Structures of R- and T-state Escherichia coli aspartokinase III. Mechanisms of the allosteric transition and inhibition by lysine

Aspartokinase III (AKIII) from Escherichia coli catalyzes an initial commitment step of the aspartate pathway, giving biosynthesis of certain amino acids including lysine. We report crystal structures of AKIII in the inactive T-state with bound feedback allosteric inhibitor lysine and in the R-state with aspartate and ADP. The structures reveal an unusual configuration for the regulatory ACT domains, in which ACT2 is inserted into ACT1 rather than the expected tandem repeat. Comparison of R- and T-state AKIII indicates that binding of lysine to the regulatory ACT1 domain in R-state AKIII instigates a series of changes that release a "latch", the beta15-alphaK loop, from the catalytic domain, which in turn undergoes large rotational rearrangements, promoting tetramer formation and completion of the transition to the T-state. Lysine-induced allosteric transition in AKIII involves both destabilizing the R-state and stabilizing the T-state tetramer. Rearrangement of the catalytic domain blocks the ATP-binding site, which is therefore the structural basis for allosteric inhibition of AKIII by lysine.     

Improved replicon cellular activity of non-nucleoside allosteric inhibitors of HCV NS5B polymerase: from benzimidazole to indole scaffolds

Benzimidazole-based allosteric inhibitors of the hepatitis C virus (HCV) NS5B polymerase were diversified to a variety of topologically related scaffolds. Replacement of the polar benzimidazole core by lipophilic indoles led to inhibitors with improved potency in the cell-based subgenomic HCV replicon system. Transposing the indole scaffold into a previously described series of benzimidazole-tryptophan amides generated the most potent inhibitors of HCV RNA replication in cell culture reported to date in this series (EC(50) approximately 50 nM).     

Sample size determination in clinical proteomic profiling experiments using mass spectrometry for class comparison

Mass spectrometric profiling approaches such as MALDI‐TOF and SELDI‐TOF are increasingly being used in disease marker discovery, particularly in the lower molecular weight proteome. However, little consideration has been given to the issue of sample size in experimental design. The aim of this study was to develop a protocol for the use of sample size calculations in proteomic profiling studies using MS. These sample size calculations can be based on a simple linear mixed model which allows the inclusion of estimates of biological and technical variation inherent in the experiment. The use of a pilot experiment to estimate these components of variance is investigated and is shown to work well when compared with larger studies. Examination of data from a number of studies using different sample types and different chromatographic surfaces shows the need for sample‐ and preparation‐specific sample size calculations.     

Characterization of a natural variant of human NDP52 and its functional consequences on mitophagy

The role of mitophagy, a process that allows the removal of damaged mitochondria from cells, remains unknown in multiple sclerosis (MS), a disease that is found associated with dysfunctional mitochondria. Here we have qualitatively and quantitatively studied the main players in PINK1-mediated mitophagy in peripheral blood mononuclear cells (PBMCs) of patients with relapsing–remitting MS. We found the variant c.491G>A (rs550510, p.G140E) of NDP52, one of the major mitophagy receptor genes, associated with a MS cohort. Through the characterization of this variant, we discovered that the residue 140 of human NDP52 is a crucial modulator of NDP52/LC3C binding, promoting the formation of autophagosomes in order to drive efficient mitophagy. In addition, we found that in the PBMC population, NDP52 is mainly expressed in B cells and by ensuring efficient mitophagy, it is able to limit the production of the proinflammatory cytokine TNF-α following cell stimulation. In sum, our results contribute to a better understanding of the role of NDP52 in mitophagy and underline, for the first time, a possible role of NDP52 in MS.Subject terms: Autophagy, Molecular modelling, Immunological disorders     

Association of practice size and pay-for-performance incentives with the quality of diabetes management in primary care

Background:

Not enough is known about the association between practice size and clinical outcomes in primary care. We examined this association between 1997 and 2005, in addition to the impact of the Quality and Outcomes Framework, a pay-for-performance incentive scheme introduced in the United Kingdom in 2004, on diabetes management.

Methods:

We conducted a retrospective open-cohort study using data from the General Practice Research Database. We enrolled 422 general practices providing care for 154 945 patients with diabetes. Our primary outcome measures were the achievement of national treatment targets for blood pressure, glycated hemoglobin (HbA_1c) levels and total cholesterol.

Results:

We saw improvements in the recording of process of care measures, prescribing and achieving intermediate outcomes in all practice sizes during the study period. We saw improvement in reaching national targets after the introduction of the Quality and Outcomes Framework. These improvements significantly exceeded the underlying trends in all practice sizes for achieving targets for cholesterol level and blood pressure, but not for HbA_1c level. In 1997 and 2005, there were no significant differences between the smallest and largest practices in achieving targets for blood pressure (1997 odds ratio [OR] 0.98, 95% confidence interval [CI] 0.82 to 1.16; 2005 OR 0.92, 95% CI 0.80 to 1.06 in 2005), cholesterol level (1997 OR 0.94, 95% CI 0.76 to 1.16; 2005 OR 1.1, 95% CI 0.97 to 1.40) and glycated hemoglobin level (1997 OR 0.79, 95% CI 0.55 to 1.14; 2005 OR 1.05, 95% CI 0.93 to 1.19).

Interpretation:

We found no evidence that size of practice is associated with the quality of diabetes management in primary care. Pay-for-performance programs appear to benefit both large and small practices to a similar extent.There is a well-established body of literature showing positive associations between volume of patients and clinical outcomes in health care, which has been documented by a systematic review.¹ However, this association has usually been examined in a limited number of discrete procedures, and most studies have involved hospital-based services rather than primary care settings.^2–5Improving our understanding of the association between volume of patients and outcomes in primary care is important for several reasons. First, most contacts with health systems occur in primary care settings, and optimizing the delivery of these services has the potential to improve the health of the population.⁶ Second, over the past decade, primary care has assumed greater responsibility for managing the growing burden of chronic disease.^7,8 Larger providers may be better resourced, through the employment of additional support staff and greater use of information technology, to deliver the systematic, structured care necessary for the effective management of chronic disease.^6,9 Third, larger providers may have been more responsive to nonfinancial and financial incentives, including pay for performance, implemented by payers aimed at improving the quality of care.^7,10 Fourth, in many countries, primary care is based around a predominance of small practices.^6,11,12 In 2006, 53% of practices in England and Wales had three or fewer family physicians.¹¹ In the same year in the United States, 30.3% of family physicians were in solo practice; 9.4% were in two-physician practices.¹²Despite the limited data available, concerns have been raised about the standards of care delivered by smaller family practices.¹³ In the United Kingdom and Canada, this has resulted in an explicit policy objective of encouraging smaller practices to amalgamate.^13,14Our study examines the associations between the size of practice and the quality of diabetes management in UK primary care settings between 1997 and 2005. We tested the hypotheses that patients attending larger family practices receive better care for diabetes and that the quality gap between larger and smaller practices has increased over the past decade. We also hypothesized that larger practices derived more benefit from the Quality and Outcomes Framework, a major pay-for-performance program in primary care introduced in 2004.