functionally crucial motifs in G-protein-coupled receptors, such as Glu/Asp-Arg-Tyr and Asn-Pro-Xaa-Xaa-Tyr motifs. In addition, the 3-D structure of CCK1R-bound CCK resembled that determined by NMR in a lipid environment. The derived computational model was also used for revealing binding modes of several nonpeptide ligands and for rationalizing ligand structure-activity relationships known from experiments. Our findings indeed support that our "validated CCK1R model" could be used to study the intrinsic mechanism of CCK1R activation and design new ligands.

Amino Acid Motifs↗
PubMed2003

Introduction to the special section on structural equation modeling.

Structural equation modeling (SEM) is a frequently used data-analytic technique in psychopathology research. This popularity is due to the unique capabilities and broad applicability of SEM and to recent advances in model and software development. Unfortunately, the popularity and accessibility of SEM is matched by its complexities and ambiguities. Thus, users are often faced with difficult decisions regarding a variety of issues. This special section is designed to increase the effective use of SEM by reviewing recently developed modeling capabilities, identifying common problems in application, and recommending appropriate strategies for analysis and evaluation.

Humans↗
PubMed1992

Bayesian analysis of stochastic constraints in structural equation models.

Structural equation models are analysed in the presence of stochastic constraints. Based on a Bayesian perspective, a prior distribution on nuisance parameters in the unknown covariance matrix of error measurements with stochastic constraints is considered. An iterative procedure is implemented to produce the various Bayesian estimates with stochastic constraints. A simulation study is conducted to illustrate the accuracy and behaviour of this Bayesian approach. A real-life example is provided to illustrate the theory.

Bayes Theorem↗
PubMed2002

Examining social-cognitive determinants of intention and physical activity among black and white adolescent girls using structural equation modeling.

Structural equation modeling was used to evaluate components within the theories of reasoned action (TRA), planned behavior (TPB), and self-efficacy (SET) for understanding moderate and vigorous physical activity among 1,797 Black and White adolescent girls. Modest to strong support was provided for components of TPB and SET; weak support was provided for components of TRA. Perceived behavioral control was related to vigorous physical activity. Self-efficacy was related to moderate and vigorous physical activity, and it accounted for the effect of intention on physical activity. The observed relationships were similar between Black and White girls. Self-efficacy and perceived behavioral control are independent influences on physical activity among Black and White adolescent girls and warrant study as potential mediators in physical activity interventions.

Adolescent↗
PubMed1997

The role of disgust and fear in blood and injection--related fainting symptoms: a structural equation model.

Structural equation models were used to examine the relationship of blood, injection, and injury (BII) fears, disgust sensitivity, and trait anxiety to having experienced fainting-related symptoms in 722 university students. The latent variable representing BII fears was highly positively related to faint symptoms whereas that relating to disgust experiences was inversely related to fainting. A second disgust sensitivity variable was not directly related to fainting. Trait anxiety added nothing directly to the model, although it was related to BII latent variable. Additional analyses included a gender-related cross-validation which showed that models developed on one gender group did not fit well when applied to the other gender group. Blood drawings were the most common faint eliciting situations and were found to be reportedly more likely to elicit faint symptoms than were injections.

Adult↗
PubMedDate not supplied

Identification, display, and use of symmetry elements in atomic and electronic structure models.

Crystallographic symmetry plays an important role in structure determination from diffraction or scattering data, in spectroscopy and in simulations. It is convenient and insightful to integrate the display and use of such symmetry data with data analysis and modeling methods. We outline the integration of a suite of crystallographic algorithms, closely coupled with interactive graphical displays. These include techniques for identifying the unit cell of a solid, for automatically determining space and point group symmetries, for generalized displays of symmetry elements overlaid on structural models, and for construction, editing, and transformation of models subject to symmetry constraints. In addition, electron densities derived from periodic density functional calculations can be symmetrized and displayed with the corresponding symmetry elements. Applications of these various capabilities in crystallographic research are illustrated by topical examples.

Aluminum Oxide↗
PubMed1982

Application of structural modeling with latent variables to adolescent drug use: a reply to Huba, Wingard, and Bentler.

I propose that strong claims about the superiority of latent variable (LV) structural modeling, compared to other causal approaches to nonexperimental data, are both overstated and premature. Focusing primarily on a recent article by Huba, Wingard, and Bentler (1981) appearing in this journal, I argue both that the authors' application of these models is seriously flawed and that the data employed to test the models are of questionable quality. I conclude that statements about powerful inferences that can be made from analyses of LV models should be moderated. A more prudent position is advocated in this paper: I argue that the evaluation and testing of LV models should proceed, but with caution and self-criticism; even highly sophisticated methods like LV modeling cannot substitute for the collection of high quality data and the clear operationalization of constructs and hypotheses.

Adolescent↗
PubMed1981

Structural models of the nicotinic acetylcholine receptor and its toxin-binding sites.

Models of the protein structure of agonist-, competitive antagonist-, and snake neurotoxin-binding sites were designed using the sequence of the first 54 residues of the acetylcholine receptor (AChR) alpha subunit from Torpedo californica. These models are based on the premise that the N-terminal portions of the subunits form the outermost extracellular surface of the AChR and that agonists bind to this portion. The models were developed by predicting the secondary structure of the alpha-subunit N-terminal segment from its sequence, then using these predictions to fold the segment into tertiary structures that should bind snake neurotoxins, agonists, and antagonists. Possible gating mechanisms and quaternary structures are suggested by the proposed tertiary structures of the subunits. Experiments are suggested to test aspects of the models.

Animals↗
PubMed1995

A three-dimensional structure model of the complex of glutamyl-tRNA synthetase and its cognate tRNA.

A docking model of glutamyl-tRNA synthetase (GluRS) and tRNAGlu was constructed, on the basis of the distinguished similarity between the X-ray crystallographic three-dimensional structures of the N-terminal halves of the Thermus thermophilus GluRS in the free state and the Escherichia coli glutaminyl-tRNA synthetase in a complex with tRNAGln. The modeled structure is energetically favorable and is also well consistent with the results of site-directed mutagenesis studies. The model indicates that the GluRS-specific insertions 2 and 3 fit and bind to the acceptor stem and the D arm, respectively, of the cognate tRNA without affecting other contacts. In particular, insertion 3 strongly interacts with the two D-stem base pairs that are essential for the tRNA-GluRS recognition.

Anticodon↗