Probing the dynamics of dihydrofolate reductase with small molecule inhibitors

High-resolution protein crystal structures have served as the template from which to devise small molecule modulators of protein function through structure-based drug design for many decades. However, protein function, such as ligand binding, dissociation and catalysis, necessitates structural flexibility of the macromolecule. Protein dynamics are often ignored in structure-based design, largely due to limited information on protein flexibility in the presence of bound ligands (e.g., peptides or small molecules). To gain insight into how protein dynamics are modulated by the binding of small molecule inhibitors, nuclear magnetic resonance spectroscopy has been used herein to characterize both fast and slow timescale motions in the pharmaceutical target protein Escherichia coli dihydrofolate reductase. A series of inhibitors of the enzyme (antifolates) that cover a broad range of binding affinity have been studied while bound to the holoenzyme complex. In the presence of two high-affinity inhibitors, dynamics appear to be essentially identical on both the fast and slow timescales. Specifically, these two inhibitors decouple functional loop switching motions on the slow timescale. One medium-affinity antifolate from the series is shown to be conformationally flexible while bound to the enzyme, eliciting a functional switching motion in a loop distal to its binding. In considering the entire panel of eight antifolates (two of high affinity, one of medium affinity, and a homologous series five of reduced-affinity antifolates), the rates of conformational switching of the enzyme on the slow timescale correlate well with ligand binding affinity and the kinetic rate of ligand dissociation. Within the sites exhibiting slow motions, a consensus set of residues is identified to be sampling a novel and structurally identical excited state that differs from physiological complexes bound to folate-derived ligands. This group of antifolate consensus residues is posited to serve as a mechanical initiator of ligand dissociation, an observation that may be quite prevalent in receptor-ligand interactions. Fast timescale motions across the series of antifolate complexes studied also suggest a correlation of flexibility with ligand binding affinity and a possible linkage between motions on the fast and slow timescales

Vascular Flora of Hooper Branch Savanna Nature Preserve, Iroquois County, Illinois

INHS Technical Report prepared for Illinois Department of Natural Resources, Division of Natural Heritag

Monitoring of Collapsed Built-Up Areas with High Resolution SAR Images

A 16-year-old male with cystic fibrosis (CF) was admitted to hospital with a severe infective exacerbation. Despite standard management, including conventionally selected intravenous antibiotics for Pseudomonas aeruginosa chest physiotherapy, and institution of noninvasive ventilation (NIV) for progressive hypercapneic respiratory failure, he continued to deteriorate. Direct sputum sensitivity testing (DSST) revealed a novel combination of antibiotics that resulted in a rapid and remarkable clinical improvement. DSST is a form of "whole" sputum sensitivity testing that provides information on antibiotic synergy, and may more accurately reflect in vivo antibiotic sensitivity patterns in cystic fibrosis.</p

Atomic Oxygen and Space Environment Effects on Aerospace Materials Flown with EOIM-3 Experiment

Polymer materials samples mounted on a passive carrier tray were flown aboard the STS-46 Atlantis shuttle as complement to the EOIM-3 (Evaluation of Oxygen Interaction with Materials) experiment to evaluate the effects of atomic oxygen on the materials and to measure the gaseous shuttle bay environment. The morphological changes of the samples produced by the atomic oxygen fluence of 2.07 x 10(exp 20) atoms/cm(exp 2) are being reported. The changes have been verified using Electron Spectroscopy for Chemical Analysis (ESCA), gravimetric measurement, microscopic observations and thermo-optical measurements. The samples, including Kapton, Delrin, epoxies, Beta Cloth, Chemglaze Z306, silver Teflon, silicone coatings, 3M tape and Uralane and Ultem, PEEK, Victrex (PES), Polyethersulfone and Polymethylpentene thermoplastic, have been characterized by their oxygen reaction efficiency on the basis of their erosion losses and the oxygen fluence. Those efficiencies have been compared to results from other experiments, when available. The efficiencies of the samples are all in the range of E-24 g/atom. The results indicate that the reaction efficiencies of the reported materials can be grouped in about three ranges of values. The least affected materials which have efficiencies varying from 1 to 10(exp 25) g/atom, include silicones, epoxies, Uralane and Teflon. A second group with efficiency from 10 to 45(exp 25) g/atom includes additional silicone coatings, the Chemglaze Z306 paint and Kapton. The third range from 50 to 75(exp 25) includes organic compound such as Pentene, Peek, Ultem, Sulfone and a 3M tape. A Delrin sample had the highest reaction efficiency of 179(exp 25) g/atom. Two samples, the aluminum Beta cloth X389-7 and the epoxy fiberglass G-11 nonflame retardant, showed a slight mass increase

Dynamic Dysfunction in Dihydrofolate Reductase Results from Antifolate Drug Binding: Modulation of Dynamics within a Structural State

The arduous task of rationally designing small molecule enzyme inhibitors is complicated by the inherent flexibility of the protein scaffold. To gain insight into the changes in dynamics associated with small molecule based inhibition, we have characterized, using NMR spectroscopy, E. coli dihydrofolate reductase in complex with two drugs: methotrexate and trimethoprim. The complexes allowed the intrinsic dynamic effects of drug binding to be revealed within the context of the “closed” structural ensemble. Binding of both drugs results in an identical decoupling of global motion on the micro- to millisecond timescale. Consistent with a change in overall dynamic character, the drugs’ perturbations to pico- to nanosecond backbone and side-chain methyl dynamics are also highly similar. These data show that the inhibitors simultaneously modulate slow concerted switching and fast motions at distal regions of DHFR, providing a dynamic link between the substrate binding site and distal loop residues known to affect catalysis

Using framework-based synthesis for conducting reviews of qualitative studies

Framework analysis is a technique used for data analysis in primary qualitative research. Recent years have seen its being adapted to conduct syntheses of qualitative studies. Framework-based synthesis shows considerable promise in addressing applied policy questions. An innovation in the approach, known as 'best fit' framework synthesis, has been published in BMC Medical Research Methodology this month. It involves reviewers in choosing a conceptual model likely to be suitable for the question of the review, and using it as the basis of their initial coding framework. This framework is then modified in response to the evidence reported in the studies in the reviews, so that the final product is a revised framework that may include both modified factors and new factors that were not anticipated in the original model. 'Best fit' framework-based synthesis may be especially suitable in addressing urgent policy questions where the need for a more fully developed synthesis is balanced by the need for a quick answer

PICADAR: a diagnostic predictive tool for primary ciliary dyskinesia

Symptoms of primary ciliary dyskinesia (PCD) are nonspecific and guidance on whom to refer for testing is limited. Diagnostic tests for PCD are highly specialised, requiring expensive equipment and experienced PCD scientists. This study aims to develop a practical clinical diagnostic tool to identify patients requiring testing.Patients consecutively referred for testing were studied. Information readily obtained from patient history was correlated with diagnostic outcome. Using logistic regression, the predictive performance of the best model was tested by receiver operating characteristic curve analyses. The model was simplified into a practical tool (PICADAR) and externally validated in a second diagnostic centre.Of 641 referrals with a definitive diagnostic outcome, 75 (12%) were positive. PICADAR applies to patients with persistent wet cough and has seven predictive parameters: full-term gestation, neonatal chest symptoms, neonatal intensive care admittance, chronic rhinitis, ear symptoms, situs inversus and congenital cardiac defect. Sensitivity and specificity of the tool were 0.90 and 0.75 for a cut-off score of 5 points. Area under the curve for the internally and externally validated tool was 0.91 and 0.87, respectively.PICADAR represents a simple diagnostic clinical prediction rule with good accuracy and validity, ready for testing in respiratory centres referring to PCD centres

Neurology and the histiocytoses: a case of Rosai-Dorfman-Destombes disease

The histiocytoses are a group of rare disorders characterised by the accumulation of neoplastic or non-neoplastic activated histiocytes in various tissues. Phenotypes vary widely from cutaneous lesions or lymphadenopathy that regress spontaneously to disseminated disease with poor prognosis. Neurological symptoms can be a presenting feature or appear during the course of disease. We present a challenging diagnostic and management case of Rosai-Dorfman-Destombes disease in a 48-year-old woman with a relapsing, partially steroid-responsive syndrome comprising patchy, non-length-dependent radiculoneuropathy with diffuse pachymeningitis and widespread systemic disease, and recent dramatic response to novel mitogen-activated kinase pathway inhibition. We discuss the clinical characteristics, diagnosis, recent breakthroughs in pathogenesis and emerging treatment options for Rosai-Dorfman disease and for the histiocytoses with neurological sequelae, including Langerhans cell histiocytosis and Erdheim-Chester disease