The proteomics of lipid droplets: structure, dynamics, and functions of the organelle conserved from bacteria to humans

Lipid droplets are cellular organelles that consists of a neutral lipid core covered by a monolayer of phospholipids and many proteins. They are thought to function in the storage, transport, and metabolism of lipids, in signaling, and as a specialized microenvironment for metabolism in most types of cells from prokaryotic to eukaryotic organisms. Lipid droplets have received a lot of attention in the last 10 years as they are linked to the progression of many metabolic diseases and hold great potential for the development of neutral lipid-derived products, such as biofuels, food supplements, hormones, and medicines. Proteomic analysis of lipid droplets has yielded a comprehensive catalog of lipid droplet proteins, shedding light on the function of this organelle and providing evidence that its function is conserved from bacteria to man. This review summarizes many of the proteomic studies on lipid droplets from a wide range of organisms, providing an evolutionary perspective on this organelle.     

A novel protein structural classes prediction method based on predicted secondary structure

Knowledge of structural classes plays an important role in understanding protein folding patterns. In this paper, features based on the predicted secondary structure sequence and the corresponding E–H sequence are extracted. Then, an 11-dimensional feature vector is selected based on a wrapper feature selection algorithm and a support vector machine (SVM). Among the 11 selected features, 4 novel features are newly designed to model the differences between α/β class and α + β class, and other 7 rational features are proposed by previous researchers. To examine the performance of our method, a total of 5 datasets are used to design and test the proposed method. The results show that competitive prediction accuracies can be achieved by the proposed method compared to existing methods (SCPRED, RKS-PPSC and MODAS), and 4 new features are demonstrated essential to differentiate α/β and α + β classes. Standalone version of the proposed method is written in JAVA language and it can be downloaded from http://web.xidian.edu.cn/slzhang/paper.html.     

Secreted phospholipase A2 involvement in neurodegeneration: differential testing of prosurvival and anti-inflammatory effects of enzyme inhibition

There is increased interest in the contribution of secreted phospholipase A2 (sPLA2) enzymes to neurodegenerative diseases. Systemic treatment with the nonapeptide CHEC-9, a broad spectrum uncompetitive inhibitor of sPLA2, has been shown previously to inhibit neuron death and aspects of the inflammatory response in several models of neurodegeneration. A persistent question in studies of sPLA2 inhibitors, as for several other anti-inflammatory and neuroprotective compounds, is whether the cell protection is direct or due to slowing of the toxic aspects of the inflammatory response. To further explore this issue, we developed assays using SY5Y (neuronal cells) and HL-60 (monocytes) cell lines and examined the effects of sPLA2 inhibition on these homogeneous cell types in vitro. We found that the peptide inhibited sPLA2 enzyme activity in both SY5Y and HL-60 cultures. This inhibition provided direct protection to SY5Y neuronal cells and their processes in response to several forms of stress including exposure to conditioned medium from HL-60 cells. In cultures of HL-60 cells, sPLA2 inhibition had no effect on survival of the cells but attenuated their differentiation into macrophages, with regard to process development, phagocytic ability, and the expression of differentiation marker CD36, as well as the secretion of proinflammatory cytokines TNF-α and IL-6. These results suggest that sPLA2 enzyme activity organizes a cascade of changes comprising both cell degeneration and inflammation, processes that could theoretically operate independently during neurodegenerative conditions. The effectiveness of sPLA2 inhibitor CHEC-9 may be due to its ability to affect both processes in isolation. Testing potential anti-inflammatory/neuroprotective compounds with these human cell lines and their conditioned media may provide a useful screening tool prior to in vivo therapeutic applications.     

T178 deletion impairs intermolecular interaction of the peptide Nramp1(164–191)

Natural resistance associated macrophage protein 1 (Nramp1), an integral membrane protein with 12 predicted transmembrane domains (TMs), is a divalent cation transporter associated with infectious and autoimmune diseases. A naturally occurring mutation G169D within TM4 of Nramp1 leads to the loss of function, suggesting potential importance of TM4 for the biological function of the protein. In this study, we determine the three‐dimensional structure and topology of a synthetic peptide, del(T178), corresponding to Nramp1(164‐191) (basically consisting of the putative TM4 of Nramp1) with Thr178 deletion in TFE and SDS micelles using NMR and CD spectroscopic techniques, and compare the results with those of the wildtype peptide. Similarly to the wildtype peptide, the del(T178) peptide still forms an amphiphilic‐like α‐helical structure in both membrane mimics and is embedded in SDS micelles. Differently, whereas the wild‐type peptide forms a helix bundle with the hydrophilic side facing the interior of the bundle, the del(T178) peptide exists as a monomer in the membrane mimics and the hydrophilic side of the helix is located near the interface of SDS micelles. Moreover, a strongly cooperative protonation occurs between intramolecular Asp residues for the del(T178) peptide in SDS micelles, while the cooperative proton binding between intermolecular Asp residues was observed for the wildtype peptide. The difference in the results of the two peptides suggests that the deletion of Thr178 impairs intermolecular interaction of the peptide. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.     

Metal ion binding of the first external loop of DCT1 in aqueous solution

The binding of the external loop1 of DCT1 with divalent metal cations was first verified by the NMR measurements of isolated peptides and the binding sites were determined.     

Extracellular DNA Inhibits Salmonella enterica Serovar Typhimurium and S. enterica Serovar Typhi Biofilm Development on Abiotic Surfaces

Extracellular DNA (eDNA) was identified and characterized in a 2-day-old biofilms developed by Salmonella enterica ser. Typhimurium SR-11 and S. enterica ser. Typhi ST6 using confocal laser scanning microscopy (CLSM) and enzymatic extraction methods. Results of microtitre plate assay and CLSM analysis showed both Salmonella strains formed significantly more biofilms in the presence of DNase I; Furthermore, a remarkable decrease of biofilm formation was observed when eDNA was added in the inoculation. However, for the pre-established biofilms on polystyrene and glass, no significant difference was observed between the DNase I treated biofilm and the corresponding non-treated controls. In conclusion, these results demonstrate that eDNA is a novel matrix component of Salmonella biofilms. This is the first evidence for the presence of eDNA and its inhibitive and destabilizing effect during biofilm development of S. enterica ser. Typhimurium and S. enterica ser. Typhi on abiotic surfaces.     

不结球白菜乙烯响应因子基因的克隆与表达分析

采用cDNA-AFLP技术,以不结球白菜雄蕊突变系‘苏白2号’及其保持系花蕾为实验材料,分离出1条编码乙烯响应转录因子的基因,命名为NhccERF1。结果显示:(1)序列分析表明,NhccERF1基因长807bp,编码268个氨基酸。(2)RT-PCR分析发现,花期NhccERF1基因在花瓣、雄蕊及花柱中表达量均显著高于保持系。(3)实时定量荧光PCR(qPCR)发现,蕾期喷施乙烯(ET)能促进NhccERF1基因的表达,外施AgNO3抑制该基因表达。研究推测NhccERF1基因可能在雄蕊变异中发挥重要作用。     

Design, synthesis, and testing of an 6-O-linked series of benzimidazole based inhibitors of CDK5/p25

Alzheimer’s disease (AD) is a progressive neurodegenerative disease resulting in cognitive and behavioral impairment. The two classic pathological hallmarks of AD include extraneuronal deposition of amyloid ?? (A??) and intraneuronal formation of neurofibrillary tangles (NFTs). NFTs contain hyperphosphorylated tau. Tau is the major microtubule-associated protein in neurons and stabilizes microtubules (MTs). Cyclin dependent kinase 5 (CDK5), when activated by the regulatory binding protein p25, phosphorylates tau at a number of proline-directed serine/threonine residues, resulting in formation of phosphorylated tau as paired helical filaments (PHFs) then in subsequent deposition of PHFs as NFTs. Beginning with the structure of Roscovitine, a moderately selective CDK5 inhibitor, we sought to conduct structural modifications to increase inhibitory potency of CDK5 and increase selectivity over a similar enzyme, cyclin dependent kinase 2 (CDK2). The design, synthesis, and testing of a series of 1-isopropyl-4-aminobenzyl-6-ether-linked benzimidazoles is presented.