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PubMed1994

Eukaryotic translation elongation factor 1 gamma contains a glutathione transferase domain--study of a diverse, ancient protein superfamily using motif search and structural modeling.

Using computer methods for multiple alignment, sequence motif search, and tertiary structure modeling, we show that eukaryotic translation elongation factor 1 gamma (EF1 gamma) contains an N-terminal domain related to class theta glutathione S-transferases (GST). GST-like proteins related to class theta comprise a large group including, in addition to typical GSTs and EF1 gamma, stress-induced proteins from bacteria and plants, bacterial reductive dehalogenases and beta-etherases, and several uncharacterized proteins. These proteins share 2 conserved sequence motifs with GSTs of other classes (alpha, mu, and pi). Tertiary structure modeling showed that in spite of the relatively low sequence similarity, the GST-related domain of EF1 gamma is likely to form a fold very similar to that in the known structures of class alpha, mu, and pi GSTs. One of the conserved motifs is implicated in glutathione binding, whereas the other motif probably is involved in maintaining the proper conformation of the GST domain. We predict that the GST-like domain in EF1 gamma is enzymatically active and that to exhibit GST activity, EF1 gamma has to form homodimers. The GST activity may be involved in the regulation of the assembly of multisubunit complexes containing EF1 and aminoacyl-tRNA synthetases by shifting the balance between glutathione, disulfide glutathione, thiol groups of cysteines, and protein disulfide bonds. The GST domain is a widespread, conserved enzymatic module that may be covalently or noncovalently complexed with other proteins. Regulation of protein assembly and folding may be 1 of the functions of GST.

Amino Acid Sequence↗

PubMed1995

Development of body image, eating disturbance, and general psychological functioning in female adolescents: covariance structure modeling and longitudinal investigations.

OBJECTIVE: Covariance structure modeling (CSM) and longitudinal analyses were used to identify a possible causal sequence for factors that might lead to the development of body image and eating disturbance in adolescent females. METHOD: In Study 1, subjects were measured for level of obesity, perceived weight status, maturational timing, history of being teased about weight/size, body image, eating disturbance, and global psychological functioning. Study 2 was a systematic replication of Study 1 using different indices of body image and a more comprehensive assessment of eating disturbance. In Study 3, subjects from Study 1 were reassessed at a 3-year follow-up. RESULTS: The findings from Study 1 indicated that level of obesity and perceived weight, but not maturational timing, had a directional influence on the other variables. In addition, teasing history was significantly related to the development of body image and eating disturbance. CSM and path analyses with Studies 2 and 3 data generally replicated and extended the results from Study 1. DISCUSSION: These findings offer important insights into possible causal sequences for the development of body image and eating disturbance.

Adaptation, Psychological↗

PubMedDate not supplied

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↗

PubMed1990

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↗

PubMed1993

Computer simulations of the differentiated pay structure model.

The differentiated pay structure (DPS) model determines a nurse's base pay on the basis of education, position, and expertise level, adjusting that base for part-time employment, differentials for nonbusiness hours, and single payment bonuses to reward longevity. Using computer simulations, the model was tested with data from two urban hospitals. The findings show that the model can be applied in a manner that is acceptable in terms of budget. By using the DPS model, administration can compensate for those objective employee behaviors that employers value the most.

Computer Simulation↗

PubMed1993

Structural models of primary cell walls in flowering plants: consistency of molecular structure with the physical properties of the walls during growth.

Advances in determination of polymer structure and in preservation of structure for electron microscopy provide the best view to date of how polysaccharides and structural proteins are organized into plant cell walls. The walls that form and partition dividing cells are modified chemically and structurally from the walls expanding to provide a cell with its functional form. In grasses, the chemical structure of the wall differs from that of all other flowering plant species that have been examined. Nevertheless, both types of wall must conform to the same physical laws. Cell expansion occurs via strictly regulated reorientation of each of the wall's components that first permits the wall to stretch in specific directions and then lock into final shape. This review integrates information on the chemical structure of individual polymers with data obtained from new techniques used to probe the arrangement of the polymers within the walls of individual cells. We provide structural models of two distinct types of walls in flowering plants consistent with the physical properties of the wall and its components.

Carbohydrate Sequence↗

PubMed1979

Structural model of leadership influence in a hospital organization.

Path analysis was used to develop a structural model of the head nurse's leadership influence in a large metropolitan hospital. The study indicates that the head nurse's consideration behavior had an inverse effect on her staff member's job related tension but also had an inverse effect on the employee's job performance. Her initiating structure behavior had a positive effect on employee terminations particularly in the structured task situations. The role of structural models in leadership research is discussed.

Group Structure↗

PubMed1992

[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↗

PubMed1998

Tertiary structural models of human interleukin-6 and evaluation by comparison with X-ray and NMR structures.

Tertiary structure models of interleukin-6 were constructed using a routine prediction method based on the X-ray crystal structures of granulocyte colony-stimulating factor (GCSF) and leukemia inhibitory factor (LIF). Those models were evaluated using a sequence-structure compatibility (3D-1D) method program Compass and a limited amount of NMR distance information when it was concluded that the model based on GCSF (IBGC) was preferable to that from LIF (Sumikawa et al., FEBS Lett., 404, 234 (1997)). We evaluated the quality of this model (IBGC) by comparing with X-ray (Somers et al., EMBO., 16, 989 (1997)) and NMR (Xu et al., J. Mol. Biol., 268, 468 (1997)) structures. Consequently, normal mode calculations were carried out for this model, giving conformation fluctuations similar to the C alpha deviation pattern between X-ray and NMR structures.

Amino Acids↗

PubMed1981

Secondary structure model for 23S ribosomal RNA.

A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the molecule into six major structural domains containing over 100 individual helices in all. Regions containing the sites of interaction with several ribosomal proteins and 5S RNA have been located. Segments of the 23S RNA structure corresponding to eucaryotic 5.8S and 25 RNA have been identified, and base paired interactions in the model suggest how they are attached to 28S RNA. Functionally important regions, including possible sites of contact with 30S ribosomal subunits, the peptidyl transferase center and locations of intervening sequences in various organisms are discussed. Models for molecular 'switching' of RNA molecules based on coaxial stacking of helices are presented, including a scheme for tRNA-23S RNA interaction.

Animals↗

PubMed1990

[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↗

PubMed1986

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↗

PubMed1994

Protein structure modelling of the bacterial light-harvesting complex.

Protein structure modelling offers a method of obtaining 3-dimensional information that can be tested and used to plan mutagenesis experiments when a crystallographically determined structure is not available. At its simplest a model may consist of little more than a secondary structure prediction coupled with a determination of the likely regions of transmembrane/membrane surface/globular configuration. These methods can yield an interesting topology map of the protein, which places the residues in their likely positions with respect to, for example, the membrane interface. If it is a member of a large family of related proteins then aligned protein sequences can be used to predict the residues that have an important function as these will be largely conserved in the alignments. Using all these methods a model can be constructed (using for example, the Nicholson Molecular Modelling Kit) to visualize the proposed structure in three dimensions following the premise of good design, that is, avoiding obvious steric clashes, packing of helices in a realistic manner, observing the correct H-bond lengths, etc. In this latter exercise the review of Chothia (Annu. Rev. Biochem. 53, 537-572, 1984) of the principles of protein structure is particularly helpful as it clearly sets out how proteins pack and their preferred configuration. There is a wealth of information about individual amino acid conformational preferences and observed frequencies of occurrence in known protein structures, which can help decide how the residues in the model can be oriented. In this article we have collated the various protein models of the bacterial light-harvesting complexes and present our own model, which is a synthesis of the available biophysical data and theoretical predictions, and show its performance in explaining recent results of site-directed mutants of the LH1 and LH2 light-harvesting complexes of Rhodobacter sphaeroides.

Amino Acid Sequence↗

PubMed1994

The mitochondrial ribosomal RNA genes of the nematodes Caenorhabditis elegans and Ascaris suum: consensus secondary-structure models and conserved nucleotide sets for phylogenetic analysis.

The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-rRNA and mt-l-rRNA) of the nematode worms Caenorhabditis elegans and Ascaris suum encode the smallest rRNAs so far reported for metazoa. These size reductions correlate with the previously described, smaller, structurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-l-rRNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus secondary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-l-rRNA genes of the two nematodes. The mt-s-rRNA secondary-structure model bears a remarkable resemblance to the previously defined universal core structure of E. coli 16S rRNA: most of the nucleotides that have been classified as variable or semiconserved in the E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed for the 3' 64% of the mt-l-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. The proposed C. elegans/A. suum mt-s-rRNA and mt-l-rRNA models include all of the secondary-structure element-forming sequences that in E. coli rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequences within the mt-s-rRNA and mt-l-rRNA core structures, derived by alignment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-rRNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likelihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergence patterns derived from more classical, morphological, and developmental data.

Animals↗

PubMed1995

Sodium channel functioning based on an octagonal structure model.

The complete amino acid sequence of a sodium channel from squid Loligo bleekeri has been deduced by cloning and sequence analysis of the complementary DNA. A unique feature of the squid sodium channel is the 1,522 residue sequence, approximately three-fourths of those of the rat sodium channels I, II and III. On the basis of the sequence, and in comparison with those of vertebrate sodium channels, we have proposed a tertiary structure model of the sodium channel where the transmembrane segments are octagonally aligned and the four linkers of S5-6 between segments S5 and S6 play a crucial role in the activation gate, voltage sensor and ion selective pore, which can slide, depending on membrane potentials, along inner walls consisting of alternating segments S2 and S4. The proposed octagonal structure model is contrasted with that of Noda et al. (Nature 320; 188-192, 1986). The octagonal structure model can explain the gating of activation and inactivation, and ion selectivity, as well as the action mechanism of both tetrodotoxin (TTX) and alpha-scorpion toxin (ScTX), and can be applied not only to the sodium channel, but also to the calcium channel, potassium channel and cGMP-gated channel.

Amino Acid Sequence↗

PubMed1987

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↗

PubMed1999

A structural model of achievement motives, performance approach and avoidance goals, and performance among Norwegian olympic athletes.

A structural model of achievement motives, performance approach and avoidance goals, and performance was applied and tested among 136 Norwegian Olympic level athletes. Achievement motives, competitive behavior over time, performance approach goal-clarity, and performance-avoidance goals were assessed, and elite performance observed. Analysis indicated that the motive to achieve success is positively correlated with competitive behavior over time (a long-term goal), whereas the motive to avoid failure is positively associated with performance avoidance goals. Both long-term competitive behavior goals and performance approach goal-clarity were positively correlated with elite performance whereas the performance-avoidance goal was negatively correlated with performance. When the proximal influences of goals are controlled, the achievement motives are not significantly related to performance. In this structural model, motives and goals shared 32% of the variance with the performance measure, whereas a more complicated model including goals, sex, and a triple interaction of sex and motives shared 42% of the variance with the performance measure.

Achievement↗

PubMed1994

Structural model of antagonist and agonist binding to the angiotensin II, AT1 subtype, G protein coupled receptor.

BACKGROUND: The family of G protein coupled receptors is the largest and perhaps most functionally diverse class of cell-surface receptors. Due to the difficulty of obtaining structural data on membrane proteins there is little information on which to base an understanding of ligand structure-activity relationships, the effects of receptor mutations and the mechanism(s) of signal transduction in this family. We therefore set out to develop a structural model for one such receptor, the human angiotensin II receptor. RESULTS: An alignment between the human angiotensin II (type 1; hAT1), human beta 2 adrenergic, human neurokinin-1, and human bradykinin receptors, all of which are G protein coupled receptors, was used to generate a three-dimensional model of the hAT1 receptor based on bacteriorhodopsin. We observed a region within the model that was congruent with the biogenic amine binding site of beta 2, and were thus able to dock a model of the hAT1 antagonist L-158,282 (MK-996) into the transmembrane region of the receptor model. The antagonist was oriented within the helical domain by recognising that the essential acid functionality of this antagonist interacts with Lys199. The structural model is consistent with much of the information on structure-activity relationships for both non-peptide and peptide ligands. CONCLUSIONS: Our model provides an explanation for the conversion of the antagonist L-158,282 (MK-996) to an agonist by the addition of an isobutyl group. It also suggests a model for domain motion during signal transduction. The approach of independently deriving three-dimensional receptor models and pharmacophore models of the ligands, then combining them, is a powerful technique which helps validate both models.

Amino Acid Sequence↗