Preliminary structural model of the G-protein alpha-chain.
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Binding Sites↗
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Results for “Models, Structural”
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Structural model for the lethal components of anthrax toxin based on ultracentrifuge studies.
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Animals↗
A structural model for the patient care operation.
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Models, Structural↗
Xenopus laevis 28S ribosomal RNA: a secondary structure model and its evolutionary and functional implications.
Based upon the three experimentally derived models of E. coli 23S rRNA (1-3) and the partial model for yeast 26S rRNA (4), which was deduced by homology to E. coli, we derived a secondary structure model for Xenopus laevis 28S rRNA. This is the first complete model presented for eukaryotic 28S rRNA. Compensatory base changes support the general validity of our model and offer help to resolve which of the three E. coli models is correct in regions where they are different from one another. Eukaryotic rDNA is longer than prokaryotic rDNA by virtue of introns, expansion segments and transcribed spacers, all of which are discussed relative to our secondary structure model. Comments are made on the evolutionary origins of these three categories and the processing fates of their transcripts. Functionally important sites on our 28S rRNA secondary structure model are suggested by analogy for ribosomal protein binding, the GTPase center, the peptidyl transferase center, and for rRNA interaction with tRNA and 5S RNA. We discuss how RNA-RNA interactions may play a vital role in translocation.
Animals↗
Modeling incomplete longitudinal and cross-sectional data using latent growth structural models.
In this paper we describe some mathematical and statistical models for identifying and dealing with changes over age. We concentrate specifically on the use of a latent growth structural equation model approach to deal with issues of: (1) latent growth models of change, (2) differences in longitudinal and cross-sectional results, and (3) differences due to longitudinal attrition. This is a methodological paper using simulated data, but we base our models on practical and conceptual principles of modeling change in developmental psychology. Our results illustrate both benefits and limitations using structural models to analyze incomplete longitudinal data.
Aging↗
Applications of covariance structure modeling in psychology: cause for concern?
Methods of covariance structure modeling are frequently applied in psychological research. These methods merge the logic of confirmatory factor analysis, multiple regression, and path analysis within a single data analytic framework. Among the many applications are estimation of disattenuated correlation and regression coefficients, evaluation of multitrait-multimethod matrices, and assessment of hypothesized causal structures. Shortcomings of these methods are commonly acknowledged in the mathematical literature and in textbooks. Nevertheless, serious flaws remain in many published applications. For example, it is rarely noted that the fit of a favored model is identical for a potentially large number of equivalent models. A review of the personality and social psychology literature illustrates the nature of this and other problems in reported applications of covariance structure models.
Analysis of Variance↗
[Latent structure model of physicians' opinions on National Health Insurance].
The purpose of this study is to construct the latent structure models of physicians' opinions on National Health Insurance (NHI). The data for the analysis came from a mail survey of 1619 physicians in January of 1990. Five latent structure models were established as follows: Structure 1. Physicians' viewpoint on NHI. Hospital physicians: Steady, 69%; Turn-Over, 26%; Career-change, 5%. Clinic physicians: Steady-with Insurance Contract, 55%; Steady-without Insurance Contract, 41%; Career-Change, 4%. Structure 2. Physicians' expected impact of NHI. Hospital physicians: Pessimistic, 45%; Disadvantaged, 38%; Constant, 17%. Clinic physicians: Pessimistic, 72%; Constant, 12%; Ambitious, 16%. Structure 3. Physicians' expected workload change due to the implement of NHI. Hospital physicians: Decreasing, 30%; No-Change, 18%; Increasing, 52%. Clinic physicians: Decreasing, 30%; Non-Change, 23%; Increasing, 48%. Structure 4. Ideal practice pattern. Hospital physicians: Traditional, 47%; Transitional, 42%; Practice Abandoned, 12%. Clinic physicians: Traditional, 20%; Transitional, 21%; Rural-Orientated 59%. Structure 5. Expected payment methods for physicians. Hospital physicians: Credentiality-Specialty-based, 44%; Specialty-Equal Pay-based, 11%; Equal Pay-Specialty-based, 42%; Equal Pay-Credentiality-based, 4%. Clinic physicians: Credentiality-based, 24%; Mixed, 11%; Equal Service-Equal Pay-based, 60%; Urbanization Level-based, 5%.
Attitude of Health Personnel↗
[An analysis of health related behavior using interpretive structural modeling].
In order for people to know about and to adopt and maintain healthy living practices, 1) a theoretical overview regarding factors associated with health behavior, and 2) an understanding of the actual pattern of behavior in given situations are needed. While theoretical models are helpful in providing a perspective, these models are not practical enough for understanding actual patterns of behavior. In the present study, the ISM (Interpretive Structural Modeling) method was utilized to understand the actual pattern of health related behaviors. The ISM method is used in systems engineering for structurally modeling complex systems. In this study, the ISM method was applied to grasp the structure of coping behavior in the case of fever caused by a common cold under the following two conditions; i) a simplified situation using eight elementary behaviors, and ii) a more complicated situation using more than eight elementary behaviors. i) Subjects were 30 students of public health nursing. The sequence of eight elementary behaviors was determined by paired comparisons using the ISM matrix. The microcomputer made a network diagram of elementary behaviors. The 30 diagrams, none of which were the same, were classified into three types: 1) simple linear (7 subjects), 2) one junction (12 subjects), 3) two or more junctions (11 subjects). After the experiment, subjects were instructed to evaluate the validity of the ISM method. More than 80 percent of the subjects rated the ISM method as effective in increasing their cognition of the hierarchical structure of health related behaviors. ii) Two subjects (A and B) were instructed to come up with as many possible coping behaviors as they could imagine.(ABSTRACT TRUNCATED AT 250 WORDS)
Health Behavior↗
A structured model for immobilized cell kinetics.
An intrinsic, structured model has been formulated to describe the kinetics of viable (living) cells immobilized within porous supports. Predictions of steady-state internal biomass concentration distributions, biocatalyst substrate profiles, and immobilized cell growth and leakage from the support are in qualitative agreement with the literature. Simulation studies indicate that carrier pore structure is a particularly important design variable to be optimized.
Catalysis↗
Drug use and personality in adolescence and young adulthood: structural models with nonnormal variables.
An introduction to structural modeling with nonnormal continuous variables is provided using the equations language of the micro-mainframe program EQS in the context of a longitudinal study of adolescent development that followed about 700 adolescents across an 8-year span into young adulthood. 2 models relating drug use and personality are developed to assess the influence of drug use on personality, and personality on drug use. A high level of self-acceptance is shown to have a small but significant inoculating effect against subsequent cannabis use in both early and late adolescence, while a small positive effect of cannabis use on subsequent self-acceptance occurs only during early adolescence. Substantial stability of self-derogation, cannabis use, and law abidance are demonstrated, with self-derogation during adolescence leading to increased law abidance during young adulthood.
Adolescent↗
A structural model of the acetylcholine receptor channel based on partition energy and helix packing calculations.
A structural model of the transmembrane portion of the acetylcholine receptor was developed from sequences of all its subunits by using transfer energy calculations to locate transmembrane alpha-helices and to calculate which helical side chains should be in contact with water inside the channel, with portions of other transmembrane helices, or with lipid hydrocarbon chains. "Knobs-into-holes" side chain packing calculations were used with other factors to stack the transmembrane alpha-helices together. In the model each subunit has the following structures in order along the sequence from the NH2 terminus: a large extracellular domain of undetermined structure, a short apolar alpha-helix that lies on the extracellular lipid surface of the membrane; three apolar transmembrane alpha-helices (I, II, and III), a cytoplasmic domain of undetermined structure, an amphipathic transmembrane alpha-helix (L) that forms the channel lining, a short extracellular alpha-helix, another apolar transmembrane alpha-helix (IV), and a small cytoplasmic domain formed by the COOH-terminal end of the chain. Three concentric layers form the pore. A bundle of five amphipathic L helices forms the channel lining. This bundle is surrounded by a bundle of 10 alternating II and III helices. Helices I and IV cover portions of the outer surface of the bundle formed by helices II and III. Positions of disulfide bridges are predicted and a mechanism for opening and closing conformational changes is proposed that requires tilting transmembrane helices and possibly a thiol-disulfide interchange reaction.
Amino Acid Sequence↗
A three-dimensional motion model of loads on the lumbar spine: I. Model structure.
Traditionally most biomechanical models that are used to estimate the loading experienced by the spine during work focus on static, two-dimensional representations of the work. However, most work tasks impose loads on the lumbar spine under dynamic, three-dimensional conditions. The objective of this study was to describe the structure and logic of a model that is capable of producing estimates of spine loading under three-dimensional motion conditions. This model is intended for use primarily under laboratory conditions. The model was designed initially for workplace simulation in which the trunk is moving under symmetric and asymmetric constant velocity lifting conditions. Future embellishments may enable the model to be used under free dynamic conditions. The model predicts lumbar spine compression, shear, and torsional forces as well as trunk torque production continuously throughout the exertion. This information may be compared with spine tolerance limits so that the risk of causing a vertebral end-plate microfracture by workplace requirements could be determined.
Biomechanical Phenomena↗
Structural models for the metal centers in the nitrogenase molybdenum-iron protein.
Structural models for the nitrogenase FeMo-cofactor and P-clusters are proposed based on crystallographic analysis of the nitrogenase molybdenum-iron (MoFe)-protein from Azotobacter vinelandii at 2.7 angstrom resolution. Each center consists of two bridged clusters; the FeMo-cofactor has 4Fe:3S and 1Mo:3Fe:3S clusters bridged by three non-protein ligands, and the P-clusters contain two 4Fe:4S clusters bridged by two cysteine thiol ligands. Six of the seven Fe sites in the FeMo-cofactor appear to have trigonal coordination geometry, including one ligand provided by a bridging group. The remaining Fe site has tetrahedral geometry and is liganded to the side chain of Cys alpha 275. The Mo site exhibits approximate octahedral coordination geometry and is liganded by three sulfurs in the cofactor, two oxygens from homocitrate, and the imidazole side chain of His alpha 442. The P-clusters are liganded by six cysteine thiol groups, two which bridge the two clusters, alpha 88 and beta 95, and four which singly coordinate the remaining Fe sites, alpha 62, alpha 154, beta 70, and beta 153. The side chain of Ser beta 188 may also coordinate one iron. The polypeptide folds of the homologous alpha and beta subunits surrounding the P-clusters are approximately related by a twofold rotation that may be utilized in the binding interactions between the MoFe-protein and the nitrogenase Fe-protein. Neither the FeMo-cofactor nor the P-clusters are exposed to the surface, suggesting that substrate entry, electron transfer, and product release must involve a carefully regulated sequence of interactions between the MoFe-protein and Fe-protein of nitrogenase.
Azotobacter vinelandii↗
Nucleotide sequence of Citrus limon 26S rRNA gene and secondary structure model of its RNA.
The complete nucleotide sequence of Citrus limon 26S rDNA has been determined. The sequence has been aligned with large ribosomal RNA (L-rRNA) sequences of Escherichia coli, Saccharomyces cerevisiae and Oryza sativa. Nine extensive expansion segments in dicot 26S rRNA relative to E. coli 23S rRNA have been identified and compared with analogous segments of monocot, yeast, amphibian and human L-rRNAs. A secondary structure model for lemon 26S rRNA has been derived based on the refined model of E. coli 23S rRNA. It has been compared with other eukaryotic L-rRNAs models in terms of location of functionally important regions. Origin and evolution of L-rRNA expansion segments are discussed.
Base Sequence↗
Structural model of human ceruloplasmin based on internal triplication, hydrophilic/hydrophobic character, and secondary structure of domains.
A molecular model for the structure of human ceruloplasmin is proposed that is based on the determination of the complete amino acid sequence, studies of the products of limited proteolytic cleavage, calculations of the hydrophilic/hydrophobic character (hydropathy profile), and predictions of the local secondary structure. This multicopper oxidase (Mr approximately 132,000) consists of a single polypeptide chain (1046 amino acid residues) with four attached glucosamine oligosaccharides. Computer-assisted statistical analysis of the internal repetition in the amino acid sequence confirms that the entire polypeptide chain is divided into three contiguous homology units, each containing about 350 amino acid residues. Each homology unit is subdivided into three domains, designated A1, A2, and B, that differ in structure and probably in function. Calculations of the hydropathy profile and predictions of the secondary structure support a molecular model based on internal repetition of three homology units and help to identify characteristic features of the interdomain junctions. The alignment scores for internal duplication of pairings of the three homology units of ceruloplasmin exceed the scores yet reported for contiguous internal duplication of any other protein. This highly significant evidence for intragenic repetition suggests that the ceruloplasmin molecule evolved by tandem triplication of ancestral genes coding for a primordial copper oxidase.
Amino Acid Sequence↗
Structure models for DNA in filamentous viruses with phosphates near the center.
DNA structure models deduced from X-ray and physicochemical data for Pfl, Xf, and fd viruses have two antiparallel chains wound in helices of approximately 15 A pitch with the phosphates near the structure axes and the bases directed outward. The models, which differ for each virus, are used to interpret ultraviolet absorbance and fluorescence data in terms of DNA protein interactions.
DNA, Viral↗
Bovine leukemia virus (BLV)--a structural model based on chemical crosslinking studies.
Nearest neighbor relationships between lipid and protein as well as between high-molecular-weight viral RNA and protein were investigated in bovine leukemia virus (BLV) particles using chemical crosslinking reagents. Separation of dimethyl suberimidate (DMS) induced lipid-protein complexes by sodium dodecyl sulfate-polyacrylamide gel electrophoresis revealed that the phosphoprotein pp 15 is linked to the lipid bilayer of the virus. By use of diepoxybutan (DEB) as crosslinking reagent p 12 and again pp 15 were found to be linked to the viral RNA. Based on these results and our previous data describing the spatial relationships of major structural proteins within BLV particles, a structural model of BLV is proposed.
Animals↗
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↗