Mapping functional interactions in a heterodimeric phospholipid pump

Type 4 P-type ATPases (P(4)-ATPases) catalyze phospholipid transport to generate phospholipid asymmetry across membranes of late secretory and endocytic compartments, but their kinship to cation-transporting P-type transporters raised doubts about whether P(4)-ATPases alone are sufficient to mediate flippase activity. P(4)-ATPases form heteromeric complexes with Cdc50 proteins. Studies of the enzymatic properties of purified P(4)-ATPase·Cdc50 complexes showed that catalytic activity depends on direct and specific interactions between Cdc50 subunit and transporter, whereas in vivo interaction assays suggested that the binding affinity for each other fluctuates during the transport reaction cycle. The structural determinants that govern this dynamic association remain to be established. Using domain swapping, site-directed, and random mutagenesis approaches, we here show that residues throughout the subunit contribute to forming the heterodimer. Moreover, we find that a precise conformation of the large ectodomain of Cdc50 proteins is crucial for the specificity and functionality to transporter/subunit interactions. We also identified two highly conserved disulfide bridges in the Cdc50 ectodomain. Functional analysis of cysteine mutants that disrupt these disulfide bridges revealed an inverse relationship between subunit binding and P(4)-ATPase-catalyzed phospholipid transport. Collectively, our data indicate that a dynamic association between subunit and transporter is crucial for the transport reaction cycle of the heterodimer.     

Homology modelling and spectroscopy, a never-ending love story

Homology modelling is normally the technique of choice when experimental structure data are not available but three-dimensional coordinates are needed, for example, to aid with detailed interpretation of results of spectroscopic studies. Herein, the state of the art of homology modelling will be described in the light of a series of recent developments, and an overview will be given of the problems and opportunities encountered in this field. The major topic, the accuracy and precision of homology models, will be discussed extensively due to its influence on the reliability of conclusions drawn from the combination of homology models and spectroscopic data. Three real-world examples will illustrate how both homology modelling and spectroscopy can be beneficial for (bio)medical research.     

Hepatocyte Growth Factor Enables Enhanced Integrin–Cytoskeleton Linkage by Affecting Integrin Expression in Subconfluent Epithelial Cells

Hepatocyte growth factor (HGF) exerts mitogenic and motogenic effects in different cell types. In the epithelial cell line mHepR1 we found that HGF induced pronounced alterations in cell morphology and promoted cell adhesion and spreading. To analyze the mechanisms how HGF affects these integrin mediated functions we studied the physical linkage of integrins with the cytoskeleton. First we found that HGF increased the expression of different integrin subunits in subconfluent cells and influenced the distribution of integrins on the cell surface. To address the physical association of integrins with the cytoskeleton we analyzed Triton X-100-extracted cell fractions using flow cytometry. Here we show that cultivation of the cells with HGF for 24 h prior to integrin cross-linking significantly enhanced the cytoskeletal anchorage of integrins. To further find out whether HGF directly induces an integrin–cytoskeleton link without subsequent cross-linking we added HGF to suspended cells but failed to detect cytoskeletally immobilized integrins in the detergent-insoluble cell fraction which could be related to the absence of a calcium response induced by HGF. Overall, the results indicate that HGF promotes the physical linkage of integrins to the cytoskeleton which requires additional stimulation of integrins.     

Psychological and social evaluation in cases of deliberate self-poisoning seen in an accident department.

The outcome in 115 consecutive patients with mild self-poisoning seen by junior medical staff and discharged from the accident department was compared with that of 98 similar patients admitted to the medical wards. Psychiatrists saw only four patients in the accident department and 25 admissions. In making their assessments the junior medical staff considered psychosocial factors as well as the patients'' physical condition. Most patients recommended for further care, and discharged from the accident department, subsequently received it. Repetition rates were similar in the two groups and there had been no suicides when patients were followed up at one year. It is feasible for junior staff in an accident department to decide whether patients with self-poisoning need admission or may be discharged with or without subsequent referral for psychiatric or social work help.     

Point Mutation Approach to Reduce Antigenicity of Interferon Beta

Interferon beta (IFNβ) is naturally occurring cytokine made and secreted by immune cells in response to stimuli. Non-glycosylated interferon beta Ser     

A catalytic defect in mitochondrial respiratory chain complex I due to a mutation in NDUFS2 in a patient with Leigh syndrome

In this study, we investigated the pathogenicity of a homozygous Asp446Asn mutation in the NDUFS2 gene of a patient with a mitochondrial respiratory chain complex I deficiency. The clinical, biochemical, and genetic features of the NDUFS2 patient were compared with those of 4 patients with previously identified NDUFS2 mutations. All 5 patients presented with Leigh syndrome. In addition, 3 out of 5 showed hypertrophic cardiomyopathy. Complex I amounts in the patient carrying the Asp446Asn mutation were normal, while the complex I activity was strongly reduced, showing that the NDUFS2 mutation affects complex I enzymatic function. By contrast, the 4 other NDUFS2 patients showed both a reduced amount and activity of complex I. The enzymatic defect in fibroblasts of the patient carrying the Asp446Asn mutation was rescued by transduction of wild type NDUFS2. A 3-D model of the catalytic core of complex I showed that the mutated amino acid residue resides near the coenzyme Q binding pocket. However, the K(M) of complex I for coenzyme Q analogs of the Asp446Asn mutated complex I was similar to the K(M) observed in other complex I defects and in controls. We propose that the mutation interferes with the reduction of coenzyme Q or with the coupling of coenzyme Q reduction with the conformational changes involved in proton pumping of complex I.     

Role of the alpha-kinase domain in transient receptor potential melastatin 6 channel and regulation by intracellular ATP

Transient receptor potential melastatin 6 (TRPM6) plays an essential role in epithelial Mg(2+) transport. TRPM6 and its closest homologue, TRPM7, both combine a cation channel with an alpha-kinase domain. However, the role of this alpha-kinase domain in TRPM6 channel activity remains elusive. The aim of this study was to investigate the regulation of TRPM6 channel activity by intracellular ATP and the involvement of its alpha-kinase domain. We demonstrated that intracellular Na- and Mg-ATP decreased the TRPM6 current in HEK293 cells heterogeneously expressing the channel, whereas Na-CTP or Na-GTP had no effect on channel activity. Whole cell recordings in TRPM6-expressing HEK293 cells showed that deletion of the alpha-kinase domain prevented the inhibitory effect of intracellular ATP without abrogating channel activity. Mutation of the conserved putative ATP-binding motif GXG(A)XXG (G1955D) in the alpha-kinase domain of TRPM6 inhibited the ATP action, whereas this effect remained preserved in the TRPM6 phosphotransferase-deficient mutant K1804R. Mutation of the TRPM6 autophosphorylation site, Thr(1851), into either an alanine or an aspartate, resulted in functional channels that could still be inhibited by ATP. In conclusion, intracellular ATP regulates TRPM6 channel activity via its alpha-kinase domain independently of alpha-kinase activity.     

Studies on the survival of enterohemorrhagic and environmental Escherichia coli strains in wastewater and in activated sludges from dairy sewage treatment plants

Survival of Escherichia coli O157:H7 strain isolated from milk in Poland and an environmental E. coli strain in wastewater from Garwolin and ?owicz dairies and in activated sludges from dairy sewage treatment plants as well as in dairy wastewater with activated sludges was examined. Environmental materials were contaminated with about 10(8) of target bacteria/ml of sample. The experiments were performed under temperature conditions typical of autumn-winter (6 degrees) and spring-summer (24 degrees C) seasons. It was found that the non-pathogenic E. coli strain survived longer in all media than the enterohemorrhagic serotype. E. coli O157:H7 bacteria were not detected (in direct plating method) in activated sludges after 21-28 days; in dairy wastewater as well as in wastewater with activated sludges after 21-25 days. These periods for environmental E. coli strain were 35-42 days (activated sludges), 25-28 days (wastewater with activated sludges). At higher temperature environmental E. coli were not detected in wastewater from ?owicz dairy sewage treatment plant after 25 days, but the bacteria were still present in wastewater from Garwolin dairy sewage tratment plant after 34 days. The obtained results show that the lack of environmental E. coli bacteria (as a indicator bacteria of fecal contamination) in dairy wastewater and in dairy wastewater with activated sludges could indicate the absence of pathogenic E. coli bacteria. Prolonged existence of the enterohemorrhagic serotype in activated sludges shows the need to treat activated sludges prior to the utilization of these materials as fertilizer.     

Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading

Background

We consider the problem of assessing inter-rater agreement when there are missing data and a large number of raters. Previous studies have shown only ‘moderate’ agreement between pathologists in grading breast cancer tumour specimens. We analyse a large but incomplete data-set consisting of 24177 grades, on a discrete 1–3 scale, provided by 732 pathologists for 52 samples.

Methodology/Principal Findings

We review existing methods for analysing inter-rater agreement for multiple raters and demonstrate two further methods. Firstly, we examine a simple non-chance-corrected agreement score based on the observed proportion of agreements with the consensus for each sample, which makes no allowance for missing data. Secondly, treating grades as lying on a continuous scale representing tumour severity, we use a Bayesian latent trait method to model cumulative probabilities of assigning grade values as functions of the severity and clarity of the tumour and of rater-specific parameters representing boundaries between grades 1–2 and 2–3. We simulate from the fitted model to estimate, for each rater, the probability of agreement with the majority. Both methods suggest that there are differences between raters in terms of rating behaviour, most often caused by consistent over- or under-estimation of the grade boundaries, and also considerable variability in the distribution of grades assigned to many individual samples. The Bayesian model addresses the tendency of the agreement score to be biased upwards for raters who, by chance, see a relatively ‘easy’ set of samples.

Conclusions/Significance

Latent trait models can be adapted to provide novel information about the nature of inter-rater agreement when the number of raters is large and there are missing data. In this large study there is substantial variability between pathologists and uncertainty in the identity of the ‘true’ grade of many of the breast cancer tumours, a fact often ignored in clinical studies.