A spatiotemporal characterization of the effect of p53 phosphorylation on its interaction with MDM2

The interaction of p53 and MDM2 is modulated by the phosphorylation of p53. This mechanism is key to activating p53, yet its molecular determinants are not fully understood. To study the spatiotemporal characteristics of this molecular process we carried out Brownian dynamics simulations of the interactions of the MDM2 protein with a p53 peptide in its wild type state and when phosphorylated at Thr18 (pThr18) and Ser20 (pSer20). We found that p53 phosphorylation results in concerted changes in the topology of the interaction landscape in the diffusively bound encounter complex domain. These changes hinder phosphorylated p53 peptides from binding to MDM2 well before reaching the binding site. The underlying mechanism appears to involve shift of the peptide away from the vicinity of the MDM2 protein, peptide reorientation, and reduction in peptide residence time relative to wild-type p53 peptide. pThr18 and pSr20 p53 peptides experience reduction in residence times by factors of 13.6 and 37.5 respectively relative to the wild-type p53 peptide, indicating a greater role for Ser20 phosphorylation in abrogating p53 MDM2 interactions. These detailed insights into the effect of phosphorylation on molecular interactions are not available from conventional experimental and theoretical approaches and open up new avenues that incorporate molecular interaction dynamics, for stabilizing p53 against MDM2, which is a major focus of anticancer drug lead development.     

Evidence for the Dimerization-Mediated Catalysis of Methionine Sulfoxide Reductase A from Clostridium oremlandii

Clostridium oremlandii MsrA (CoMsrA) is a natively selenocysteine-containing methionine-S-sulfoxide reductase and classified into a 1-Cys type MsrA. CoMsrA exists as a monomer in solution. Herein, we report evidence that CoMsrA can undergo homodimerization during catalysis. The monomeric CoMsrA dimerizes in the presence of its substrate methionine sulfoxide via an intermolecular disulfide bond between catalytic Cys16 residues. The dimeric CoMsrA is resolved by the reductant glutaredoxin, suggesting the relevance of dimerization in catalysis. The dimerization reaction occurs in a concentration- and time-dependent manner. In addition, the occurrence of homodimer formation in the native selenoprotein CoMsrA is confirmed. We also determine the crystal structure of the dimeric CoMsrA, having the dimer interface around the two catalytic Cys16 residues. A central cone-shaped hole is present in the surface model of dimeric structure, and the two Cys16 residues constitute the base of the hole. Collectively, our biochemical and structural analyses suggest a novel dimerization-mediated mechanism for CoMsrA catalysis that is additionally involved in CoMsrA regeneration by glutaredoxin.     

Antitcoagulant and antiplatelet activities of scolymoside

Cyclopia subternata is a medicinal plant commonly used in traditional medicine to relieve pain. Here, the anticoagulant effects of scolymoside, an active compound in C. subternata, were examined by monitoring activated partial thromboplastin time (aPTT), prothrombin time (PT), and the activities of thrombin and activated factor X (FXa). The effects of scolymoside on plasminogen activator inhibitor type 1 (PAI-1) and tissue-type plasminogen activator (t-PA) expression were evaluated in tumor necrosis factor (TNF)-α-activated human endothelial cells. Treatment with scolymoside resulted in prolonged aPTT and PT and the inhibition of thrombin and FXa activities and production. In addition, scolymoside inhibited thrombin-catalyzed fibrin polymerization and platelet aggregation. Scolymoside also elicited anticoagulant effects in mice, including a significant reduction in the PAI-1 to t-PA ratio. Collectively, these findings indicate that scolymoside possesses anticoagulant activities and could be developed as a novel anticoagulant. [BMB Reports 2015; 48(10): 577-582]     

Predicting fine‐scale distributions of peripheral aquatic species in headwater streams

Headwater species and peripheral populations that occupy habitat at the edge of a species range may hold an increased conservation value to managers due to their potential to maximize intraspecies diversity and species' adaptive capabilities in the context of rapid environmental change. The southern Appalachian Mountains are the southern extent of the geographic range of native Salvelinus fontinalis and naturalized Oncorhynchus mykiss and Salmo trutta in eastern North America. We predicted distributions of these peripheral, headwater wild trout populations at a fine scale to serve as a planning and management tool for resource managers to maximize resistance and resilience of these populations in the face of anthropogenic stressors. We developed correlative logistic regression models to predict occurrence of brook trout, rainbow trout, and brown trout for every interconfluence stream reach in the study area. A stream network was generated to capture a more consistent representation of headwater streams. Each of the final models had four significant metrics in common: stream order, fragmentation, precipitation, and land cover. Strahler stream order was found to be the most influential variable in two of the three final models and the second most influential variable in the other model. Greater than 70% presence accuracy was achieved for all three models. The underrepresentation of headwater streams in commonly used hydrography datasets is an important consideration that warrants close examination when forecasting headwater species distributions and range estimates. Additionally, it appears that a relative watershed position metric (e.g., stream order) is an important surrogate variable (even when elevation is included) for biotic interactions across the landscape in areas where headwater species distributions are influenced by topographical gradients.     

Coarse Woody Debris Increases Microbial Community Functional Diversity but not Enzyme Activities in Reclaimed Oil Sands Soils

Forest floor mineral soil mix (FMM) and peat mineral soil mix (PMM) are cover soils commonly used for upland reclamation post open-pit oil sands mining in northern Alberta, Canada. Coarse woody debris (CWD) can be used to regulate soil temperature and water content, to increase organic matter content, and to create microsites for the establishment of microorganisms and vegetation in upland reclamation. We studied the effects of CWD on soil microbial community level physiological profile (CLPP) and soil enzyme activities in FMM and PMM in a reclaimed landscape in the oil sands. This experiment was conducted with a 2 (FMM vs PMM) × 2 (near CWD vs away from CWD) factorial design with 6 replications. The study plots were established with Populus tremuloides (trembling aspen) CWD placed on each plot between November 2007 and February 2008. Soil samples were collected within 5 cm from CWD and more than 100 cm away from CWD in July, August and September 2013 and 2014. Microbial biomass was greater (p<0.05) in FMM than in PMM, in July, and August 2013 and July 2014, and greater (p<0.05) near CWD than away from CWD in FMM in July and August samplings. Soil microbial CLPP differed between FMM and PMM (p<0.01) according to a principal component analysis and CWD changed microbial CLPP in FMM (p<0.05) but not in PMM. Coarse woody debris increased microbial community functional diversity (average well color development in Biolog Ecoplates) in both cover soils (p<0.05) in August and September 2014. Carbon degrading soil enzyme activities were greater in FMM than in PMM (p<0.05) regardless of distance from CWD but were not affected by CWD. Greater microbial biomass and enzyme activities in FMM than in PMM will increase organic matter decomposition and nutrient cycling, improving plant growth. Enhanced microbial community functional diversity by CWD application in upland reclamation has implications for accelerating upland reclamation after oil sands mining.     

Efficacy and Safety of Sorafenib Therapy on Metastatic Renal Cell Carcinoma in Korean Patients: Results from a Retrospective Multicenter Study

Objective

To evaluate the efficacy and safety of sorafenib for Korean patients with metastatic renal cell carcinoma (mRCC).

Methods

A total of 177 mRCC patients using sorafenib as first- (N = 116), second- (N = 43), and third-line (N = 18) therapies were enrolled from 11 Korean centers between 2006 and 2012. The patient characteristics, therapy duration, tumor response, disease control rate, and tolerability were assessed at baseline and at routine follow-ups, and the progression-free survival (PFS) and overall survival (OS) times and rates were analyzed.

Results

Among all patients, 18 (10.2%) stopped sorafenib treatment for a median of 1.7 weeks, including 15 (8.5%) who discontinued the drug, while 40 (22.6%) and 12 (6.8%) patients required dose reductions and drug interruptions, respectively. Severe adverse events (AEs) or poor compliance was observed in 64 (36.2%) patients, with 118 (7.4%) ≥grade 3 AEs. During the treatment, one myocardial infarction was observed. The number of ≥grade 3 AEs in the first-line sorafenib group was 71 (6.8% of the total 1048 AEs). During a median follow-up of 17.2 months, the radiologically confirmed best objective response rate, disease control rate, median PFS, and median OS were 22.0%, 53.0%, 6.4 months (95% confidence interval [CI], 5.2–8.9), and 32.6 months (95% CI, 27.3–63.8) for the total 177 sorafenib-treated patients, respectively, and 23.2%, 56.0%, 7.4 months (95% CI, 5.5–10.5), and not reached yet (95% CI, 1.0–31.1) for the first-line sorafenib group, respectively.

Conclusions

Sorafenib produced tolerable safety, with a ≥grade 3 AE rate of 7.4% and an acceptable disease control rate (53.0%) in Korean mRCC patients.     

Comparison of Bacterial Community of Healthy and Erwinia amylovora Infected Apples

Fire blight disease, caused by Erwinia amylovora, could damage rosaceous plants such as apples, pears, and raspberries. In this study, we designed to understand how E. amylovora affected other bacterial communities on apple rhizosphere; twig and fruit endosphere; and leaf, and fruit episphere. Limited studies on the understanding of the microbial community of apples and changes the community structure by occurrence of the fire blight disease were conducted. As result of these experiments, the infected trees had low species richness and operational taxonomic unit diversity when compared to healthy trees. Rhizospheric bacterial communities were stable regardless of infection. But the communities in endosphere and episphere were significanlty affected by E. amylovora infection. We also found that several metabolic pathways differ significantly between infected and healthy trees. In particular, we observed differences in sugar metabolites. The finding provides that sucrose metabolites are important for colonization of E. amylovora in host tissue. Our results provide fundamental information on the microbial community structures between E. amylovora infected and uninfected trees, which will contribute to developing novel control strategies for the fire blight disease.     

NAD-linked alcohol dehydrogenase 1 regulates methylglyoxal concentration in Candida albicans

We purified a fraction that showed NAD⁺-linked methylglyoxal dehydrogenase activity, directly catalyzing methylglyoxal oxidation to pyruvate, which was significantly increased in glutathione-depleted Candida albicans. It also showed NADH-linked methylglyoxal-reducing activity. The fraction was identified as a NAD⁺-linked alcohol dehydrogenase (ADH1) through mass spectrometric analyses. In ADH1-disruptants of both the wild type and glutathione-depleted cells, the intracellular methylglyoxal concentration increased significantly; defects in growth, differentiation, and virulence were observed; and G2-phase arrest was induced.     

The cardioprotective effects of zileuton, a 5-lipoxygenase inhibitor, are mediated by COX-2 via activation of PKCδ

Zileuton has been demonstrated to act as an anti-inflammatory agent by virtue of its well-known ability to inhibit 5-lipoxygenase (5-LO). However, the effects of zileuton on cardiovascular disease and cardiomyocyte apoptosis are unclear. Here, we investigated the effects of zileuton on apoptosis of cardiac myogenic H9c2 cells and neonatal rat cardiomyocytes (NRCMs), and examined the possible role of PKCδ-mediated induction of COX-2 in these effects. Treatment of H9c2 cells with zileuton efficiently induced COX-2 expression and PGE₂ biosynthesis in a time- and dose-dependent manner. Zileuton also exerted a profound protective effect against H₂O₂-induced oxidative stress, a mimic of reperfusion damage in vitro, and this protective effect was abolished by COX-2-selective inhibitor. When we investigated the signalling pathways involved in zileuton-induced COX-2 expression, we found that zileuton acts as a PKCδ activator, causing it to translocate from the cytosol to nucleus. Inhibition of PKCδ activation with rottlerlin, a PKCδ-specific inhibitor, abolished the zileuton-induced protection against H₂O₂-induced cell death and inhibited zileuton-induced COX-2 expression and PGE₂ production. The protective effect of zileuton was dramatically diminished by treatment with LY294002 or PD98059. Furthermore, zileuton-stimulated ERK1/2 and Akt phosphorylation was attenuated by rottlerin, indicating that PKCδ might act upstream of ERK1/2 and Akt. Moreover, inhibition of either ERK1/2 or Akt activation abolished zileuton-induced COX-2 expression. Knockdown of PKCδ with siRNA also reversed the protective effect of zileuton and blocked the induction of COX-2. These results suggest that zileuton-induced COX-2 expression is sequentially mediated through PKCδ-dependent activation of ERK1/2 and Akt. Based on these findings, we propose that zileuton might provide a new therapeutic strategy for ischemia/reperfusion injury of the heart.     

2,4-Diaminopyrimidine MK2 inhibitors. Part I: Observation of an unexpected inhibitor binding mode

MK2 is a Ser/Thr kinase of significant interest as an anti-inflammatory drug discovery target. Here we describe the development of in vitro tools for the identification and characterization of MK2 inhibitors, including validation of inhibitor interactions with the crystallography construct and determination of the unique binding mode of 2,4-diaminopyrimidine inhibitors in the MK2 active site. Use of these tools in the optimization of a potent and selective inhibitor lead series is described in the accompanying Letter.