Predicting estrogen receptor binding of chemicals using a suite of in silico methods - Complementary approaches of (Q)SAR, molecular docking and molecular dynamics.

With the aim of obtaining reliable estimates of Estrogen Receptor (ER) binding for diverse classes of compounds, a weight of evidence approach using estimates from a suite of in silico models was assessed. The predictivity of a simple Majority Consensus of (Q)SAR models was assessed using a test set of compounds with experimental Relative Binding Affinity (RBA) data. Molecular docking was also carried out and the binding energies of these compounds to the ERα receptor were determined. For a few selected compounds, including a known full agonist and antagonist, the intrinsic activity was determined using low-mode molecular dynamics methods. Individual (Q)SAR model predictivity varied, as expected, with some models showing high sensitivity, others higher specificity. However, the Majority Consensus (Q)SAR prediction showed a high accuracy and reasonably balanced sensitivity and specificity. Molecular docking provided quantitative information on strength of binding to the ERα receptor. For the 50 highest binding affinity compounds with positive RBA experimental values, just 5 of them were predicted to be non-binders by the Majority QSAR Consensus. Furthermore, agonist-specific assay experimental values for these 5 compounds were negative, which indicates that they may be ER antagonists. We also showed different scenarios of combining (Q)SAR results with Molecular docking classification of ER binding based on cut-off values of binding energies, providing a rational combined strategy to maximize terms of toxicological interest.

Objectively measured physical activity and longitudinal changes in adolescent body fatness: an observational cohort study.

BACKGROUND: The data regarding prospective associations between physical activity (PA) and adiposity in youth are inconsistent. OBJECTIVE: The objective of this study was to investigate associations between baseline levels of objectively measured PA and changes in adiposity over 2.5 years from mid-to-late adolescence. METHODS: This was an observational cohort study in 728 school students (43% boys) from Cambridgeshire, United Kingdom. Fat mass index (FMI, kg m(-2) ) was estimated at baseline (mean ± standard deviation age: 15 ± 0.3 years) and follow-up (17.5 ± 0.3 years) by anthropometry and bioelectrical impedance. Habitual PA was assessed at baseline by ≥3 d combined heart rate and movement sensing. Average daily PA energy expenditure (PAEE) and the time (min d(-1) ) spent in light, moderate and vigorous intensity PA (LPA, MPA and VPA, respectively) was estimated. Multilevel models were used to investigate associations between baseline PA and change in FMI (ΔFMI). Adjustment for baseline age, sex, follow-up duration, area-level socioeconomic status, season of PA assessment, sedentary time, energy intake and sleep duration was made; baseline FMI was also added in a second model. RESULTS: FMI increased significantly over follow-up (0.6 ± 1.2 kg m(-2) , P < 0.001). Baseline PAEE and LPA positively predicted ΔFMI in overfat participants (P ≤ 0.030), as did VPA in initially normal fat participants (P ≤ 0.044). There were further positive associations between PAEE and ΔFMI in normal fat participants, and between MPA and ΔFMI in both fat groups, when adjusted for baseline FMI (P ≤ 0.024). CONCLUSIONS: Baseline PAEE and its subcomponents were positively associated with small and unlikely clinically relevant increases in ΔFMI. These counter-intuitive findings may be explained by behavioural changes during the course of study follow-up.

Myocardial function in hypothyroidism. Relation to disease severity and response to treatment.

Systolic time intervals (ST) were used to evaluate myocardial function prospectively in 29 hypothyroid patients. The patients were divided into three categories of disease severity: (1) severe hypothyroidism, (2) mild hypothyroidism, and (3) decreased thyroid reserve or "prehypothyroidism." Groups 1 and 2 showed decreased myocardial contractility with a prolonged preejection period (PEP), shortened left ventricular ejection time (LVET), and increase PEP/LVET, compared with normal controls. The STI were more abnormal (P less than .05) in group 1 than in group 2, suggesting that the severity of myocardial dysfunction correlates with the severity of the hypothyroidism. Group 3 had normal STI. Ten patients were restudied when euthyroid and showed complete normalization of their STI, supporting the thesis that hypothyroidism was the sole cause of the initial myocardial dysfunction.

Type VI microfilaments interact with a specific region of banded collagen fibrils in skin.

Immunolocalization studies demonstrate that Type VI collagen forms a flexible network that interweaves among collagen fibrils in the dermis of skin as well as in other loose connective tissues. Although binding of Type VI collagen with other matrix components has been suggested, no structural evidence supporting these studies has been reported. In this study, we demonstrate that Type VI microfilaments consistently crossbanded collagen fibrils near the "d" band, indicating that the interaction of Type VI collagen with banded fibrils is not passive. This "d" band is also the location of the binding domain of decorin to banded fibrils, suggesting that decorin mediates the interaction of Type VI microfilaments with banded fibers. Examination of the architecture of the Type VI network in a decorin nullizygous mouse demonstrates a continuance of this specific interaction, indicating that the association is not entirely dependent on the presence of decorin. At least one other component, whose identity is uncertain, persists near the "d" band, which may also serve to mediate the attachment of Type VI collagen to collagen fibrils.

Fibrillin-1 in human cartilage: developmental expression and formation of special banded fibers.

The molecular basis for Marfan's syndrome (MS), a heritable disorder of connective tissue, is now known to reside in mutations in FBN1, the gene for fibrillin-1. Classic phenotypic manifestations of MS include several skeletal abnormalities associated primarily with overgrowth of long bones. As a first step towards understanding how mutations in FBN1 result in skeletal abnormalities, the developmental expression of fibrillin-1 (Fib-1) in human skeletal tissues is documented using immunohistochemistry and monoclonal antibodies demonstrated here to be specific for Fib-1. At around 10-11 weeks of fetal gestation, Fib-1 is limited in tissue distribution to the loose connective tissue surrounding skeletal muscle and tendon in developing limbs. By 16 weeks, Fib-1 is widely expressed in developing limbs and digits, especially in the perichondrium, but it is apparently absent within cartilage matrix. Fib-1 appears as a loose meshwork of fibers within cartilage matrix by 20 weeks of fetal gestation. Until early adolescence, Fib-1 forms loose bundles of microfibrils within cartilage. However, by late adolescence, broad banded fibers composed of Fib-1 are found accumulated pericellularly within cartilage. Because these fibers can be extracted from cartilage using dissociative conditions, we postulate that they are laterally packed and crosslinked microfibrils. On the basis of these findings, we suggest that the growth-regulating function of Fib-1 may reside persistently within the perichondrium. In addition, the accumulation of special laterally crosslinked Fib-1 microfibrils around chondrocytes during late adolescence suggests that growth-regulating activities may also be performed by Fib-1 at these sites.

Modelling of the void space of tablets compacted over a range of pressures.

A previously developed computer model, named Pore-Cor, has been used to simulate the changes in the void-space dimensions which occur during the compaction of tablets over a range of pressures. The tablets were made by mixing pharmaceutical grade crystalline lactose and an anti-inflammatory compound in the proportion 4:1. Compacts were made by placing a weighed amount of the mixed powder into a stainless-steel die and applying pressure with a hand-operated calibrated hydraulic press. Compacts were prepared at eight pressures over the hydraulic pressure range 1 to 8 ton in-2 (15.4-123.2 MPa) in 1 ton in-2 increments. Mercury-intrusion curves were measured for the eight samples by use of a porosimeter and the Pore-Cor package was then used to simulate the mercury-intrusion curves and generate void-space models of the correct porosity. The experimental and simulated characteristic throat diameter, the experimental and simulated porosity, and the simulated permeability of the tablets have all been shown to follow expected trends. The successful modelling of void-structure parameters, which are difficult or impossible to measure experimentally, opens the way to an improved understanding of the strength of compacts.

Evaluation of a vertical mouth stretching orthosis: two case reports.

Burns around the mouth frequently result in contractures or microstomia. Orthoses used in the past have usually been designed to stretch the mouth horizontally. Finding a comfortable effective way to stretch the mouth vertically proved to be a challenge. A jaw positioner was used for vertical mouth stretching in two case studies and was evaluated for effectiveness of preventing mouth contractures and for comfort, durability, ease of use, adaptability for children, and ease of measuring results. Vertical and horizontal passive range of motion increased with initial use and then was maintained in both patients. The jaw positioner was comfortable and easy to use. This orthosis could be adapted to fit in a child's mouth and was impossible to swallow. Progress was easy to monitor with the numeric scale on the orthosis. Though no single orthosis will be ideal for every oral burn, this jaw positioner is recommended for pediatric and adult patients with extensive circumoral burns who demonstrate fair to good compliance.

Serial casting as a technique to correct burn scar contractures. A case report.

Serial casting is a fast, relatively simple, and inexpensive way to effectively correct burn scar contractures. Plaster casts provide circumferential pressure and a prolonged stretch to contracted tissue and cannot be removed by the patient. When casts are applied well and padded appropriately, there is little risk of pressure areas, since the casts are conforming and do not slip distally. Serial casting may be a successful alternative when low-force dynamic splinting cannot be sized small enough for a child, or when patient compliance is unreliable. A case study of a 2-year-old male patient with severe plantar-flexion contractures of the ankles is presented.

A prospective study of burn scar maturation in pediatrics: does age matter?

A prospective study was performed to determine whether patterns of burn scar maturation varied among different pediatric age groups. Patients were divided into three groups according to age at the time of burn injury: birth to 3 years, 4 to 11 years, and 12 to 18 years. Scarring of sheet grafts on an extremity was assessed throughout the maturation process in three areas: vascularity, pliability, and height. A 1-inch square was selected on the graft edge adjacent to unburned skin. Two experienced therapists independently evaluated the test area and averaged their scores. There were no significant differences in rate of scar maturation between age groups. Burn scar maturation of sheet skin grafts in the pediatric patient with burns demonstrated a rapid peak of scarring (1 to 2 months) and scar maturation (9 to 13 months).

Short timescale inkjet ink component diffusion: an active part of the absorption mechanism into inkjet coatings.

The structures of inkjet coatings commonly contain a high concentration of fine diameter pores together with a large pore volume capacity. To clarify the interactive role of the porous structure and the coincidentally occurring swelling of binder during inkjet ink vehicle imbibition, coating structures were studied in respect to their absorption behaviour for polar and non-polar liquid. The absorption measurement was performed using compressed pigment tablets, based on a range of pigment types and surface charge polarity, containing either polyvinyl alcohol (PVOH) or styrene acrylic latex (SA) as the binder, by recording the liquid uptake with a microbalance. The results indicate that, at the beginning of liquid uptake, at times less than 2 s, the small pores play the dominant role with respect to the inkjet ink vehicle imbibition. Simultaneously, water molecules diffuse into and within the hydrophilic PVOH binder causing binder swelling, which diminishes the number of active small pores and reduces the diameter of remaining pores, thus slowing the capillary flow as a function of time. The SA latex does not absorb the vehicle, and therefore the dominating phenomenon is then capillary absorption. However, the diffusion coefficient of the water vapour across separately prepared PVOH and SA latex films seems to be quite similar. In the PVOH, the polar liquid diffuses into the polymer network, whereas in the SA latex the hydrophobic nature prevents the diffusion into the polymer matrix and there exists surface diffusion. At longer timescale, permeation flow into the porous coating dominates as the resistive term controlling the capillary driven liquid imbibition rate.

Fat-free mass mediates the association between birth weight and aerobic fitness in youth.

OBJECTIVE: To investigate whether birth weight acts as a biological determinant of later aerobic fitness, and whether fat-free mass may mediate this association. METHODS: The European Youth Heart Study (EYHS) is a population-based cohort of two age groups (9 and 15 years) from Denmark, Portugal, Estonia and Norway. Children with parentally reported birth weight >1.5 kg were included (n = 2 749). Data were collected on weight, height, and skinfold measures to estimate fat mass and fat-free mass. Aerobic fitness (peak power, watts) was assessed using a maximal, progressive cycle ergometer test. Physical activity was collected in a subset (n = 1 505) using a hip-worn accelerometer and defined as total activity counts/wear time, all children with >600 minutes/day for ≥3 days of wear were included. RESULTS: Lower birth weight was associated with lower aerobic fitness, after adjusting for sex, age group, country, sexual maturity and socio-economic status (ß = 5.4; 95% CI: 3.5, 7.3 W per 1 kg increase in birth weight, p < 0.001). When fat-free mass was introduced as a covariate in the model, the association between birth weight and aerobic fitness was almost completely attenuated (p = 0.7). Birth weight was also significantly associated with fat-free mass (ß = 1.4; 95% CI: 1.1, 1.8, p < 0.001) and fat-free mass was significantly associated with aerobic fitness (ß = 3.6; 95% CI: 3.4, 3.7, p < 0.001). Further adjustment for physical activity did not alter the findings. CONCLUSION: Birth weight may have long-term influences on fat-free mass and differences in fat-free mass mediate the observed association between birth weight and aerobic fitness.

Triple helix formation of procollagen type I can occur at the rough endoplasmic reticulum membrane.

One key problem in understanding the biosynthesis of collagens remains the assembly of the three alpha-chains. How and when are the different gene products selected, aligned, and folded into a triple helix? As the spatial arrangement during biosynthesis might be important, we concentrated on whether the rough endoplasmic reticular membrane is involved in this process. Microsomes were prepared from biosynthetically labeled chick tendon fibroblasts. Vesicles were spread as a monomolecular film which was then transferred over several compartments of a filmbalance containing fresh subphase. Fluorograms of the surface film showed that the monolayer contains procollagen chains. When the monolayer was transferred onto a chymotrypsin/trypsin-containing subphase, the gel bands of the proalpha-chains were shifted into the position of mature alpha-chains, indicating that only the propeptides were digested and the collagenous regions were protected due to triple helix formation. Our results suggest that newly synthesized proalpha-chains can associate as trimers and fold into a triple helical conformation while they are still associated with the membranes of the rough endoplasmic reticulum. These processes also occur when interchain disulfide linkage is inhibited, indicating that chain selection and registration is not dependent on formation of covalent bonds among the carboxyl propeptides.

Temperature effects on the catalytic efficiency, rate enhancement, and transition state affinity of cytidine deaminase, and the thermodynamic consequences for catalysis of removing a substrate "anchor".

To obtain a clearer understanding of the forces involved in transition state stabilization by Escherichia coli cytidine deaminase, we investigated the thermodynamic changes that accompany substrate binding in the ground state and transition state for substrate hydrolysis. Viscosity studies indicate that the action of cytidine deaminase is not diffusion-limited. Thus, K(m) appears to be a true dissociation constant, and k(cat) describes the chemical reaction of the ES complex, not product release. Enzyme-substrate association is accompanied by a loss of entropy and a somewhat greater release of enthalpy. As the ES complex proceeds to the transition state (ES), there is little further change in entropy, but heat is taken up that almost matches the heat that was released with ES formation. As a result, k(cat)/K(m) (describing the overall conversion of the free substrate to ES is almost invariant with changing temperature. The free energy barrier for the enzyme-catalyzed reaction (k(cat)/K(m)) is much lower than that for the spontaneous reaction (k(non)) (DeltaDeltaG = -21.8 kcal/mol at 25 degrees C). This difference, which also describes the virtual binding affinity of the enzyme for the activated substrate in the transition state (S), is almost entirely enthalpic in origin (DeltaDeltaH = -20.2 kcal/mol), compatible with the formation of hydrogen bonds that stabilize the ES complex. Thus, the transition state affinity of cytidine deaminase increases rapidly with decreasing temperature. When a hydrogen bond between Glu-91 and the 3'-hydroxyl moiety of cytidine is disrupted by truncation of either group, k(cat)/K(m) and transition state affinity are each reduced by a factor of 10(4). This effect of mutation is entirely enthalpic in origin (DeltaDeltaH approximately 7.9 kcal/mol), somewhat offset by a favorable change in the entropy of transition state binding. This increase in entropy is attributed to a loss of constraints on the relative motions of the activated substrate within the ES complex. In an Appendix, some objections to the conventional scheme for transition state binding are discussed.

Secondary structure and shape of plasma sex steroid-binding protein--comparison with domain G of laminin results in a structural model of plasma sex steroid-binding protein.

We have analyzed the secondary structure, shape and dimensions of plasma sex steroid-binding protein (SBP) by CD, size-exclusion chromatography and electron microscopy. CD spectra show extrema at 186 nm and 216 nm characteristic for beta-sheet structures. Analysis with different algorithms indicates 15% alpha-helix, 43% beta-sheet and 10-16% beta-turn structures. An irreversible structural change is observed upon heating above 60 degrees C, which correlates with the loss of steroid-binding activity. As the SBP sequence shows similarity with domains of several multidomain proteins, including laminins, we evaluated the structure of domain G of laminin-1. The CD spectrum shows extrema at 200 nm and 216 nm. Deconvolution results in 13% alpha-helix, 32% beta-sheet and 15% beta-turn structures. Steroid-binding assays indicate that laminin and fragments thereof have no activity. Size-exclusion chromatography reveals that SBP has an extended shape and can be modeled as a cylinder with a length and diameter of 23 nm and 3 nm, respectively. This shape and the dimensions are in agreement with the appearance on electron micrographs. We propose a model for the structure of SBP in which two monomers assemble head to head with the steroid-binding site located in the center of the rod-like particle.

The fate of cartilage oligomeric matrix protein is determined by the cell type in the case of a novel mutation in pseudoachondroplasia.

We have identified a novel missense mutation in a pseudoachondroplasia (PSACH) patient in one of the type III repeats of cartilage oligomeric matrix protein (COMP). Enlarged lamellar rough endoplasmic reticulum vesicles were shown to contain accumulated COMP along with type IX collagen, a cartilage-specific component. COMP was secreted and assembled normally into the extracellular matrix of tendon, demonstrating that the accumulation of COMP in chondrocytes was a cell-specific phenomenon. We believe that the intracellular storage of COMP causes a nonspecific aggregation of cartilage-specific molecules and results in a cartilage matrix deficient in required structural components leading to impaired cartilage growth and maintenance. These data support a common pathogenetic mechanism behind two clinically related chondrodysplasias, PSACH and multiple epiphyseal dysplasia.