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PubMed2002

Testing the grief to personal growth model using structural equation modeling.

The belief that loss can result in growth has been hypothesized for centuries.Yet, traditional grief theories have viewed grief work as a process of resolving grief and returning to normal. Formal conceptualizations of grief to growth models have been recently delineated by several grief theorists. The Grief to Personal Growth model represents one emergent perspective of the qualitative changes resulting from the loss of a loved one. The model delineates a pathway through grief that indicates the bereft experience despair and detachment followed by intrusive thoughts and later avoidance of intense preoccupation with grief. Social support is shown to facilitate the bereft as they reconstruct their lives and find new meaning in life. A second path indicates that some bereaved individuals become mired in grief and need help to proceed toward personal growth. The model was tested in a sample of bereaved parents using structural equation modeling as a method of theory testing. The results of testing this model are presented within a framework of theory testing as a mechanism to bridge the gaps between theory, practice, and research. Implications for practice are considered.

Adult↗

PubMed1999

Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5'-phosphate-dependent decarboxylase: a functional study.

The pyridoxal-5'-phosphate-dependent enzymes (B6 enzymes) are grouped into three main families named alpha, beta, and gamma. Proteins in the alpha and gamma families share the same fold and might be distantly related, while those in the beta family exhibit specific structural features. The rat aromatic L-amino acid decarboxylase (AADC; EC(4.1.1.28)) catalyzes the synthesis of two important neurotransmitters: dopamine and serotonin. It binds the cofactor pyridoxal-5'-phosphate and belongs to the alpha family. Despite the low level of sequence identity (approximately 10%) shared by the rat AADC and the sequences of the enzymes belonging to the B6 enzymes family, including the known three-dimensional structures, a multiple sequence alignment was deduced. A model was built using segments belonging to seven of the eleven known structures. By homology, and based on knowledge of the biochemistry of the aspartate aminotransferase, structurally and functionally important residues were identified in the rat AADC. Site-directed mutagenesis of the conserved residues D271, T246, and C311 was carried out in order to confirm our predictions and highlight their functional role. Mutation of D271A and D271N resulted in complete loss of enzyme activity, while the D271E mutant exhibited 2% of the wild-type activity. Substitution of T246A resulted in 5% of the wild-type activity while the C311A mutant conserved 42% of the wild-type activity. A functional model of the AADC is discussed in view of the structural model and the complementary mutagenesis and labelling studies.

Amino Acid Sequence↗

PubMed2005

Novel properties of malarial S-adenosylmethionine decarboxylase as revealed by structural modelling.

In the malaria parasite, the two main regulatory activities of polyamine biosynthesis, ornithine decarboxylase (ODC) and S-adenosylmethionine decarboxylase (AdoMetDC) occur in a single bifunctional protein. The AdoMetDC domain was modeled using the human and potato X-ray crystal structures as templates. Three parasite-specific inserts and the core active site region was identified using a structure-based alignment approach. The domain was modeled without the two largest inserts, to give a root mean square deviation of 1.85 angstroms from the human template. Contact with the rest of the bifunctional complex is predicted to occur on one face of the Plasmodium falciparum AdoMetDC (PfAdoMetDC) domain. In the active site there are four substitutions compared to the human template. One of these substitutions may be responsible for the lack of inhibition by Tris, compared to mammalian AdoMetDC. The model also provides an explanation for the lack of putrescine stimulation in PfAdoMetDC compared to mammalian AdoMetDC. A network of residues that connects the putrescine-binding site with the active site in human AdoMetDC is conserved in the malarial and plant cognates. Internal basic residues are found to assume the role of putrescine, based on the model and site-directed mutagenesis: Arg11 is absolutely required for normal activity, while disrupting Lys15 and Lys215 each cause 50% inhibition of AdoMetDC activity. These novel features of malarial AdoMetDC suggest possibilities for the discovery of parasite-specific inhibitors.

Adenosylmethionine Decarboxylase↗

PubMed2004

Patterns of retinal light absorption related to retinitis pigmentosa mutants from in silico model structures of rhodopsin.

Changes induced by mutations in rhodopsin that are associated with the degenerative visual disease retinitis pigmentosa result in an altered pattern of light absorption according to quantum mechanical simulations and reference experimental works. Eleven single-point mutations associated with retinitis pigmentosa at and in the proximity to the retinal binding pocket of rhodopsin have been modeled in silico and their spectra calculated with the NDOL (Neglect of Differential Overlap accounting L azimuthal quantum number) a priori method. The altered pattern of absorption found would lead to cumulative consequences in energy dissipation with aging. Different energy balances in the case of mutants at the very molecular level, compared to native nonmutated rhodopsin, can cause permanent cellular stress and would play a role in the progression of the retine degenerative process. It could explain the worsening of the pathological condition mostly in adults and suggests the probable beneficial effects of using quenching drugs and protection devices against excess of light in the early stages of life for avoiding or reducing potential damage.

Absorption↗

PubMed1998

Antecedents and consequences of victimization of lesbian, gay, and bisexual young people: a structural model comparing rural university and urban samples.

Research indicates that antigay victimization is widespread and that lesbian, gay, and bisexual young people may be very vulnerable to such victimization. The current study builds upon previous work by Hershberger and D'Augelli (1995), who studied the consequences of sexual orientation-based victimization in 194 urban lesbian, gay, and bisexual youths. Using structural equation modeling, the present study models both antecedents and consequences (including psychological distress, self-esteem, and suicidality) of victimization via a secondary analysis of their data set. In addition, a second sample of 54 lesbian, gay, and bisexual youths from a rural university setting was examined to cross-validate and generalize the relationships found in urban settings. Results indicated that a revised model of victimization exhibited sufficient fit to the urban sample data and provided preliminary support for the generalizability of the model beyond the initial sample. Additional similarities were found between the urban and rural university community samples, including a high prevalence of reported suicide attempts: 42% of the urban sample and 32% of the rural university sample had attempted suicide at least once. Results indicated that victimization based on sexual orientation has similar correlates for young people in different community settings.

Bisexuality↗

PubMed1999

Deduced structural model for animal rhabdovirus glycoproteins.

The G protein sequences of fourteen animal rhabdoviruses, representing all four recognized genera (Vesiculovirus, Lyssavirus, Ephemerovirus and Novirhabdovirus) and the ungrouped sigma virus, were aligned using CLUSTAL W and adjusted to account for obvious sequence similarities not detected by the algorithm. Analysis of the alignment indicated remarkable preservation of G protein structural features including cysteine residues, antigenic sites and significant elements of secondary structure (alpha-helices, beta-strands and loops). Twelve highly conserved cysteine residues were assigned numbers (C(I) to C(XII)) according to their location in the alignment. Other cysteine residues were assigned numbers (C0 to C(XIIe)) according to their position relative to the conserved cysteines. The pattern of conservation of cysteine residues and the structural characteristics of identified discontinuous antigenic sites were used to deduce a model for G protein structure. Six absolutely conserved cysteines are predicted to associate in three disulphide bridges (C(I)-C(XII); C(VIII)-C(XI); C(IX)-C(X)) that form the core of the G protein structure and define the common discontinuous antigenic site. The associations of six other highly conserved cysteines (C(II)-C(IV); C(III)-C(V); C(VI)-C(VII)) are predicted by the absence of a specific pair in all viruses within a genus. Of the other cysteines, one pair occurs only in ephemeroviruses and novirhabdoviruses (C0-C(XIIa)); two pairs occur only in ephemeroviruses (C(Ib)-C(VIIIa); C(XIIb)-C(XIIe)); and two pairs occur only in lyssaviruses (C(Ia)-C(VIIIb); C(XIIc)-C(XIId)). The structures predicted by the model account for the preservation of conformational antigenic sites, accommodate genus-specific variations, and are generally consistent with previous observations of G protein structure.

Amino Acid Sequence↗

PubMed1998

A structured model for evaluation of information retrieval (IR).

The paper reviews methods of evaluation of information retrieval (IR), in particular relevance (recall and precision) based approaches and their limitations and proposes a new model of IR which emphasizes the difference between the IR process and the technical IR system supporting the process. The model is proposed as basis for the structured evaluation of the IR process, and the planning, analysis and comparison of results of experiments using different methodologies.

Evaluation Studies as Topic↗

PubMed2000

A structural modeling approach to the understanding of parenting stress.

Tested and cross-validated a multidimensional model of predictors of parenting stress on data from a population-based sample of Swedish mothers (N = 1,081) with children ages 6 months to 3 years. The study was a cross-sectional questionnaire study, focusing on the explanation of variance in parenting stress. Structural equation modeling procedures permitted disentanglement of total, direct, and indirect effects. A Swedish instrument based on parts of the Parent Domain in the Parenting Stress Index was used as a measure of stress. The results provided general support for the proposed model. High workload, low social support, perception of the child as fussy-difficult, negative life events, child caretaking hassles, more children in the family, and high maternal age related directly to more stress. Child irregularity contributed indirectly to mother's experienced stress. No buffering effects of social support were found. Forty-eight percent of the variance in the parenting stress measure was explained by the model. Implications for interventions were discussed.

Adult↗

PubMed1994

Protein structure modelling from remote sequence similarity.

Many methods exist for taking a sequence that exhibits similarity to another of known structure and building a molecular model. However, when the sequence similarity is very remote and fragmentary, this 'modelling-by-homology' approach is less reliable. Current methods that tackle this problem are reviewed below, taking as an example the construction of a predicted model for the retroviral protease. This earlier work, which was only partially automatic, identified many of the outstanding difficulties that have subsequently been automated in computer programs, developed both by the author and many others. Because of the rapid proliferation of methods and their variants, an exhaustive review of the literature has not been possible and the following survey concentrates on the developments of the author and colleagues to explain the basic methods.

Algorithms↗

PubMed2003

Comparing the modeled structures of PR-4 proteins from wheat.

We have constructed three-dimensional models of four pathogenesis-related (PR) proteins from wheat (wheatwins) belonging to the PR-4 family. All the models were based on the knowledge of the tertiary structure of barwin, a highly homologous protein from barley. Wheatwin1 and wheatwin2 differ in two amino acid residues (positions 62 and 68) out of 125. Wheatwin4 differs from wheatwin2 in one residue at position 78, while wheatwin3 differs from wheatwin1 in one residue at position 88. The global folding and the secondary structures were very similar through all the sequences, including the regions of the amino acid substitutions. The main differences were found in the traits 15-21, 84-86 and 91-93. Trait 15-21 was predicted as ss-sheet in wheatwin4 and random-coil in the other proteins. Trait 84-86 was predicted as ss-sheet in wheatwin3 and random-coil in the other proteins. Trait 91-93 was predicted as random coil in wheatwin1 and wheatwin3 and ss-sheet in the other two proteins. Traits 15-21 and 84-86 were exposed, while trait 91-93 was quite hidden in all the proteins. The antifungal activities of the four proteins towards the specific pathogenic fungus Fusarium culmorum were distinct and well correlated to the structural differences. These results suggest that these regions may have a role in the action mechanism, which is still unknown.

Amino Acid Sequence↗

PubMed1982

Secondary structure model for the complete simian virus 50 late precursor mRNA.

Structures for all sequences containing less than 1790 nucleotides in the 2600 nucleotide late region of the SV40 virus have been computed and saved on magnetic tape. Previously the longest sequence whose secondary structure was calculated in a single computer run contained 950 nucleotides. In the past, analysis of long molecules required numerous repeated, partially overlapping computations on much shorter segments. The structure obtained for the late half of the SV40 is Y-shaped with two unequal arms. It has 52 short hairpins. Two long range interactions between nucleotides near 650 and 1350 and between 1450 and 2450 appear to play an important role. The first is within the 16S intron; the second is in the 3' exon. The 5' and 3' ends of the molecule are close to each other and are found in the major elongated stem in the vicinity of the fork.

Base Sequence↗

PubMed1976

Spectroscopic studies and a structural model for blue copper centers in proteins.

Low temperature absorption, circular dichroism, and magnetic circular dichroism spectral studies of the blue copper proteins Rhus vernicifera stellacyanin, bean plastocyanin, and Pseudomonas aeruginosa azurin have been made. Low energy bands attributable to the d-d transitions 2B2 leads to 2E and 2B2 leads to 2B1 in a flattened tetrahedral (D 2d) copper-(II) center are observed in these proteins at about 5000 and 10,000 cm-1, respectively. The band positions accord well with ligand field calculations based on a tetrahedral structure that is distorted approximately 6 degrees toward a square plane. The ligands in this flattened tetrahedral coordination unit in bean plastocyanin are identified from various spectroscopic experiments as His-38, Cys-85, His-88, and a deprotonated peptide nitrogen (N) a few residues above His-38.

Azurin↗

PubMed2006

An age-structured model of dendritic cell trafficking in the lung.

As the sentinels of the immune system, dendritic cells (DC) play a critical role in initiating and maintaining appropriate T cell responses through capture and presentation of antigen, costimulation, and mediator release. Although much is known about certain aspects of DC function, the exact relationship between lung epithelial DC precursor populations in the blood and their functional role in antigen presentation are not clearly understood. I created an age-structured mathematical model for DC trafficking into the lung to address this question. While capturing experimentally observed system dynamics, I found that blood DC are preferentially recruited over blood monocytes. For short-lived antigens, the model results suggest that lung epithelial DC derived from blood DC exhibit a 625% increase in antigen density compared with those derived from blood monocytes. Finally, these results motivate future experimental studies to clarify aspects of DC trafficking in the lung.

Aging↗

PubMed2002

Peptide analysis, stability studies, and structural modeling explain contradictory peptide motifs and unique properties of the NOD mouse MHC class II molecule H2-A(g7).

The MHC class II molecule H2-A(g7) is the chief genetic determinant in insulin-dependent diabetes mellitus of the non-obese diabetic (NOD) mice. Poor peptide binding ability, as well as presentation of a unique subset of peptides by this molecule was suggested to promote autoimmunity in this strain. However, several laboratories have presented results in favor of an H2-A(g7) molecule that can avidly bind many different peptides. The crystal structures of H2-A(g7) in complex with two different peptides did not completely resolve this issue. To analyze the peptide binding capacity and the motif requirements of H2-A(g7), we eluted natural ligands from purified H2-A(g7) molecules isolated from the H2-A(g7)-transfected M12-C3 cells. A low peptide yield dominated by a few peptide ligands was found. Pool sequencing and alignment of individual ligands on the basis of molecular modeling revealed a peptide-binding motif with basic/aliphatic/small hydrophilic amino acids at relative position 1 (p1), aliphatic amino acids at p4, Ala at p6, and acidic amino acids and Ser/Gly at p9, as well as acidic residues at p10/11. Though weak, the binding of individual ligands, as well as the importance of an acidic C-terminal residue was confirmed by peptide binding studies to isolated H2-A(g7) molecules. Furthermore, the H2-A(g7) molecule incompletely dissociated into its constituent chains in SDS-electrophoresis under nonreducing conditions. This provides additional evidence of its weak affinity for peptides, which probably arises from the combination of beta56His/beta57Ser/beta78Ala and other unique H2-A(g7) residues in contact with the antigenic peptide. These results allow a better understanding of the role of this molecule in the development of autoimmunity and the identification of epitopes relevant to diabetes.

Amino Acid Motifs↗

PubMed2006

Sources of motivation, interpersonal conflict management styles, and leadership effectiveness: a structural model.

126 leaders and 624 employees were sampled to test the relationship between sources of motivation and conflict management styles of leaders and how these variables influence effectiveness of leadership. Five sources of motivation measured by the Motivation Sources Inventory were tested-intrinsic process, instrumental, self-concept external, self-concept internal, and goal internalization. These sources of work motivation were associated with Rahim's modes of interpersonal conflict management-dominating, avoiding, obliging, complying, and integrating-and to perceived leadership effectiveness. A structural equation model tested leaders' conflict management styles and leadership effectiveness based upon different sources of work motivation. The model explained variance for obliging (65%), dominating (79%), avoiding (76%), and compromising (68%), but explained little variance for integrating (7%). The model explained only 28% of the variance in leader effectiveness.

Adolescent↗

PubMed2006

Structural model of the OPA1 GTPase domain may explain the molecular consequences of a novel mutation in a family with autosomal dominant optic atrophy.

Autosomal dominant optic atrophy (ADOA) is the most frequent hereditary optic neuropathy. Three loci have been reported for ADOA: a major locus, harboring all identified mutations to date, maps to 3q28 (OPA1), a second locus is linked to 18q12.2-q12.3 (OPA4) and a third locus on 22q12.1-q13.1 (OPA5) has been reported recently. We describe a six-generation Iranian family in which optic atrophy runs as an autosomal dominant trait with an age of onset at 14-15years. We performed linkage analysis with markers mapping to 3q28 and 18q12.2-q12.3 and found linkage to 3q28. Subsequent sequencing of OPA1 identified a novel heterozygous missense mutation (c.1313A>G) replacing aspartic acid by glycine (p.D438G) in the GTPase domain of OPA1. Interestingly, another missense mutation at the same position (c.1313A>T, D438V) has been reported before in two unrelated German families, indicating a possible mutation hot spot. Further evidence supporting the importance of D438 is its conservation from human to acoelomata. OPA1 is believed to be the human orthologue of yeast MGM1, a dynamin-related protein required for the integrity of mitochondrial DNA. Homology modeling of the OPA1 GTPase domain revealed extensive structural similarity to the Dictyostelium dynamin A GTPase domain and showed that D438 may interact with residues of the G1 and the G4 motifs, which are crucial in coordinating GTP. Based on this analysis, we propose a mechanism which explains the gradual decline of vision in ADOA patients with OPA1 mutations at position 438.

Adolescent↗

PubMed1997

Structure model and physicochemical properties of the C-U mismatch pair in the double stranded RNA in solution.

Structure of the C-U mismatch pair was reported only in crystal but none in solution. Here we have studied the structure and physicochemical properties of the C-U mismatch pair in a double stranded RNA in solution. RNA oligomers r(CGACUCAGG) and r(CCUGCGUCG) form a double stranded structure with the C-U pair. The arrangement of the C-U pair derived from the model building based on nOe gives a similar structural feature to that in crystal. The modeling reveals that the amino-proton of cytidine and the keto-oxygen of uridine are located within hydrogen bonding distance, and the imino proton of uridine is exposed to bulk water. From the melting experiment which monitors chemical shifts of non-exchangeable protons, the melting of all the base-pairs including the C-U pair occurs simultaneously. This suggests the possibility where the C-U mismatch pair is stacked on the neighboring base-pairs in the double helix until the duplex is denatured to single strands.

Base Composition↗

PubMedDate not supplied

A structural model of the relationships among self-efficacy, psychological adjustment, and physical condition in Japanese advanced cancer patients.

We made detailed research for relationships among physical condition, self-efficacy and psychological adjustment of patients with advanced cancer in Japan. The sample consisted of 85 (42 males and 43 females) advanced cancer patients. Interviews were conducted with some measurement scales including the Self-efficacy scale for Advanced Cancer (SEAC), and the Hospital Anxiety and Depression Scale (HADS). Karnofsky Performance Status (KPS) and medication status were also recorded from the evaluation by physicians. We used structural equation modeling (SEM) for statistical analysis. The analysis revealed that the model, including three self-efficacy subscales, depression, anxiety, KPS, meal-, liquid-intake, prognosis and three latent variables: 'Self-efficacy', 'Emotional Distress', and 'Physical Condition,' fit the data (chi-square(24)=28.67, p=0.23; GFI=0.93; CFI=0.98; RMSEA=0.05). In this model, self-efficacy accounted for 71% of the variance in emotional distress and physical condition accounted for 8% of the variance in self-efficacy. Overall, our findings suggest clearly that close relationships existed among physical condition, self-efficacy and emotional distress. That is, patients in good physical condition had a high self-efficacy, and patients with high self-efficacy were less emotionally distressed. These results imply that psychological intervention which emphasizes self-efficacy would be effective for advanced cancer patients.

Adaptation, Psychological↗