c-Cbl acts as a mediator of Src-induced activation of the PI3K-Akt signal transduction pathway during TRAIL treatment

We have previously observed that TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) induces acquired TRAIL resistance by increasing Akt phosphorylation and Bcl-xL expression. In this study, we report that Src, c-Cbl, and PI3K are involved in the phosphorylation of Akt during TRAIL treatment. Data from immunoprecipitation and immunoblotting assay reveal that Src interacts with c-Cbl and PI3K. Data from immune complex kinase assay demonstrate that Src can directly phosphorylate c-Cbl and PI3K p85 subunit protein. Data from gene knockdown experiments with an RNA interference (RNAi) technique show that c-Cbl is involved in the interaction between Src and PI3K p85 during TRAIL treatment, playing an important role in TRAIL-induced Akt phosphorylation. Taken together, c-Cbl may act as a mediator to regulate the Src-PI3K-Akt signal transduction pathway during TRAIL treatment.     

Subtype-specific role of phospholipase C-β in bradykinin and LPA signaling through differential binding of different PDZ scaffold proteins

Among phospholipase C (PLC) isozymes (β, γ, δ, ε, ζ and η), PLC-β plays a key role in G-protein coupled receptor (GPCR)-mediated signaling. PLC-β subtypes are often overlapped in their distribution, but have unique knock-out phenotypes in organism, suggesting that each subtype may have the different role even within the same type of cells. In this study, we examined the possibility of the differential coupling of each PLC-β subtype to GPCRs, and explored the molecular mechanism underlying the specificity. Firstly, we found that PLC-β1 and PLC-β3 are activated by bradykinin (BK) or lysophosphatidic acid (LPA), respectively. BK-triggered phosphoinositides hydrolysis and subsequent Ca²⁺ mobilization were abolished specifically by PLC-β1 silencing, whereas LPA-triggered events were by PLC-β3 silencing. Secondly, we showed the evidence that PDZ scaffold proteins is a key mediator for the selective coupling between PLC-β subtype and GPCR. We found PAR-3 mediates physical interaction between PLC-β1 and BK receptor, while NHERF2 does between PLC-β3 and LPA₂ receptor. Consistently, the silencing of PAR-3 or NHERF2 blunted PLC signaling induced by BK or LPA respectively. Taken together, these data suggest that each subtype of PLC-β is selectively coupled to GPCR via PDZ scaffold proteins in given cell types and plays differential role in the signaling of various GPCRs.     

c-Cbl-mediated degradation of TRAIL receptors is responsible for the development of the early phase of TRAIL resistance

We previously reported two modes of development of acquired TRAIL resistance: early phase and late phase [1]. In these studies, we observed that greater Akt activity and the expression of Bcl-xL were related mainly to the late phase of acquired TRAIL resistance.Recently we became aware of a possible mechanism of early phase TRAIL resistance development through internalization and degradation of TRAIL receptors (DR4 and DR5). Our current studies demonstrate that TRAIL receptors rapidly diminish at the membrane as well as the cytoplasm within 4 h after TRAIL exposure, but recover completely after one or two days. Our studies also reveal that Cbl, a ubiquitously expressed cytoplasmic adaptor protein, is responsible for the rapid degradation of TRAIL receptors; Cbl binds to them and induces monoubiquitination of these receptors concurrent with their degeneration soon after TRAIL exposure, creating the early phase of acquired TRAIL resistance.     

Effects of microclimate,litter type,and mesh size on leaf litter decomposition along an elevation gradient in the Wuyi Mountains,China

Litter decomposition is an important ecosystem process regulated by both biotic factors (e.g., decomposers and litter types) and abiotic factors (e.g., temperature and moisture). This study examined the regulatory effects of soil fauna and microclimate on decomposition of two substrates (Castanopsis carlesii and Pinus taiwanensis) along an elevation gradient in four ecosystems of zonal vegetation types in southeastern China: evergreen broadleaf forest (EVB), coniferous forest (COF), dwarf forest (DWF), and alpine meadow (ALM). Our objective was to identify the mechanisms by which microclimate, substrate, and fauna control litter decomposition, especially where variations in ecosystem structure and environment are markedly shown across an elevation gradient. The hypotheses were as follows: (1) litter decomposition within the same litter type would decrease across the elevation gradient, (2) litter decomposition would be lower in poorer nutrient quality substrate across the four sites, and (3) litter dynamics, influenced by strong interactions among ecosystem type, litter type, and decomposers, would vary by elevation gradient due to microclimate effects (i.e., temperature and moisture). The decomposition rates of C. carlesii were significantly higher than those of P. taiwanensis at EVB, COF, and DWF sites; however, they were not significantly different at the ALM site. Low elevation forests possessed a microclimate (warm and humid) that favors decomposer activities and also appeared to possess a decomposer community adapted to consuming large amounts of leaf litter, as indicated by the rapid leaf litter loss. Litter decomposition in micro-mesh bags proceeded more slowly compared to litter in meso-mesh and macro-mesh litterbags across the elevation gradient, indicating that restricting some detritivore access to litter reduced litter mass loss. We suggest that microclimate and faunal contributions to plant litter decomposition differ markedly across the ecosystems in the Wuyi Mountains.     

SANA: an algorithm for sequential and non-sequential protein structure alignment

Protein structure alignment algorithms play an important role in the studies of protein structure and function. In this paper, a novel approach for structure alignment is presented. Specifically, core regions in two protein structures are first aligned by identifying connected components in a network of neighboring geometrically compatible aligned fragment pairs. The initial alignments then are refined through a multi-objective optimization method. The algorithm can produce both sequential and non-sequential alignments. We show the superior performance of the proposed algorithm by the computational experiments on several benchmark datasets and the comparisons with the well-known structure alignment algorithms such as DALI, CE and MATT. The proposed method can obtain accurate and biologically significant alignment results for the case with occurrence of internal repeats or indels, identify the circular permutations, and reveal conserved functional sites. A ranking criterion of our algorithm for fold similarity is presented and found to be comparable or superior to the Z-score of CE in most cases from the numerical experiments. The software and supplementary data of computational results are available at .     

Investigating the disorder–order transition of calmodulin binding domain upon binding calmodulin using molecular dynamics simulation

We have studied the conformational transition of the calmodulin binding domains (CBD) in several calmodulin‐binding kinases, in which CBD changes from the disordered state to the ordered state when binding with calmodulin (CaM). Targeted molecular dynamics simulation was used to investigate the binding process of CaM and CBD of CaM‐dependent kinase I (CaMKI–CBD). The results show that CaMKI–CBD began to form an α‐helix and the interaction free energy between CaM and CaMKI–CBD increased once CaM fully encompassed CaMKI–CBD. Two series of CaM/CBD complex systems, including the complexes of CaM with the initially disordered and the final ordered CBD, were constructed to study the interaction using molecular dynamics simulations. Our analyses suggest that the VDW interaction plays a dominant role in CaM/CBD binding and is a key factor in the disorder–order transition of CBD. Additionally, the entropy effect is not in favor of the formation of the CaM/CBD complex, which is consistent with the experimental evidence. Based on the results, it appears that the CBD conformational change from a non‐compact extended structure to compact α‐helix is critical in gaining a favorable VDW interaction and interaction free energy. Copyright © 2009 John Wiley & Sons, Ltd.     

Quality control of Pulsatilla koreana based on the simultaneous determination of triterpenoidal saponins by HPLC‐ELSD and principal component analysis

Introduction – Pulsatilla koreana Nakai, with triterpenoidal saponins as its main pharmacological effective compounds, is known to have several biological activities, including hypoglycaemic, antitumour, cognition‐enhancing, neuroprotective, cytotoxic and antiangiogenic activities. However, few analytical methods have been reported on the quality assessment of P. koreana roots. Obejective – To establish a high‐performance liquid chromatography coupled with evaporative light scattering detection for the simultaneous determination of five triterpenoidal saponins, including pulsatilloside E (1), pulsatilla saponin H (2), anemoside B₄ (3), hederacolchiside E (4) and cussosaponin C (5) in P. koreana. Methodology – The chromatographic separation was performed on a Shiseido CapCell PAK C₁₈ analytical column efficiently using gradient elution with acetonitrile and water. Results – All calibration curves showed excellent linear regressions (R² > 0.9996) within the range of tested concentrations. The intra‐ and inter‐day variations were below 4.78% in terms of RSD. The recoveries were 94.82–102.97% with RSD of 0.27–3.92% for spiked P. koreana samples. Conclusion – The validated method was successfully used for the analysis of five saponins in P. koreana from different locations. Moreover, the different samples were clustered in accordance with contents of triterpenoidal saponins based on aglycon type by a principal component analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

The conserved and divergent roles of carbonic anhydrases in the filamentous fungi Aspergillus fumigatus and Aspergillus nidulans

Carbon dioxide (CO₂) and its hydration product bicarbonate (HCO₃^‐) are essential molecules in various physiological processes of all living organisms. The reversible interconversion between CO₂ and HCO₃^‐ is in equilibrium. This reaction is slow without catalyst, but can be rapidly facilitated by Zn²⁺‐metalloenzymes named carbonic anhydrases (CAs). To gain an insight into the function of multiple clades of fungal CA, we chose to investigate the filamentous fungi Aspergillus fumigatus and A. nidulans. We identified four and two CAs in A. fumigatus and A. nidulans, respectively, named cafA‐D and canA‐B. The cafA and cafB genes are constitutively, strongly expressed whereas cafC and cafD genes are weakly expressed but CO₂‐inducible. Heterologous expression of the A. fumigatus cafB, and A. nidulans canA and canB genes completely rescued the high CO₂‐requiring phenotype of a Saccharomyces cerevisiaeΔnce103 mutant. Only the ΔcafAΔcafB and ΔcanB deletion mutants were unable to grow at 0.033% CO₂, of which growth defects can be restored by high CO₂. Defects in the CAs can affect Aspergilli conidiation. Furthermore, A. fumigatusΔcafA, ΔcafB, ΔcafC, ΔcafD and ΔcafAΔcafB mutant strains are fully virulent in a low‐dose murine infection.     

Structure-based design,synthesis and biological evaluation of new N-carboxyphenylpyrrole derivatives as HIV fusion inhibitors targeting gp41

A new series of N-carboxyphenylpyrrole ligands were designed using GeometryFit based on an X-ray crystal structure of gp41. The synthesized ligands showed significant inhibitory activities against HIV gp41 6-helix bundle formation, HIV-1 mediated cell–cell fusion and HIV-1 replication.