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At least 325 records · Page 18Linked to original sources
PubMed2005

Analysis of the interaction between human steroid 21-hydroxylase and various monoclonal antibodies using comparative structural modelling.

OBJECTIVE: To study the interaction between human steroid 21-hydroxylase (21-OH) and monoclonal antibodies (MAbs) to 21-OH directed to 3 different epitopes recognised by 21-OH autoantibodies characteristic of autoimmune Addison's disease. DESIGN: Build comparative structural models of 21-OH, 21-OH MAbs and complexes of 21-OH-21-OH MAbs and study the effects of 21-OH MAbs on 21-OH enzyme activity. Then, analyse the relationship between sites important for binding of 21-OH MAbs and 21-OH autoantibodies and sites important for 21-OH enzyme activity. METHODS: Variable (V) regions of 21-OH MAbs (M21-OH1, M21-OH3, M21-OH5) were sequenced and models of the MAbs built using structures of antibodies in the database as templates. A comparative model of 21-OH was built using the crystal structure of rabbit cytochrome p450 2c5/3LVdH as template. 21-OH enzyme activity was measured in terms of conversion of [3H]progesterone to deoxycorticosterone and the effect of purified MAb IgGs on 21-OH enzyme activity was assessed. RESULTS: M21-OH1, M21-OH3 and control MAb had no effect on 21-OH enzyme activity with 88.8% +/- 24% (n = 6), 86.7% +/- 7.6% (n = 6) and 86.5% +/- 10.6% (n = 6) of activity remaining in the presence of the respective IgGs. This was consistent with the epitopes for M21-OH1 and M21-OH3 being located distant from 21-OH enzyme active sites in our 21-OH model. The epitope for M21-OH5 which inhibited 21-OH enzyme activity (48.5 +/- 8.3% activity remaining; P < 0.001 compared with control MAb IgG) was found close to the redox protein binding site in our 21-OH model. CONCLUSIONS: A comparative model of 21-OH has been produced. Analysis of experimental data in the context of the model suggests that M21-OH5 inhibits 21-OH enzyme activity through interference with redox protein binding.

Animals↗
PubMed2004

Structural modeling of dual-affinity purified Pho84 phosphate transporter.

The phosphate transporter Pho84 of Saccharomyces cerevisiae is predicted to contain 12 transmembrane (TM) regions, divided into two partially duplicated parts of 6 TM segments. The three-dimensional (3D) organization of the Pho84 protein has not yet been determined. However, the 3D crystal structure of the Escherichia coli MFS glycerol-3-phosphate/phosphate antiporter, GlpT, and lactose transporter, LacY, has recently been determined. On the basis of extensive prediction and fold recognition analyses (at the MetaServer), GlpT was proposed as the best structural template on which the arrangement of TM segments of the Pho84 transporter was fit, using the comparative structural modeling program MODELLER. To initiate an evaluation of the appropriateness of the Pho84 model, we have performed two direct tests by targeting spin labels to putative TM segments 8 and 12. Electron paramagnetic resonance spectroscopy was then applied on purified and spin labeled Pho84. The line shape from labels located at both positions is consistent with the structural environment predicted by the template-generated model, thus supporting the model.

Amino Acid Sequence↗
PubMed1998

The determinants of child mortality in the Philippines: estimation of a structural model.

"This paper employs a longitudinal data set from the Philippines to estimate a structural model of the determinants of infant mortality. To control for the endogeneity of some explanatory variables, a set of reduced form equations for these outcomes is estimated simultaneously with the mortality hazard. A non-parametric discrete factor method is used to control for common unobservable factors in the error terms. Birth interval and parity lose explanatory power once biological measures are considered in the model. The results indicate significant correlations across the equations' error terms. The significant effects of breastfeeding and growth on mortality are quantified in simulation experiments." The data are from a longitudinal survey conducted in metropolitan Cebu between 1983 and 1986.

Asia↗
PubMedDate not supplied

Application of a variable structure model in observation and control of an anaerobic digestor.

In this work, a variable structure model (VSM) of an anaerobic digestion process was developed. The anaerobic biodegradation process was described by four nonlinear submodels representing methanogenic, chemical oxygen demand overload, acidogenic, and hydrogen-inhibited states of the anaerobic process. At any instant, process dynamics was modeled only by one of the submodels, while the others were considered trailing. The choice of a leading submodel was handled by a knowledge-based system, which analyzed available process variables, such as off-gas composition and reactor pH. The feasibility of the proposed method was demonstrated both by using the VSM to predict the outputs of a comprehensive process model, and the experimental results obtained in a pilot scale anaerobic fixed-bed bioreactor.

Algorithms↗
PubMed2003

Effect of highly active antiretroviral therapy on time to acquired immunodeficiency syndrome or death using marginal structural models.

To estimate the net (i.e., overall) effect of highly active antiretroviral therapy (HAART) on time to acquired immunodeficiency syndrome (AIDS) or death, the authors used inverse probability-of-treatment weighted estimation of a marginal structural model, which can appropriately adjust for time-varying confounders affected by prior treatment or exposure. Human immunodeficiency virus (HIV)-positive men and women (n = 1,498) were followed in two ongoing cohort studies between 1995 and 2002. Sixty-one percent (n = 918) of the participants initiated HAART during 6,763 person-years of follow-up, and 382 developed AIDS or died. Strong confounding by indication for HAART was apparent; the unadjusted hazard ratio for AIDS or death was 0.98. The hazard ratio from a standard time-dependent Cox model that included time-varying CD4 cell count, HIV RNA level, and other time-varying and fixed covariates as regressors was 0.81 (95% confidence interval: 0.61, 1.07). In contrast, the hazard ratio from a marginal structural survival model was 0.54 (robust 95% confidence interval: 0.38, 0.78), suggesting a clinically meaningful net benefit of HAART. Standard Cox analysis failed to detect a clear net benefit, because it does not appropriately adjust for time-dependent covariates, such as HIV RNA level and CD4 cell count, that are simultaneously confounders and intermediate variables.

Acquired Immunodeficiency Syndrome↗
PubMed2002

Long-term effects of child punishment on Mexican women: a structural model.

OBJECTIVE: The aim of this study was to investigate long-term effects of parental use of physical and verbal punishment on Mexican women. To study both direct and indirect effects of these phenomena, a structural model was developed and tested. METHOD: One hundred and fifty Mexican women were interviewed with regard to their history of child abuse, their level of depression, alcohol use, antisocial behavior, and punishment of their own children. Factors representing such constructs were specified within a structural equation model and their inter-relations were estimated. Women's history of abuse was considered as an exogenous latent variable directly affecting three other factors: mothers' antisocial behavior, their alcohol consumption, and their levels of depression or anxiety. These factors, in turn, were specified as influencing mothers' harsh discipline of their own children. RESULTS: Data supported this model, indicating that a history of abuse has long-term effects on women's behavior and psychological functioning, which in turn cause women's punitive behavior against their children. CONCLUSIONS: These results are discussed in terms of the theoretical framework of intergenerational transmission of violence. The direct consequences (depression, anxiety, alcohol consumption, and antisocial behavior) of child punishment act as risk factors for the next generation of child abuse.

Adult↗
PubMed2004

Molecular docking of the scorpion toxin Tc1 to the structural model of the voltage-gated potassium channel Kv1.1 from human Homo sapiens.

In this study, structural model of the pore loop region of the voltage-gated potassium channel Kv1.1 from human Homo sapiens was constructed based on the crystallographic structure of KcsA by structural homology. The pore loop region of Kv1.1 exhibits similar folds as that of KcsA. The structural feature of the selectivity filter of Kv1.1 is nearly identical to that of KcsA, whereas most of the structural variations occur in the turret as well as in the inner and outer helices. Molecular docking experiments of the scorpion toxin Tc1 from Tityus cambridgei to the outer vestibule of KcsA as well as Kv1.1 were subsequently performed with various initial Tc1 orientations. Tc1 was found to form the most stable complexes with these two K+ channels when the side chain of Lys14 occupies the pore of the selectivity filter through electrostatic interaction. Tc1 binds preferentially towards Kv1.1 than KcsA due to stronger hydrophobic and electrostatic interactions formed between the toxin and the selectivity filter and outer vestibule of Kv1.1. Furthermore, surface complementarity of the outer vestibules of the channels to the Tc1 spatial conformations also plays an important role in stabilizing both the Tc1/KcsA and Tc1/Kv1.1 complexes.

Amino Acid Sequence↗
PubMed2006

Hyaluronan: the absence of amide-carboxylate hydrogen bonds and the chain conformation in aqueous solution are incompatible with stable secondary and tertiary structure models.

Contradictory descriptions for the aqueous solution conformation of the glycosaminoglycan hyaluronan (HA) exist in the literature. According to hydrodynamic and simulation data, HA molecules are stiffened by a rapidly interchanging network of transient hydrogen bonds at the local level and do not significantly associate at the global level. In marked contrast, models derived from NMR data suggest that the secondary structure involves persistent hydrogen bonds and that strong associations between chains can occur to form vast stable tertiary structures. These models require an extended 2-fold helical conformation of the HA chain and specific hydrogen bonds between amide and carboxylate groups. To test these descriptions, we have used 15N-labelled oligosaccharides and high-field NMR to measure pertinent properties of the acetamido group. The amide proton chemical shift perturbation and carboxylate group pK(a) value are inconsistent with a highly populated hydrogen bond between the amide and carboxylate groups. Amide proton temperature coefficients and chemical exchange rates confirm this conclusion. Comparison of oligomer properties with polymeric HA indicates that there is no discernible difference in amide proton environment between the centre of octasaccharides and the polymer, inconsistent with the formation of tertiary structures. A [1H-1H-15N] NOESY-HSQC (heteronuclear single-quantum correlation) spectrum recorded on an HA octasaccharide revealed that amide groups in the centre are in a trans orientation and that the average solution conformation is not an extended 2-fold helix. Therefore the two key aspects of the secondary and tertiary structure models are unlikely to be correct. Rather, these new NMR data agree with descriptions from hydrodynamic and simulations data.

Amides↗
PubMed2004

[A structural model for symptom management of the patients with chronic fatigue].

PURPOSE: This study was designed to construct a structural model for symptom management of life of the patients with chronic fatigue. The hypothetical model was developed based on the literature review and Self-regulating Model. METHOD: Data were collected by questionnaires from 252 patients with chronic fatigue in the 8 community from December 2002 to April 2003 in Seoul. Data analysis was done with SAS for descriptive statistics and PC-LISREL Program for Covariance structural analysis. RESULT: The fit of the hypothetical model to the data was moderate, thus it was modified by excluding 4 path and including free parameters and 3 path to it. The modified model with path showed a good fitness to the empirical data(chi2=318.11, p=0.0, GFI=.98, AGFI=.98, NNFI=.95, RMSR=.03, RMSEA=.05). The symptoms of stress, self-efficacy, and present fatigue level were found to have significant direct effect on symptom management of the patients with chronic fatigue. The ways of coping, perceived stress, and fatigue symptom were found to have indirect effects on symptom management of the patients with chronic fatigue. CONCLUSION: The derived model is considered appropriate in explaining and predicting symptom management of the patients with chronic fatigue. Therefore, it can effectively be used as a reference model for further studies and suggested direction in nursing practice.

Adult↗
PubMed1989

Nucleotide sequence of bovine herpesvirus type 1 glycoprotein gIII, a structural model for gIII as a new member of the immunoglobulin superfamily, and implications for the homologous glycoproteins of other herpesviruses.

The gene encoding bovine herpesvirus type 1 (BHV-1) glycoprotein gIII was mapped, cloned, and sequenced. The gene is situated between map units 0.122 and 0.135 and encodes a predicted protein of 521 amino acids. The identity of the sequenced gene has been verified previously by expression of immunologically authentic recombinant BHV-1 gIII (Fitzpatrick et al. (1988) J. Virol. 62, 4239-4248). Comparison of the BHV-1 gIII amino acid sequence with the homologous glycoproteins of other alphaherpesviruses revealed significant homology in the carboxy-terminal half of the molecules, including six invariant cysteine residues. A 96 amino acid domain with significant homology to class II major histocompatibility complex (MHC) antigen constant domains was identified in the conserved carboxy-terminal half of BHV-1 gIII. This domain is flanked by two other similarly sized domains which may be related to other immunoglobulin (Ig) superfamily domains. These homologies support a model for the structure of BHV-1 gIII as a new member of the Ig superfamily. Elements of the model may be applicable to the homologous glycoproteins of other herpesviruses and relevant to the immunobiology of herpesvirus infections.

Amino Acid Sequence↗
PubMed2004

Morphologically structured model for antitumoral retamycin production during batch and fed-batch cultivations of Streptomyces olindensis.

A morphologically structured model is proposed to describe trends in biomass growth, substrate consumption, and antitumoral retamycin production during batch and fed-batch cultivations of Streptomyces olindensis. Filamentous biomass is structured into three morphological compartments (apical, subapical, and hyphal), and the production of retamycin, a secondary metabolite, is assumed to take place in the subapical cell compartment. Model accounts for the effect of glucose as well as complex nitrogen source on both the biomass growth and retamycin production. Laboratory data from bench-scale batch and fed-batch fermentations were used to estimate some model parameters by nonlinear regression. The predictive capability of the model was then tested for additional fed-batch and continuous experiments not used in the previous fitting procedure. The model predictions show fair agreement to the experimental data. The proposed model can be useful for further studies on process optimization and control.

Anthracyclines↗
PubMedDate not supplied

Structural model for quality of life of patients with chronic cardiovascular disease in Korea.

BACKGROUND: Health promotion among those with chronic illness has been proposed as a strategy to contain health care cost and enhance quality of life (QOL), but little research has been done in Korea on QOL focused on health promotion of patients with chronic cardiovascular disease (CCVD). OBJECTIVES: This study was designed to estimate a structural model to represent the QOL of patients with CCVD, on the basis of a literature review and Pender's health promotion model (HPM). METHODS: Data were collected by questionnaire from 436 patients with CCVD in a university hospital in Seoul from August 2001 to July 2002. Data analysis included descriptive statistics and covariance structural analysis. RESULTS: As the fit of the hypothetical model to the data was only moderate, it was modified by excluding 10 paths and including free parameters. The modified model with path showed a good fit to the empirical data (chi = 508.12, p = .001, GFI = .95, AGFI = .93, NFI = .98, NNFI = .98, RMSEA = .04). Health-promoting behavior (HPB) and self-efficacy were found to have a significant direct effect on QOL. Health perception, self-esteem, perceived barriers to action, and preference were found to have indirect effects on QOL. The variables of this model explain 63% of the variance in QOL. DISCUSSION: The modified model is considered appropriate to explain and predict QOL of patients with CCVD. Therefore, it can effectively be used as a reference model for further studies and to suggest directions in nursing practice.

Attitude to Health↗
PubMed1999

A structural model for the rolA protein and its interaction with DNA.

The study of the plant oncogene rolA has been hampered by a lack of structural information. Here we show that, despite a lack of significant sequence similarity to proteins of known structure, the rolA sequence adopts a known fold; that of the papillomavirus E2 DNA-binding domain. This fold is reliably identified by modern threading programs, which consider predicted secondary structure, but not by others. Although the rolA sequence is only around 16% identical to those of the available template structures, a structural model could be built that performed well against protein structure verification programs. The adopted strategy involved alignment corrections, justified by multiple model building and evaluation, with particular attention paid to the hydrophobic core residues. We find that rolA protein is predicted to resemble the template proteins in two key aspects; existence as a dimer and ability to bind DNA. rolA protein has recently been shown experimentally to possess DNA binding ability. This model predicts Lys 24 and Arg 27 to be involved in sequence-specific interactions and eight other residues to hydrogen-bond phosphate groups of the DNA.

Amino Acid Sequence↗
PubMed2003

An accurately-constructed structural model for an active site of Fe-containing superoxide dismutases (Fe-SODs).

A novel structural model, [Fe(bpga)(N(3))(OCH(3))] (1) (BPGA: bis(6-pivalamido-2-pyridylmethyl)(carboxy-methyl)amine), for an active site of Fe-containing SOD enzyme with N(3)(-) has been accurately designed and prepared, which has been characterized by X-ray structure analysis and UV-vis, ESR, and IR spectroscopies. Reaction of 1 with acid/base in methanol has shown that the superoxide-accessible site is the N(3)(-)-coordination site in the equatorial plane.

Binding Sites↗
PubMed2002

Structural model of the regulatory domain of smooth muscle heavy meromyosin.

The goal of this study was to provide structural information about the regulatory domains of double-headed smooth muscle heavy meromyosin, including the N terminus of the regulatory light chain, in both the phosphorylated and unphosphorylated states. We extended our previous photo-cross-linking studies (Wu, X., Clack, B. A., Zhi, G., Stull, J. T., and Cremo, C. R. (1999) J. Biol. Chem. 274, 20328-20335) to determine regions of the regulatory light chain that are cross-linked by a cross-linker attached to Cys(108) on the partner regulatory light chain. For this purpose, we have synthesized two new biotinylated sulfhydryl reactive photo-cross-linking reagents, benzophenone, 4-(N-iodoacetamido)-4'-(N-biotinylamido) and benzophenone, 4-(N-maleimido)-4'-(N-biotinylamido). Cross-linked peptides were purified by avidin affinity chromatography and characterized by Edman sequencing and mass spectrometry. Labeled Cys(108) from one regulatory light chain cross-linked to (71)GMMSEAPGPIN(81), a loop in the N-terminal half of the regulatory light chain, and to (4)RAKAKTTKKRPQR(16), a region for which there is no atomic resolution data. Both cross-links were to the partner regulatory light chain and occurred in unphosphorylated but not phosphorylated heavy meromyosin. Using these data, data from our previous study, and atomic coordinates from various myosin isoforms, we have constructed a structural model of the regulatory domain in an unphosphorylated double-headed molecule that predicts the general location of the N terminus. The implications for the structural basis of the phosphorylation-mediated regulatory mechanism are discussed.

Amino Acid Sequence↗
PubMed2002

Global self-esteem in relation to structural models of personality and affectivity.

Three studies examined global self-esteem in relation to structural models of personality and affectivity. In every study, self-esteem was strongly negatively correlated with Neuroticism/Negative Affectivity and moderately to strongly related to Extraversion/Positive Affectivity. Additional findings, however, revealed that self-esteem is better viewed at the lower order level. For instance, global self-esteem correlated -.79 with the Depression facet of the Revised NEO Personality Inventory (P. T. Costa, Jr., & R. R. McCrae, 1992) in Study 3. Moreover, confirmatory factor analyses produced very strong correlations between self-esteem and depression in both Study 2 (r = -.82) and Study 3 (r = -.86). Taken together, the data suggest that global self-esteem measures define one end of a bipolar continuum, with trait indicators of depression defining the other.

Adult↗
PubMedDate not supplied

[Discussion of the hypothetical structural model of the active center in a manganese-protein complex].

It is discussed the structural model of the management-protein complex centre participating in the O2-evolution process. The points of the model are the followings: the protein complex appears to contain only one manganese ion Mn2+. It is supposed that the manganese is complexed with the peptide chains fragment as the ligand. According to the crystallite field theory the active centre is the complex of octahedral symmetry. It is proposed that complex is formed by the skeleton of the peptide chain by the donor-accepting bonds of Mn2+ and four peptide nitrogens (d2sp3-hybridization), and two vacant orbitals are for the complex functioning.

Binding Sites↗