287 research outputs found
The 1.1 angstrom resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank
During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement using MOLREP in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate-binding protein from Stenotrophomonas maltophilia (UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of the S. maltophilia protein has been refined to an R factor of 10.15% and an Rfree of 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles
Integrating the promotion of physical activity within a smoking cessation programme: Findings from collaborative action research in UK Stop Smoking Services
Background: Within the framework of collaborative action research, the aim was to explore the feasibility of
developing and embedding physical activity promotion as a smoking cessation aid within UK 6/7-week National
Health Service (NHS) Stop Smoking Services.
Methods: In Phase 1 three initial cycles of collaborative action research (observation, reflection, planning,
implementation and re-evaluation), in an urban Stop Smoking Service, led to the development of an integrated
intervention in which physical activity was promoted as a cessation aid, with the support of a theoretically based
self-help guide, and self monitoring using pedometers. In Phase 2 advisors underwent training and offered the
intervention, and changes in physical activity promoting behaviour and beliefs were monitored. Also, changes in
clients’ stage of readiness to use physical activity as a cessation aid, physical activity beliefs and behaviour and
physical activity levels were assessed, among those who attended the clinic at 4-week post-quit. Qualitative data
were collected, in the form of clinic observation, informal interviews with advisors and field notes.
Results: The integrated intervention emerged through cycles of collaboration as something quite different to
previous practice. Based on field notes, there were many positive elements associated with the integrated
intervention in Phase 2. Self-reported advisors’ physical activity promoting behaviour increased as a result of
training and adapting to the intervention. There was a significant advancement in clients’ stage of readiness to use physical activity as a smoking cessation aid.
Conclusions: Collaboration with advisors was key in ensuring that a feasible intervention was developed as an aid to smoking cessation. There is scope to further develop tailored support to increasing physical activity and
smoking cessation, mediated through changes in perceptions about the benefits of, and confidence to do physical activity
Zirconium-catalyzed alkene hydrophosphination and dehydrocoupling with an air-stable, fluorescent primary phosphine
Zirconium-catalyzed alkene hydrophosphination and dehydrocoupling with an air-stable, fluorescent primary phosphine 8-[(4-phosphino)phenyl]-4,4-dimethyl-1,3,5,7-tetramethyl-2,6-diethyl- 4-bora-3a,4a-diaza-s-indacene furnishes fluorescent phosphine products. Hydrophosphination of the fluorescent phosphine produces products with a complete selectivity for the secondary product. A key intermediate in catalysis, a zirconium phosphido compound, was isolated
Parental bonding and identity style as correlates of self-esteem among adult adoptees and nonadoptees
Adult adoptees (n equals 100) and non-adoptees (n equals 100) were compared with regard to selfesteem, identity processing style, and parental bonding. While some differences were found with regard to self-esteem, maternal care, and maternal overprotection, these differences were
qualified by reunion status such that only reunited adoptees differed significantly from nonadoptees.
Moreover, hierarchical regression analyses indicated that parental bonding and identity processing style were more important than adoptive status per se in predicting self esteem. Implications for practitioners who work with adoptees are discussed
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
©2008 Pandit and Skolnick; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is available from: http://www.biomedcentral.com/1471-2105/9/531doi:10.1186/1471-2105-9-531Background: Protein tertiary structure comparisons are employed in various fields of
contemporary structural biology. Most structure comparison methods involve generation of an
initial seed alignment, which is extended and/or refined to provide the best structural superposition
between a pair of protein structures as assessed by a structure comparison metric. One such
metric, the TM-score, was recently introduced to provide a combined structure quality measure
of the coordinate root mean square deviation between a pair of structures and coverage. Using the
TM-score, the TM-align structure alignment algorithm was developed that was often found to have
better accuracy and coverage than the most commonly used structural alignment programs;
however, there were a number of situations when this was not true.
Results: To further improve structure alignment quality, the Fr-TM-align algorithm has been
developed where aligned fragment pairs are used to generate the initial seed alignments that are
then refined using dynamic programming to maximize the TM-score. For the assessment of the
structural alignment quality from Fr-TM-align in comparison to other programs such as CE and TMalign,
we examined various alignment quality assessment scores such as PSI and TM-score. The
assessment showed that the structural alignment quality from Fr-TM-align is better in comparison
to both CE and TM-align. On average, the structural alignments generated using Fr-TM-align have
a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr-
TM-align uses an exhaustive procedure to generate initial seed alignments. Hence, the algorithm is
computationally more expensive than TM-align.
Conclusion: Fr-TM-align, a new algorithm that employs fragment alignment and assembly provides
better structural alignments in comparison to TM-align. The source code and executables of Fr-
TM-align are freely downloadable at: http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/
Electrohydrodynamic Dispersion of Deformable Aerosols in the Presence of an Electric Field and Chemical Reaction Using Taylor Dispersion Model
Financial considerations in the conduct of multi-centre randomised controlled trials: evidence from a qualitative study.
National Coordinating Centre for Research Methodology; Medical Research Council, UK Department of Health; Chief Scientist OfficeNot peer reviewedPublisher PD
Lethal Injection for Execution: Chemical Asphyxiation?
Data from executions in the US suggest that current lethal injection protocols do not effect death through the mechanisms intended, and that potentially aware inmates could die through pancuronium-induced asphyxiation
Microtubule-severing enzymes: From cellular functions to molecular mechanism.
Microtubule-severing enzymes generate internal breaks in microtubules. They are conserved in eukaryotes from ciliates to mammals, and their function is important in diverse cellular processes ranging from cilia biogenesis to cell division, phototropism, and neurogenesis. Their mutation leads to neurodegenerative and neurodevelopmental disorders in humans. All three known microtubule-severing enzymes, katanin, spastin, and fidgetin, are members of the meiotic subfamily of AAA ATPases that also includes VPS4, which disassembles ESCRTIII polymers. Despite their conservation and importance to cell physiology, the cellular and molecular mechanisms of action of microtubule-severing enzymes are not well understood. Here we review a subset of cellular processes that require microtubule-severing enzymes as well as recent advances in understanding their structure, biophysical mechanism, and regulation
Maternal iodine status in a multi-ethnic UK birth cohort:Associations with child cognitive and educational development
Background: Maternal iodine requirements increase during pregnancy to supply thyroid hormones critical for fetal neurodevelopment. Iodine insufficiency may result in poorer cognitive or child educational outcomes but current evidence is sparse and inconsistent. Objectives: To quantify the association between maternal iodine status and child educational outcomes. Methods: Urinary iodine concentrations (UIC) and iodine/creatinine ratios (I:Cr) were measured in 6971 mothers at 26-28 weeks' gestation participating in the Born in Bradford cohort. Maternal iodine status was examined in relation to child school achievement (early years foundation stage (EYFS), phonics, and Key Stage 1 (KS1)), other learning outcomes, social and behavioural difficulties, and sensorimotor control in 5745 children aged 4-7 years. Results: Median (interquartile range) UIC was 76 µg/L (46, 120), and I:Cr was 83 µg/g (59, 121). Overall, there was no strong or consistent evidence to support associations between UIC or I:Cr and neurodevelopmental outcomes. For instance, predicted EYFS and phonics scores (primary outcomes) at the 25th vs 75th I:Cr percentiles (99% confidence intervals) were similar, with no evidence of associations: EYFS scores were 32 (99% CI 31, 33) and 33 (99% CI 32, 34), and phonics scores were 34 (99% CI 33, 35) and 35 (99% CI 34, 36), respectively. Conclusions: In the largest single study of its kind, there was little evidence of detrimental neurodevelopmental outcomes in children born to pregnant women with iodine insufficiency as defined by World Health Organization–outlined thresholds. Alternative functional biomarkers for iodine status in pregnancy and focused assessment of other health outcomes may provide additional insight.</p
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