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Critical examination of the supermolecule density functional theory calculations of intermolecular interactions.

The results of calculations employing twelve different combinations of exchange and correlation functionals are compared with results of ab initio calculations for two different configurations of the water dimer and three different configurations of the thymine-adenine complex. None of the density functional theory (DFT) treatments could properly reproduce the results of coupled-cluster calculations for all configurations examined. The DFT approaches perform well when the interaction energy is dominated by the electrostatic component and the dispersion energy is less important. Two mechanisms that compensate for the missing dispersion component were identified. The first one is the decrease of the magnitude of the intermolecular exchange-repulsion and the second one is the increase of the magnitude of the attractive deformation energy. For some functionals both effects are observed together, but for some other ones only the second effect occurs. The three correlation functionals that were examined were found to make only very small contributions to the deformation energy. The examination of angular and distance dependence of the interactions shows that the currently available DFT approaches are not suitable for developing intermolecular potential energy surfaces. They could however be used to find global minima on potential energy surfaces governed by intermolecular electrostatic interactions. Additional single point ab initio calculations are recommended as the means of validating optimized structures.

Adenine↗

Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist.

Recently we predicted the 3D structure of the human beta2-adrenergic receptor (beta2AR) and of the binding site of several agonists and antagonists to beta2AR. These predictions (MembStruk and HierDock) included no explicit water and only a few lipid molecules. Here we include explicit H(2)O and an infinite lipid bilayer membrane in molecular dynamics (MD) simulations of three systems: apo-beta2AR, epinephrine-bound beta2AR, and butoxamine-bound beta2AR (epinephrine is an endogenous agonist, and butoxamine is a beta2AR selective antagonist). The predicted structures for apo-beta2AR and butoxamine-beta2AR are stable in MD, but in epinephrine-beta2AR, extracellular water trickles into the binding pocket to mediate hydrogen bonding between the catechol of epinephrine and Ser-204 on helix 5. The epinephrine-beta2AR structure shows dynamic flexibility with small, piston-like movements of helices 3 and 6 and transient interhelical hydrogen bonding between Ser-165 on transmembrane 4 and Ser-207 on transmembrane 5. These couplings and motions may play a role in protein activation. The apo-beta2AR shows less dynamic flexibility, whereas the antagonist-beta2AR structure is quite rigid. This MD validation of the structure predictions for G protein-coupled receptors in explicit lipid and water suggests that these methods can be trusted for studying the mechanism of activation and the design of subtype-specific agonists and antagonists.

Adrenergic beta-2 Receptor Agonists↗

A membrane-distal segment of the integrin alpha IIb cytoplasmic domain regulates integrin activation.

Previous evidence suggests that interactions between integrin cytoplasmic domains regulate integrin activation. We have constructed and validated recombinant structural mimics of the heterodimeric alpha(IIb)beta(3) cytoplasmic domain. The mimics elicited polyclonal antibodies that recognize a combinatorial epitope(s) formed in mixtures of the alpha(IIb) and beta(3) cytoplasmic domains but not present in either isolated tail. This epitope(s) is present within intact alpha(IIb)beta(3), indicating that interaction between the tails can occur in the native integrin. Furthermore, the combinatorial epitope(s) is also formed by introducing the activation-blocking beta(3)(Y747A) mutation into the beta(3) tail. A membrane-distal heptapeptide sequence in the alpha(IIb) tail ((997)RPPLEED) is responsible for this effect on beta(3). Membrane-permeant palmitoylated peptides, containing this alpha(IIb) sequence, specifically blocked alpha(IIb)beta(3) activation in platelets. Thus, this region of the alpha(IIb) tail causes the beta(3) tail to resemble that of beta(3)(Y747A) and suppresses activation of the integrin.

Amino Acid Sequence↗

Prevalence and impact of premenstrual syndrome in adolescent schoolgirls in the United Arab Emirates.

BACKGROUND: Our objective was to determine the prevalence, sociodemographics, and impact of premenstrual syndrome in adolescent schoolgirls in the United Arab Emirates, as there are no national data on this subject. METHODS: Adolescent girls aged 12-18 years who were at least 1 year postmenarchal were selected from five private and five public schools (n=70 x 10 = 700) in Al-Ain city using a multistage stratified cluster-sampling technique. Subjects were interviewed about cyclic and recurrent behavioral and somatic premenstrual symptoms during the last 3 months based on the American College of Obstetricians and Gynecologists' criteria and their impact on quality of life using a structured and validated questionnaire. RESULTS: The prevalence of premenstrual syndrome was 16.4% (n=115). On logistic regression analysis, premenstrual syndrome was significantly associated with Emirati nationality (p=0.001), presence of the condition in sister(s) (p=0.002), and dysmenorrhea (p<0.001). Only 52 affected subjects (45.2%) were currently taking treatment for premenstrual syndrome and the majority (60%) used pharmacological therapy. Premenstrual syndrome had a moderate but significant negative impact (p<0.001) on the quality of life of affected girls, particularly school performance, social interactions, lifestyle, and emotional well-being. Difficulty in performing school functions and decrease in stigma were the two most adversely affected parameters. CONCLUSION: Premenstrual syndrome is a prevalent, yet undertreated, disorder in adolescent schoolgirls in the United Arab Emirates, which adversely affects their emotional well-being and educational performance, representing a significant public health problem. Premenstrual syndrome is significantly associated with ethnicity, family history, and dysmenorrhea in this group.

Adaptation, Psychological↗

Structure of an 11-mer DNA duplex containing the carbocyclic nucleotide analog: 2'-deoxyaristeromycin.

2'-deoxyaristeromycin (dAr) is a nucleoside analogue that is resistant to the action of DNA glycosylases. High-resolution NMR spectroscopy and molecular dynamics simulations were used to determine the three-dimensional structure of an 11-mer DNA containing a single dAr.T base pair at its center. Analysis of the spectra revealed the existence of a right-handed duplex in solution, stabilized by Watson-Crick hydrogen bonding and base-stacking interactions. The carbocyclic sugar adopted a C1'-exo conformation and sugars of the 3'-flanking base pair had puckers in the O4'-endo range. The dAr.T base pair was mildly propeller twisted, and the dAr analogue showed a positive roll with the 3'-flanking base. Our findings indicate that the observed resistance of dAr-containing oligodeoxynucleotides to the catalytic action of DNA glycosylases relates to its electronic properties rather than structure, and validate the use of dAr and related carbocyclic nucleoside analogues for biological and structure/function relationship studies.

Computer Simulation↗

Specificity of membrane specializations in mechanoreceptors of birds--A freeze-etching study.

The detailed knowledge of the molecular process of mechanotransduction is still an unsolved question. The investigation of the intramembranous structure of the cutaneous mechanoreceptors may play an important role in elucidating this problem. In this relation, Herbst sensory corpuscles in ducks were studied for the first time using the freeze-etching and thin sectioning techniques. Herbst corpuscles have the basic structural components valid for most of the encapsulated mechanoreceptors in mammals: a capsule made of perineural cells, a lamellar complex of modified Schwann cells, surrounding the non-myelinated part of the receptor nerve fiber and its ending. Freeze-etching replicas reveal that the plasmalemmae of the capsule cells, modified Schwann cells and axolemmae of parts of the nerve fiber differ in both density and pattern of distribution of intramembranous particles (IMPs) as well as IMP size. On all the plasmalemmae the IMP density is higher on the P-face (2000-3300 microm(-2)) than the respective E-face (800-1500 microm(-2)). The axolemma of the ending of the receptor nerve fiber expresses higher density of IMPs than its shaft. The mean IMP size for all the plasmalemmae varies between 5.5 and 7.5 nm. Many tight junctions occur between the capsule cells. These results indicate that the non-myelinated axolemma as well as the plasmalemmae of other components of Herbst corpuscles are specialized in terms of content and distribution of IMPs. The IMPs may represent various kinds of mechanosensitive channel proteins or related membrane-bound proteins participating in the process of mechanotransduction.

Animals↗

Sequences of three molluscan 5 S ribosomal RNAs confirm the validity of a dynamic secondary structure model.

The collection of known 5 S rRNA primary structures is enriched with the sequences from three mollusca, the snails Helix pomatia and Arion rufus, and the mussel Mytilus edulis. The three sequences can be fitted in a five-helix secondary structure model previously shown (De Wachter et al. (1982) Biochimie 64, 311-329) to apply to all 5 S RNAs regardless of their origin. One of the helices in this model can undergo a bulge-internal loop transition. Within the metazoan kingdom, the dimensions of each helix and loop are rigidly conserved, except for one helix which can comprise either 6 or 7 base pairs.

Animals↗

Protein engineering tests of a homology model of Plasmodium falciparum lactate dehydrogenase.

This paper describes the testing of a homology model of Plasmodium falciparum lactate dehydrogenase (pfLDH) by protein engineering. The model had been validated in structural terms. It suggests explanations of the unusual properties of pfLDH (compared with all other LDHs). These unusual features are a lack of substrate inhibition, high activity with the synthetic coenzyme 3-acetylpyridine adenine dinucleotide (APAD+) and changes in residues at previously conserved positions. pfLDH shows several amino acid insertions and deletions in an alignment with protein sequences from all other known LDHs. The most notable is a five amino acid insertion into the active-site loop. In addition, a conserved serine at position 163 is replaced by leucine. The results showed that when the unique pfLDH structural features were engineered into Bacillus stearothermophilus lactate dehydrogenase, the thermophilic enzyme acquired the properties previously uniquely associated with the malarial enzyme. We conclude that the homology model of the malarial enzyme is adequate for the prediction of successful redesigns and, in the regions tested, is accurate.

Amino Acid Sequence↗

Undergraduate musculoskeletal examination teaching by trained patient educators--a comparison with doctor-led teaching.

BACKGROUND: To compare the core hand and knee examination skills gained by undergraduates taught either by trained patient educators (PEs) or by doctors. METHODS: A total of 50 final year medical students were randomized to receive training from PEs or doctors. Group A were taught hand examination by a PE with rheumatoid arthritis, and knee examination by a PE with osteoarthritis. Group B was taught hand and knee examination by a consultant rheumatologist plus an untrained patient with appropriate signs. All students were taught an established core skills set in small group workshops. Students then undertook two validated objective structured clinical examination (OSCE) stations with two blinded assessors. Pre- and post-teaching questionnaires established the students' self-reported levels of skills (SRS) and a student evaluation of teaching (SET). The study was analysed as an equivalence trial. A mean difference in OSCE scores of 10% was assumed to be of educational significance. RESULTS: Although the SET scores of both groups were high, the doctor-led group received higher scores. Aside from this, the two student groups did not differ significantly. There were no significant differences in mean hand OSCE (mean difference = 0.88, P = 0.28, 95% CI = -0.73 to 2.49) or knee OSCE (mean difference = 0.28, P = 0.7, 95% CI = -1.19 to 1.75) scores. Both the upper and lower confidence intervals for each mean difference fell within the 10% range (-2.8 to 2.8 for the hand, and -2.5 to 2.5 for the knee) and equivalence was assumed. CONCLUSIONS: Adequately trained PEs can deliver clearly structured undergraduate skills, teaching with equivalent learning outcomes to those of rheumatology consultants. PEs are a valuable development to augment musculoskeletal education in the face of expanding student numbers.

Adult↗

Effects of an organized critical care service on outcomes and resource utilization: a cohort study.

OBJECTIVE: To determine whether the presence of an on-site, organized, supervised critical service improves care and decreases resource utilization. DESIGN: The study compared two patient cohorts admitted to a surgical intensive care unit during the same period of time. The study cohort was cared for by an on-site critical care team supervised by an intensivist. The control cohort was cared for by a team with patient care responsibilities in multiple sites supervised by a general surgeon. The main outcome measures were duration of stay, resource utilization, and complication rate. SETTING: Study patients were general surgical patients in an academic medical center. RESULTS: Despite having higher Acute Physiology and Chronic Health Evaluation II scores, patients cared for by the critical care service spent less time in the surgical intensive care unit, used fewer resources, had fewer complications and had lower total hospital charges. The difference between the two cohorts was most evident in patients with the worst APACHE II score. CONCLUSIONS: Critical care interventions are expensive and have a narrow safety margin. It is essential to develop structured and validated approaches to study the delivery of this resource. In this study, the critical care service model performed favorably both in terms of quality and cost.

APACHE↗

Ten-year follow-up of adolescent-onset anorexia nervosa: personality disorders.

OBJECTIVE: To study the development of personality disorders, especially those involving obsessions, compulsions, and social interaction problems, in a representative group of anorexia nervosa (AN) cases. METHOD: The prevalence of personality disorders, obsessive-compulsive disorder, and autism spectrum disorders at mean age 24 years (10 years after reported onset) was examined in 51 adolescent-onset AN cases recruited after community screening and 51 comparison cases matched for age, sex, and school. All 102 cases had originally been examined at age 16 years and followed up at 21 years. At 24 years, structured and validated psychiatric diagnostic interviews were performed by a psychiatrist who was blind to original diagnosis. The majority of AN cases (94%) were weight-restored. RESULTS: Personality disorders, particularly cluster C, and autism spectrum disorders were overrepresented in the AN group. Obsessive-compulsive personality disorder and/or autism spectrum disorder was diagnosed in a subgroup of AN cases in all 3 studies. This subgroup had a very poor psychosocial outcome. CONCLUSIONS: Persistent problems with obsessions, compulsions, and social interaction characterized a substantial minority of weight-restored AN cases at 10-year follow-up. These problems appear to be constitutional rather than a result of AN, and they may warrant a different treatment approach.

Adolescent↗

Development and testing of the caregiver reciprocity scale.

The purpose of this study was to develop and validate the dimensions of caregiver reciprocity. Social exchange and equity theory served as a conceptual framework for examining recprocal intergenerational exchanges of assistance and support. In the first phase of the study, 12 caregivers of elderly parents, including in-laws, were interviewed to provide narrative data from which items were developed. Content validity was judged by two separate panels of experts. The revised CRS was tested with 303 adult children for reliability and validity, including internal consistency, test-retest reliability, exploratory factor analysis, and convergent and discriminant validity testing using structural equation modeling. Support for construct validity was demonstrated for four factors: Warmth and Regard, Intrinsic Rewards of Giving, Love and Affection, and Balance within Family Caregiving.

Aged↗

Measuring the functional status of patients with low back pain. Assessment of the quality of four disease-specific questionnaires.

STUDY DESIGN: This study was a literature review of the quality of four disease-specific functional status questionnaires for patients with low back pain: Oswestry; Million; Roland; and Waddell disability questionnaire. OBJECTIVES: The questionnaires were evaluated in terms of general description, scale structure, reliability, validity, responsiveness, and clinical research applications. SUMMARY OF BACKGROUND DATA: Functional status is an outcome of great interest for clinical trials of low back pain. METHODS: A computer-aided search was conducted of articles published between 1981 and 1993 and references given in selected relevant publications. Articles were selected if at least one of the four functional status questionnaires was used or if the authors gave relevant information about the methodology of these questionnaires. RESULTS: There was not enough information available about the criteria of item selection used for the development of the questionnaires. The test-retest reproducibility of the questionnaires seemed satisfactory. The Oswestry and Roland disability questionnaires have been used and evaluated more frequently than the Million and Waddell. Therefore, we can be more certain about the validity and responsiveness of the former pair of questionnaires. CONCLUSION: In the absence of a gold standard, direct comparisons of evaluative functional status questionnaires in a single patient group are needed. Through direct comparisons, comparative validity and responsiveness can be assessed. Functional status measures are not currently used in many settings in which they would be valuable. It is important to encourage their wider use in clinical trials. Additional research is needed to compare and improve the existing questionnaires.

Activities of Daily Living↗

Use of a standardized menopause symptom rating scale in a sample of women with physical disabilities.

OBJECTIVE: To determine the psychometric properties of a menopause symptom rating scale developed on nondisabled women in a sample of women polio survivors with physical disabilities. DESIGN: The 25-item Menopause Symptom List (MSL) was administered to 190 women between ages 40 and 65 not taking hormone or estrogen therapy. Factor analysis, bivariate correlation, and analysis of variance were performed to determine the scale's underlying structure, construct validity, and association with menopausal status. RESULTS: Factor analysis revealed four factors: (1) psychological, (2) somatic-sensory, (3) somatic-sleep, and (4) vasomotor. Factors 1 and 3 were associated with postpolio sequelae, self-rated health, positive and negative affect, life satisfaction, and perceived stress. Factor 2 was associated with postpolio sequelae, basic activities of daily living, self-rated health, negative affect, life satisfaction, and perceived stress. Factor 4 was associated with postpolio sequelae, self-rated health, negative affect, and perceived stress. Comparison by menopause status found Factors 1 and 3 significantly differed between groups (F(2,181) = 6.68 and 4.17, respectively; P = 0.02). Contrary to expectations, vasomotor factor severity was not distinguished by menopause status. CONCLUSIONS: Menopause symptom scales standardized on nondisabled women should be used cautiously with women with physical disabilities. Associations between construct validity measures and menopause symptomatology suggest a complex relationship between physical disability and menopause.

Adult↗

Impact of a long asylum procedure on the prevalence of psychiatric disorders in Iraqi asylum seekers in The Netherlands.

Clinically, a long asylum procedure seems to be associated with psychiatric disorders. However, data on this issue are lacking. In a national community-based study, using random sampling, we compared two groups of Iraqi asylum seekers, who had resided less than 6 months (N = 143) and more than 2 years (N= 151), respectively, in The Netherlands. Respondents were interviewed with fully structured, culturally validated, translated questionnaires. Psychiatric (DSM-IV) disorders were measured with the Composite International Diagnostic Interview 2.1 and evaluated in relation with premigration and postmigration adverse life events. Overall prevalence of psychiatric disorders was 42% in the first group and 66.2% in the second. The prevalence rates of anxiety, depressive, and somatoform disorders were significantly higher in the second group. Posttraumatic stress disorder was high in both groups but did not differ (p > .05). On logistic regression of all relevant risk factors, a long asylum procedure showed an odds ratio of 2.16 (confidence interval = 1.15-4.08) for psychopathology. The conclusion is that, indeed, the duration of the asylum procedure is an important risk factor for psychiatric problems. Both politicians and mental health workers should take note of this finding.

Adolescent↗

Postmigration living problems and common psychiatric disorders in Iraqi asylum seekers in the Netherlands.

In a previous community-based, national study among Iraqi asylum seekers, a long asylum procedure was found to have a higher risk for common psychiatric disorders than adverse life events in Iraq. In the present article, the postmigration period is considered in more detail and evaluated in relationship with psychiatric disorders. Respondents were interviewed with fully structured, culturally validated, translated questionnaires. With the use of a Post- migration Living Problems questionnaire, worries about all kinds of problems were gathered. Psychiatric (DSM-IV) disorders were measured with the Composite International Diagnostic Interview 2.1. Factor analysis was done on the postmigration living problems, and in univariate and multivariate analyses, associations with psychopathology were calculated. Results show that clusters of postmigration living problems could be identified: family issues, discrimination, asylum procedure, socioeconomic living conditions, socioreligious aspects, and work-related issues. There was a significant relationship between all clustered postmigration living problems and psychopathology, except for socioreligious aspects. Multivariate logistic regression showed that lack of work, family issues, and asylum procedure stress had the highest odds ratios for psychopathology. The findings appeal to governments to shorten the asylum procedures, allow asylum seekers to work, and give preference to family reunion. Mental health workers should recognize the impact of postmigration living problems and consider focusing their treatment on coping with these problems instead of traumas from the past.

Adaptation, Psychological↗

Neural systems underlying episodic memory: insights from animal research.

Two strategies used to uncover neural systems for episodic-like memory in animals are discussed: (i) an attribute of episodic memory (what? when? where?) is examined in order to reveal the neuronal interactions supporting that component of memory; and (ii) the connections of a structure thought to be central to episodic memory in humans are studied at a level of detail not feasible in humans. By focusing on spatial memory (where?) and the hippocampus, it has proved possible to bring the strategies together. A review of lesion, disconnection and immediate early-gene studies in animals reveals the importance of interactions between the hippocampus and specific nuclei in the diencephalon (most notably the anterior thalamic nuclei) for spatial memory. Other parts of this extended hippocampal system include the mammillary bodies and the posterior cingulate (retrosplenial) cortex. Furthermore, by combining lesion and immediate early-gene studies it is possible to show how the loss of one component structure or tract can influence the remaining regions in this group of structures. The validity of this convergent approach is supported by new findings showing that the same set of regions is implicated in anterograde amnesia in humans.

Amnesia↗

Protein structure and evolutionary history determine sequence space topology.

Understanding the observed variability in the number of homologs of a gene is a very important unsolved problem that has broad implications for research into coevolution of structure and function, gene duplication, pseudogene formation, and possibly for emerging diseases. Here, we attempt to define and elucidate some possible causes behind the observed irregularity in sequence space. We present evidence that sequence variability and functional diversity of a gene or fold family is influenced by quantifiable characteristics of the protein structure. These characteristics reflect the structural potential for sequence plasticity, i.e., the ability to accept mutation without losing thermodynamic stability. We identify a structural feature of a protein domain-contact density-that serves as a determinant of entropy in sequence space, i.e., the ability of a protein to accept mutations without destroying the fold (also known as fold designability). We show that (log) of average gene family size exhibits statistical correlation (R(2) > 0.9.) with contact density of its three-dimensional structure. We present evidence that the size of individual gene families are influenced not only by the designability of the structure, but also by evolutionary history, e.g., the amount of time the gene family was in existence. We further show that our observed statistical correlation between gene family size and contact density of the structure is valid on many levels of evolutionary divergence, i.e., not only for closely related sequence, but also for less-related fold and superfamily levels of homology.

Amino Acid Sequence↗