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Results for “Models, Structural”

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At least 631 records · Page 35Linked to original sources

PubMed1989

Envelope structure model of human immunodeficiency virus type 1.

The envelope structure of human immunodeficiency virus type 1 (HIV-1) was examined using a computer image processor combined with an image rotation-averaging system. Our results indicate that the envelope of the HIV-1 particle is constructed of a T-7 laevo icosahedral surface net, and the knobs are distributed in the positions of pentamer-hexamer clustering, the total number being 72, which correspond to the results obtained by Gelderblom et al. and Ozel et al.

HIV-1↗

PubMed2005

Structural model of the amino propeptide of collagen XI alpha1 chain with similarity to the LNS domains.

Fibrillar collagens are the principal structural molecules of connective tissues. The assembly of collagen fibrils is regulated by quantitatively minor fibrillar collagens, types V and XI. A unique amino-terminal propeptide domain of these collagens has been attributed this regulatory role. The structure of the amino terminal propeptide has yet to be determined. Low sequence similarity necessitated a secondary structure-based method to carry out homology modeling based upon the determined structure of LNS family members, named for a common structure in the laminin LG5 domain, the neurexin 1B domain and the sex hormone binding globulin. Distribution of amino acids within the model suggested glycosaminoglycan interaction and calcium binding. These activities were tested experimentally. Sequence analyses of existing genes for collagens indicate that 16 known collagen alpha chains may contain an LNS domain. A similar approach may prove useful for structure/function studies of similar domains in other collagens with similar domains. This will provide mechanistic details of the organization and assembly of the extracellular matrix and the underlying basis of structural integrity in connective tissues. The absolute requirement for collagen XI in skeletal growth is indicated by collagen XI deficiencies such as chondrodystrophies found in the cho/cho mouse and in humans with Stickler syndrome.

Amino Acid Sequence↗

PubMed1991

A structured model for vegetative growth and sporulation in Bacillus thuringiensis.

A mathematical model has been developed for the delta-endotoxin producing Bacillus thuringiensis. The structure of the model involves the processes taking place during vegetative growth, those leading to the initiation of sporulation under conditions of carbon and/or nitrogen limitation, and the sporulation events. The key features in the model are the pools of compounds, such as PRPP, IMP, ADP/ATP, GDP/GTP, pyrimidine nucleotides, NAD/NADH2, amino acids, nucleic acids, cell wall, and vegetative and sporulation proteins. These, along with sigma-factors that control the nature of RNA-polymerase during the different phases, effectively stimulate the vegetative growth and sporulation. The initiation of sporulation is controlled by the intracellular concentration of GTP. Results of simulation of vegetative growth, initiation of sporulation, spore protein formation, and production of delta-endotoxin under C- or N-limitation are presented.

Ammonia↗

PubMed2006

Structure model for the tau(mu) phase in Al-Cr-Si alloys deduced from the lambda phase by the strong-reflections approach.

There are very obvious common features in the electron diffraction patterns of the lambda and tau(mu) phases in the Al-Cr-Si system. The positions of the strong reflections and their intensity distributions are similar for the two structures. The relation of the reciprocal lattices of the lambda and tau(mu) phases is studied. By applying the strong-reflections approach, the structure factors of tau(mu) are deduced from the corresponding structure factors of the known lambda phase. Rules for selecting reflections for the strong-reflections approach are described. Similar to that of lambda, the structure of tau(mu) contains six layers stacked along the c axis in each unit cell. There are 752 atoms in each unit cell, 53 of them are unique. The corresponding composition of the tau(mu) model is Al(3.82 - x)CrSi(x). Simulated electron diffraction patterns from the structure model are in good agreement with the experimental ones. The arrangement of interpenetrated icosahedral clusters in the tau(mu) phase is discussed.

Journal Article↗

PubMed2006

The influence of individual characteristics and contraceptive beliefs on parent-teen sexual communications: a structural model.

PURPOSE: To explore relationships between parent and teen demographic characteristics, parent beliefs about the effectiveness, safety and usability of condoms and oral contraceptives, and parent-teen sexual communication. METHODS: One thousand parents of 13-17-year-olds were surveyed. Structural equation modeling was used to test direct and indirect relationships between parent and teen characteristics, parent effectiveness beliefs, and amount of parent-teen communication about the negative consequences of sex and where to obtain birth control. RESULTS: Parent effectiveness beliefs were directly related to parent-teen communication levels. Minority, religious, politically conservative, and low income parents reported lower effectiveness beliefs than other parent groups. Low income, minority parents reported more discussion with their teens about the negative consequences of sex and where to obtain birth control than high income, White parents. Politically conservative, religious parents reported more discussion with their teen about the negative consequences of sex than their liberal and nonreligious counterparts. In general, nonreligious parents reported more discussion about where to obtain birth control than religious parents. Parents were less likely to talk with males, younger teens, and teens not believed to be romantically involved. Parent and teen gender interacted to predict the amount of parent-teen communication. CONCLUSIONS: Parent beliefs about condom and oral contraceptive efficacy, safety and usability related directly to amount of parent-teen sexual communication. Parent beliefs and communication levels varied across a number of demographic groups. Educating parent groups may result in more frequent and accurate sexual communications with their teenage children.

Adolescent↗

PubMed2001

Binaural processing model based on contralateral inhibition. I. Model structure.

This article presents a quantitative binaural signal detection model which extends the monaural model described by Dau et al. [J. Acoust. Soc. Am. 99, 3615-3622 (1996)]. The model is divided into three stages. The first stage comprises peripheral preprocessing in the right and left monaural channels. The second stage is a binaural processor which produces a time-dependent internal representation of the binaurally presented stimuli. This stage is based on the Jeffress delay line extended with tapped attenuator lines. Through this extension, the internal representation codes both interaural time and intensity differences. In contrast to most present-day models, which are based on excitatory-excitatory interaction, the binaural interaction in the present model is based on contralateral inhibition of ipsilateral signals. The last stage, a central processor, extracts a decision variable that can be used to detect the presence of a signal in a detection task, but could also derive information about the position and the compactness of a sound source. In two accompanying articles, the model predictions are compared with data obtained with human observers in a great variety of experimental conditions.

Attention↗

PubMed1979

A structural model for the kinetic behavior of hemoglobin.

The tertiary structures of all liganded hemoglobins in the R state differ in detail. Steric hindrance arising from nonbonded ligand-globin interactions affects the binding of ligands such as CO and cyanide which preferentially form linear axial complexes to heme; these ligands bind in a strained off-axis configuration. Ligands such as O2 and NO, which preferentially form bent complexes, encounter less steric hindrance and can bind in their (preferred) unstrained configuration. Linear complexes distort the ligand pockets in the R state (and by inference, in the T state) more than bent complexes. These structural differences between linear and bent complexes are reflected in the kinetic behavior of hemoglobin. Structural interpretation of this kinetic behavior indicates that the relative contributions of nonbonded ligand-globin interactions and nonbonded heme interactions to transition state free energies differ for linear and bent ligands. The relative contributions of these interactions to the free energy of cooperativity may also differ for linear and bent ligands. Thus the detailed molecular mechanism by which the affinity of heme is regulated differs for different ligands.

Allosteric Regulation↗

PubMed1994

X-ray structure of a pokeweed antiviral protein, coded by a new genomic clone, at 0.23 nm resolution. A model structure provides a suitable electrostatic field for substrate binding.

We have determined the crystal structure of alpha-pokeweed antiviral protein, a member of ribosome-inactivating proteins, at 0.23 nm resolution, by the molecular-replacement method. The crystals belong to the space group P2(1)2(1)2 with unit-cell dimensions a = 4.71, b = 11.63 and c = 4.96 nm, and contain one protein molecule/asymmetric unit based on a crystal volume/unit protein molecular mass of 2.1 x 10(-3) nm3/Da. The crystallographic residual value was reduced to 17.2% (0.6-0.23 nm resolution) with root-mean-square deviations in bond lengths of 1.9 pm and bond angles of 2.2 degrees. The C alpha-C alpha distance map shows that alpha-pokeweed antiviral protein is composed of three modules, the N-terminal (Ala1-Leu76), the central (Tyr77-Lys185) and the C-terminal (Tyr186-Thr266) modules. The substrate-binding site is formed as a cleft between the central and C-terminal modules and all the active residues exist on the central module. The electrostatic potential around the substrate-binding site shows that the central and C-terminal module sides of this cleft have a negatively and a positively charged region, respectively. This charge distribution in the protein seems to provide a suitable interaction with the substrate rRNA.

Amino Acid Sequence↗

PubMed2001

A structural model of acculturation and mental health status among Chinese Americans.

This study examined the role of acculturation and its direct and indirect impact on depressive symptom severity through various correlates, including socioeconomic status (SES), stress, social support, personality negativity, and physical health perception. Using structural equation modeling, the proposed model was tested with 983 employed Chinese Americans from a representative community sample, the majority of whom were immigrants. The results demonstrated that acculturation, correlated with SES, contributed to depressive symptom severity only through indirect pathways. Higher acculturation was found associated with higher stress that in turn contributed to more elevated depressive symptoms. On the other hand, higher acculturation was also found strongly correlated with higher SES, which was associated with lower depressive symptoms directly or indirectly through several mediators. Better support, lower personality negativity, better health perception, and lower stress were found mediating the relationship between higher SES and lower depressive symptom severity. The simultaneous multigroup analysis showed that the final model was comparable for both men and women with very few differences.

Acculturation↗

PubMed2006

Acculturation and aggression in Latino adolescents: a structural model focusing on cultural risk factors and assets.

The specific aim of this investigation was to map cultural factors associated with aggressive behavior in Latino adolescents. Interviews were conducted with a sample of 481 foreign- and U.S.-born Latino adolescents living in North Carolina and Arizona. Structural Equation Modeling was used to validate a conceptual model linking adolescent and parent culture-of-origin and U.S. cultural involvement, acculturation conflicts, and perceived discrimination to family processes (familism and parent-adolescent conflict) and adolescent aggression. Parent-adolescent conflict was the strongest cultural risk factor followed by perceived discrimination. Familism and adolescent culture-of-origin involvement were key cultural assets associated with less aggressive behavior. Exploratory mediation analyses suggested that familism and parent-adolescent conflict mediated the effects of acculturation conflicts, parent and adolescent culture-of-origin involvement, and parent U.S. cultural involvement on adolescent aggression. Implications for prevention programming were discussed.

Acculturation↗

PubMed1994

Structural model of the ATP-binding domain of the F1-beta subunit based on analogy to the RecA protein.

In contrast to the previous topological model of the ATP binding domain of the F1-ATPase beta subunit based on analogies to those of ras p21 and adenylate kinase, a more consistent model can be constructed with the known structure of the recA protein as a reference. The secondary structure of the F1-ATPase beta subunit predicted from the primary structure agrees well with that of the recA protein. The topology includes a repetitive beta alpha c beta alpha beta alpha beta alpha beta structure where all beta strands are parallel and surround the central alpha c helix above which bound ATP is located. Several residues thought to be located at catalytic site as reported in genetic and chemical labeling work can be consistently positioned in this model.

Adenosine Triphosphate↗

PubMed2003

Structural models of gender, alcohol consumption, and health.

BACKGROUND: Gender differences exist in patterns of alcohol consumption and in the health and social effects of alcohol use, but little is known about gender differences in how alcohol use is affected by mental and physical health conditions. METHODS: We used structural equation modeling techniques to examine gender differences in the relationships among alcohol consumption, physical and mental health, functional status, and social and demographic characteristics. Data were obtained from a random sample of the adult membership of a health maintenance organization in the U.S. Pacific Northwest. Simultaneous models evaluated gender differences in predictors of drinking vs. nondrinking status and, among drinkers, amount of alcohol consumed. RESULTS: Physical health was twice as strong a predictor of drinker/nondrinker status among women compared with men, but among drinkers, there were no gender differences in predictors of amount of alcohol consumed. Mental health predicted drinking status and alcohol consumption among drinkers, but these relationships did not differ by gender. Overall, sociodemographic characteristics and physical health were stronger predictors of alcohol use among women than among men. CONCLUSIONS: Women may be more amenable than men to alcohol-related preventive messages that target physical health concerns. Treating mental health conditions may be an important method for reducing alcohol consumption.

Adult↗

PubMed1984

An age-structured model of pre- and post-vaccination measles transmission.

An infection like measles does not spread uniformly in populations from Europe and North America. Of special importance is a pronounced age-dependency in the contact rates, because of increased infection transmission within schools. Therefore an age-structured epidemiologic model is investigated here, which also pays attention to the fact that children are promoted grade-wise into and out of school. Simulation results are contrasted with pre- and post-vaccination measles data from England and Wales and the model is shown to perform better than previous global mass-action models.

Age Factors↗

PubMed2001

Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate.

High-resolution nitrite soaked oxidized and reduced crystal structures of two active site mutants, D98N and H255N, of nitrite reductase (NIR) from Alcaligenes faecalis S-6 were determined to better than 2.0 A resolution. In the oxidized D98N nitrite-soaked structures, nitrite is coordinated to the type II copper via its oxygen atoms in an asymmetric bidentate manner; however, elevated B-factors and weak electron density indicate that both nitrite and Asn98 are less ordered than in the native enzyme. This disorder likely results from the inability of the N delta 2 atom of Asn98 to form a hydrogen bond with the bound protonated nitrite, indicating that the hydrogen bond between Asp98 and nitrite in the native NIR structure is essential in anchoring nitrite in the active site for catalysis. In the oxidized nitrite soaked H255N crystal structure, nitrite does not displace the ligand water and is instead coordinated in an alternative mode via a single oxygen to the type II copper. His255 is clearly essential in defining the nitrite binding site despite the lack of direct interaction with the substrate in the native enzyme. The resulting pentacoordinate copper site in the H255N structure also serves as a model for a proposed transient intermediate in the catalytic mechanism consisting of a hydroxyl and nitric oxide molecule coordinated to the copper. The formation of an unusual dinuclear type I copper site in the reduced nitrite soaked D98N and H255N crystal structures may represent an evolutionary link between the mononuclear type I copper centers and dinuclear Cu(A) sites.

Alcaligenes↗

PubMed2003

Crystal structures of cyanide complexes of P450cam and the oxygenase domain of inducible nitric oxide synthase-structural models of the short-lived oxygen complexes.

The crystal structure of the ternary cyanide complex of P450cam and camphor was determined to 1.8A resolution and found to be identical with the structure of the active oxygen complex [I. Schlichting et al., 2000, Science 287, 1615]. Notably, cyanide binds in a bent mode and induces the active conformation that is characterized by the presence of two water molecules and a flip of the carbonyl of the conserved Asp251. The structure of the ternary complex of cyanide, L-arginine, and the oxygenase domain of inducible nitric oxide synthase was determined to 2.4A resolution. Cyanide binds essentially linearly, interacts with L-Arg, and induces the binding of a water molecule at the active site. This water is positioned by backbone interactions, located 2.8A from the nitrogen atom of cyanide, and could provide a proton required for O-O bond scission in the hydroxylation reaction of nitric oxide synthase.

Animals↗

PubMed1996

Substrate recognition mechanism of human beta-adrenergic receptor kinase 1 based on a three-dimensional model structure.

Although its detailed substrate specificity is not precisely known, beta-adrenergic receptor kinase 1 phosphorylates beta 2-adrenergic receptors and other G protein-coupled receptors. To elucidate the ligand recognition mechanism of the enzyme and the consensus sequence required for substrates, a three-dimensional structure of the catalytic domain of the enzyme was modeled based on the X-ray crystal structure of the catalytic subunit of cyclic AMP-dependent protein kinase A. When the phosphorylation residue of the substrate was defined as the p position in the model of beta-adrenergic receptor kinase 1, the present study suggested that the consensus sequence recognized by this enzyme would consist of a basic residue at p-3 and an acidic residue at p-2.

Amino Acid Sequence↗

PubMed2004

A quasi-linear, viscoelastic, structural model of the plantar soft tissue with frequency-sensitive damping properties.

Little is known about the structural properties of plantar soft-tissue areas other than the heel; nor is it known whether the structural properties vary depending on location. Furthermore, although the quasi-linear viscoelastic (QLV) theory has been used to model many soft-tissue types, it has not been employed to model the plantar soft tissue. The structural properties of the plantar soft tissue were quantified via stress relaxation experiments at seven regions (subcalcaneal, five submetatarsal, and subhallucal) across eight cadaveric feet. The cadaveric feet were 36.9 +/- 17.4 (mean +/- S.D.) years of age, all free from vascular diseases and orthopedics disorders. All tests were performed at a constant environmental temperature of 35 degrees C. Stress relaxation experiments were performed; different loads were employed for different areas based on normative gait data. A modification of the relaxation spectrum employed within the QLV theory allowed for the inclusion of frequency-sensitive relaxation properties in addition to nonlinear elastic behavior. The tissue demonstrated frequency-dependent damping properties that made the QLV theory ill suited to model the relaxation. There was a significant difference between the elastic structural properties (A) of the subcalcaneal tissue and all other areas (p = 0.004), and a trend (p = 0.067) for the fifth submetatarsal to have less viscous damping (c1) than the subhallucal, or first, second, or third submetatarsal areas. Thus, the data demonstrate that the structural properties of the foot can vary across regions, but careful consideration must be given to the applied loads and the manner in which the loads were applied.

Adolescent↗

PubMed2001

The search for a new model structure of beta-factor XIIa.

We present the search for a new model of beta-factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modelers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and beta-factor XIIa, in particular.

Amino Acid Sequence↗