Evaluation of coupling conditions for the incorporation of Nα-Fmoc-Tyr(PO3H2)-OH in solid-phase peptide synthesis

Summary In order to minimise the formation of the pyrophosphate derivative of the target peptide when side-chain-unprotected phopshotyrosine is used in solid-phase peptide synthesis, this building block can be incorporated using benzotriazolyloxy-tris-(dimethylamino)phosphonium hexafluorophosphate/1-hydroxybenzotriazole/N-methylmorpholine (1:1:2.3) in the presence of a chaotropic salt (0.4 M LiCl in N-methyl-2-pyrrolidinone).Abbreviations BOP benzotriazolyloxy-tris-(dimethylamino)phosphonium hexafluorophosphate - DIEA diisopropylethylamine - Fmoc 9-fluorenylmethoxycarbony - HATU N-[(dimethylamino)1H-1,2,3-triazolo[4,5-b]pyridin-1-ylmethylene]-N-methylmethan-aminium hexafluorophosphate N-oxide - HOBt 1-hydroxybenzotriazole - HPLC high-performance liquid chromatography - MALDI-TOF matrix-assisted laser-desorption ionization time-of-flight mass spectrometry - NMM N-methylmorpholine - NMP N-methyl-2-pyrrolidinone - Pmc 2,2,5,7,8-pentamethyl-chroman-6-sulfonyl - ® solid support - TFA trifluoroacetic acid - TPTU 2-(2-pyridon-1-yl)-1,1,3,3-tetramethyluroniumfluoroborate. Abbreviations used for amino acids follow the recommendations of the IUPAC-IUB Commission of Biochemical Nomenclature [Eur. J. Biochem., 138 (1984) 9]     

ADAM17在恶性肿瘤中的研究及其进展

去整合素-金属蛋白酶17(adisintegrin and metalloproteinase 17,ADAM17)是近年来发现的金属蛋白酶解聚素(adisintegrin and metalloproteinase,ADAMs)家族成员之一,参与肿瘤发生发展的重要过程.去整合素-金属蛋白酶17(ADAM17)又称为肿瘤坏死因子转换酶(TACE),因此除了具有解聚素和金属蛋白酶的活性,还可以将没有活性的肿瘤坏死因子(TNF-α)从细胞膜上切割下来,并与其受体相结合,从而激活TNF-α下游的EGFR信号传导,此外还可以激活多条信号传导途径如Notch传导通路等,进而影响肿瘤细胞的粘附、凋亡、转移、增殖等生物学行为.纵观ADAM17的研究,在多种恶性肿瘤中呈高表达状态,且这种高表达状态与肿瘤侵润程度及转移情况相关.随着人们对ADAM17基础科学的研究不断深入,ADAM17的临床应用前景也正被不断开发,鉴于其在多种恶性肿瘤组织中高表达的情况,可将其作为许多肿瘤的诊断标志物、及判断其转移和预后情况.靶向药物的研究给恶性肿瘤患者带来了新的福音,利用EGFR为研究扳机点成功研制出许多靶向药物,在EGFR的配体释放环节,ADAM17尤为重要.本文总结了ADAM17在恶性肿瘤发展中的作用及其机制,对其在癌症治疗的应用前景进行展望.     

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

Signal transduction networks have only been studied at a small scale because large-scale reconstructions and suitable in silico analysis methods have not been available. Since reconstructions of large signaling networks are progressing well there is now a need to develop a framework for analysing structural properties of signaling networks. One such framework is presented here, one that is based on systemically independent pathways and a mass-balanced representation of signaling events. This approach was applied to a prototypic signaling network and it allowed for: (1) a systemic analysis of all possible input/output relationships, (2) a quantitative evaluation of network crosstalk, or the interconnectivity of systemically independent pathways, (3) a measure of the redundancy in the signaling network, (4) the participation of reactions in signaling pathways, and (5) the calculation of correlated reaction sets. These properties emerge from network structure and can only be derived and studied within a defined mathematical framework. The calculations presented are the first of their kind for a signaling network, while similar analysis has been extensively performed for prototypic and genome-scale metabolic networks. This approach does not yet account for dynamic concentration profiles. Due to the scalability of the stoichiometric formalism used, the results presented for the prototypic signaling network can be obtained for large signaling networks once their reconstruction is completed.     

Robustness analysis of EGFR signaling network with a multi-objective evolutionary algorithm

Robustness, the ability to maintain performance in the face of perturbations and uncertainty, is believed to be a necessary property of biological systems. In this paper, we address the issue of robustness in an important signal transduction network--epidermal growth factor receptor (EGFR) network. First, we analyze the robustness in the EGFR signaling network using all rate constants against the Gauss variation which was described as "the reference parameter set" in the previous study [Kholodenko, B.N., Demin, O.V., Moehren, G., Hoek, J.B., 1999. Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274, 30169-30181]. The simulation results show that signal time, signal duration and signal amplitude of the EGRR signaling network are relatively not robust against the simultaneous variation of the reference parameter set. Second, robustness is quantified using some statistical quantities. Finally, a multi-objective evolutionary algorithm (MOEA) is presented to search reaction rate constants which optimize the robustness of network and compared with the NSGA-II, which is a representation of a class of modern multi-objective evolutionary algorithms. Our simulation results demonstrate that signal time, signal duration and signal amplitude of the four key components--the most downstream variable in each of the pathways: R-Sh-G-S, R-PLP, R-G-S and the phosphorylated receptor RP in EGRR signaling network for the optimized parameter sets have better robustness than those for the reference parameter set and the NSGA-II. These results can provide valuable insight into experimental designs and the dynamics of the signal-response relationship between the dimerized and activated EGFR and the activation of downstream proteins.     

Hepatocyte growth factor exerts a proliferative effect on oval cells through the PI3K/AKT signaling pathway

Hepatocyte growth factor (HGF) is a potent mitogen for a variety of cells including hepatocytes. While rat oval cells are supposed to be one of hepatic stem cells, biological effects of HGF on oval cells and their relevant signal transduction pathways remain to be determined. We sought to investigate them on OC/CDE22 rat oval cells, which are established from the liver of rats fed a choline-deficient/DL-ethionine-supplemented diet. The oval cells were cultured on fibronectin-coated dishes and stimulated with recombinant HGF, transforming growth factor-alpha (TGF-alpha), and thrombopoietin (TPO) under the serum-free medium condition. HGF treatment enhanced [3H]thymidine incorporation into oval cells in a dose-dependent manner. On the contrary, treatment with TGF-alpha or TPO had no significant effects on [3H]thymidine incorporation into the oval cells. c-Met protein was phosphorylated at the tyrosine residues after the HGF treatment. AKT, extracellular signal-regulated kinase 1/2 (ERK1/2), and p70(s6k) were simultaneously activated after the HGF stimulation, peaking at 30min after the treatment. The activation of AKT, p70(s6k), and ERK1/2 induced by HGF was abolished by pre-treatment with LY294002, a phosphoinositide 3-OH kinase (PI3K) inhibitor, and U0126, a mitogen-activated protein kinase/ERK kinase (MEK) inhibitor, respectively. When the cells were pre-treated with LY294002 prior to the HGF stimulation, the proliferative action of HGF was completely abrogated, implying that the PI3K/AKT signaling pathway is responsible for the biological effect of HGF. These in vitro data indicate that HGF exerts a proliferative action on hepatic oval cells via activation of the PI3K/AKT signaling pathway.     

Interactions of the NPXY microdomains of the low density lipoprotein receptor‐related protein 1

The low density lipoprotein receptor‐related protein 1 (LRP1) mediates internalization of a large number of proteins and protein–lipid complexes and is widely implicated in Alzheimer's disease. The cytoplasmic domain of LRP1 (LRP1‐CT) can be phosphorylated by activated protein‐tyrosine kinases at two NPXY motifs in LRP1‐CT; Tyr 4507 is readily phosphorylated and must be phosphorylated before phosphorylation of Tyr 4473 occurs. Pull‐down experiments from brain lysate revealed numerous proteins binding to LRP1‐CT, but the results were highly variable. To separate which proteins bind to each NPXY motif and their phosphorylation dependence, each NPXY motif microdomain was prepared in both phosphorylated and non‐phosphorylated forms and used to probe rodent brain extracts for binding proteins. Proteins that bound specifically to the microdomains were identified by LC‐MS/MS, and confirmed by Western blot. Recombinant proteins were then tested for binding to each NPXY motif. The NPXY₄₅₀₇ (membrane distal) was found to interact with a large number of proteins, many of which only bound the tyrosine‐phosphorylated form. This microdomain also bound a significant number of other proteins in the unphosphorylated state. Many of the interactions were later confirmed to be direct with recombinant proteins. The NPXY₄₄₇₃ (membrane proximal) bound many fewer proteins and only to the phosphorylated form.     

基于Unscented卡尔曼滤波器的信号转导通路参数与不可观测状态估计

系统生物学的一个主要目的是建立细胞信号转导通路的数学模型。然而细胞信号转导通路多具有较强非线性、参与生化反应物质多等特点,同时测量数据往往不完备,并且混有来自实验各个阶段的各种噪声,这些都给模型参数估计带来很大困难。该文采用Unscented卡尔曼滤波器估计信号转导通路未知参数与模型不可观测状态。以肿瘤坏死因子诱导的核转录因子κB信号转导通路为例进行了仿真,结果表明,采用该方法可以在噪声干扰下较准确地的估计系统未知参数和不能观测状态。     

Synthetic modular systems--reverse engineering of signal transduction

During the last decades, biology has decomposed cellular systems into genetic, functional and molecular networks. It has become evident that these networks consist of components with specific functions (e.g., proteins and genes). This has generated a considerable amount of knowledge and hypotheses concerning cellular organization. The idea discussed here is to test the extent of this knowledge by reconstructing, or reverse engineering, new synthetic biological systems from known components. We will discuss how integration of computational methods with proteomics and engineering concepts might lead us to a deeper and more abstract understanding of signal transduction systems. Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs and rewiring of biological pathways.