Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

Small-probe contact dot surface analysis, with all explicit hydrogen atoms added and their van der Waals contacts included, was used to choose between the two possible orientations for each of 1554 asparagine (Asn) and glutamine (Gln) side-chain amide groups in a dataset of 100 unrelated, high-quality protein crystal structures at 0.9 to 1.7 AÊ resolution. For the movable-H groups, each connected, closed set of local H-bonds was optimized for both H-bonds and van der Waals overlaps. In addition to the Asn/Gln ``¯ips'', this process included rotation of OH, SH, NH 3, and methionine methyl H atoms, ¯ip and protonation state of histidine rings, interaction with bound ligands, and a simple model of water interactions. However, except for switching N and O identity for amide ¯ips (or N and C identity for His ¯ips), no non-H atoms were shifted. Even in these very high-quality structures, about 20 % of the Asn/Gln side-chains required a 180 ¯ip to optimize H-bonding and/o

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing

Preparing potential teachers for the transition from employment to teacher training: an evaluative case study of a Maths Enhancement Course

In response to a UK government drive to improve maths teaching in schools, the South West London Maths Enhancement Course (MEC) has been set up though collaboration between three Higher Education institutions (HEIs) to provide an efficient route for non maths graduates in employment to upgrade their subject knowledge and give a smooth transition into teacher training (PGCE). An evaluation of the scheme, measured against Teacher Development Agency (TDA) objectives and success criteria agreed by university staff, involved thematic analysis of focus group discussions and interviews with students and staff during both the MEC and PGCE courses. This has revealed a high level of satisfaction and success related to a number of underlying issues, particularly around student recruitment, curriculum design, peer support and staff collaboration. The model offers an example of practice transferable to a range of programmes aimed at supporting students in the transition between levels and institutions

Protein imperfections: separating intrinsic from extrinsic variation of torsion angles

In this paper, the variation of the values of dihedral angles in proteins is divided into two categories by analyzing distributions in a database of structures determined at a resolution of 1.8 A or better [Lovell et al. (2003), Proteins Struct. Funct. Genet. 50, 437-450]. The first analysis uses the torsion angle for the Calpha-Cbeta bond (chi1) of all Gln, Glu, Arg and Lys residues ('unbranched set'). Plateaued values at low B values imply a root-mean-square deviation (RMSD) of just 9 degrees for chi1 related to intrinsic structural differences between proteins. Extrapolation to high resolution gives a value of 11 degrees , while over the entire database the RMSD is 13.4 degrees . The assumption that the deviations arise from independent intrinsic and extrinsic sources gives approximately 10 degrees as the RMSD for chi1 of these unbranched side chains arising from all disorder and error over the entire set. It is also found that the decrease in chi1 deviation that is correlated with higher resolution structures is almost entirely a consequence of the higher percentage of low-B-value side chains in those structures and furthermore that the crystal temperature at which diffraction data are collected has a negligible effect on intrinsic deviation. Those intrinsic aspects of the distributions not related to statistical or other errors, data incompleteness or disorder correlate with energies of model compounds computed with high-level quantum mechanics. Mean side-chain torsion angles for specific rotamers correlate well with local energy minima of Ace-Leu-Nme, Ace-Ile-Nme and Ace-Met-Nme. Intrinsic RMSD values in examples with B < or = 20 A2 correlate inversely with calculated values for the relevant rotational energy barriers: from a low of 6.5 degrees for chi1 of some rotamers of Ile to a high of 14 degrees for some Met chi3 for fully tetrahedral angles and much higher for chi angles around bonds that are tetrahedral at one end and planar at the other (e.g. 30 degrees for chi2 of the gauche- rotamer of Phe). For the lower barrier Met chi3 rotations there are relatively more well validated cases near eclipsed values and calculated torques from the rest of the protein structure either confine or force the Cepsilon atom into the strained position. These results can be used to evaluate the variability and accuracy of chi angles in crystal structures and also to decide whether to restrain side-chain angles in refinement as a function of the resolution and atomic B values, depending on whether one aims for a realistic distribution of values or a spread that is statistically suitable to the probable data-set errors

Implementation and evaluation of the VA DPP clinical demonstration: protocol for a multi-site non-randomized hybrid effectiveness-implementation type III trial.

BackgroundThe Diabetes Prevention Program (DPP) study showed that lifestyle intervention resulted in a 58% reduction in incidence of type 2 diabetes among individuals with prediabetes. Additional large randomized controlled trials have confirmed these results, and long-term follow-up has shown sustained benefit 10-20 years after the interventions ended. Diabetes is a common and costly disease, especially among Veterans, and despite strong evidence supporting the feasibility of type 2 diabetes prevention, the DPP has not been widely implemented. The first aim of this study will evaluate implementation of the Veterans Affairs (VA) DPP in three VA medical centers. The second aim will assess weight and hemoglobin A1c (A1c) outcomes, and the third aim will determine the cost-effectiveness and budget impact of implementation of the VA DPP from a health system perspective.Methods/designThis partnered multi-site non-randomized systematic assignment study will use a highly pragmatic hybrid effectiveness-implementation type III mixed methods study design. The implementation and administration of the VA DPP will be funded by clinical operations while the evaluation of the VA DPP will be funded by research grants. Seven hundred twenty eligible Veterans will be systematically assigned to the VA DPP clinical demonstration or the usual care VA MOVE!® weight management program. A multi-phase formative evaluation of the VA DPP implementation will be conducted. A theoretical program change model will be used to guide the implementation process and assess applicability and feasibility of the DPP for VA. The Consolidated Framework for Implementation Research (CFIR) will be used to guide qualitative data collection, analysis, and interpretation of barriers and facilitators to implementation. The RE-AIM framework will be used to assess Reach, Effectiveness, Adoption, Implementation, and Maintenance of the VA DPP. Twelve-month weight and A1c change will be evaluated for the VA DPP compared to the VA MOVE!ProgramMediation analyses will be conducted to identify whether program design differences impact outcomes.DiscussionFindings from this pragmatic evaluation will be highly applicable to practitioners who are tasked with implementing the DPP in clinical settings. In addition, findings will determine the effectiveness and cost-effectiveness of the VA DPP in the Veteran population

KinImmerse: Macromolecular VR for NMR ensembles

<p>Abstract</p> <p>Background</p> <p>In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case.</p> <p>Methods</p> <p>The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE.</p> <p>Results</p> <p>In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs).</p> <p>Conclusion</p> <p>The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis.</p

Pesticide use and risk of end-stage renal disease among licensed pesticide applicators in the Agricultural Health Study

Experimental studies suggest a relationship between pesticide exposure and renal impairment, but epidemiological evidence is limited. We evaluated the association between exposure to 41 specific pesticides and end-stage renal disease (ESRD) incidence in the Agricultural Health Study (AHS), a prospective cohort study of licensed pesticide applicators in Iowa and North Carolina

A woman living with osteoarthritis: A case report

Osteoarthritis is a common condition that is typically associated with older adults. Other causes of osteoarthritis, such as those cases resulting from childhood Perthes disease, can affect younger people and frequently have a major impact on the lives of those affected. This case report describes the experiences of one patient with osteoarthritis, using examples of her poetry to illustrate her social, psychological and emotional transformation

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution