Prediction of protein loop geometries in solution

The ability to determine the structure of a protein in solution is a critical tool for structural biology, as proteins in their native state are found in aqueous environments. Using a physical chemistry based prediction protocol, we demonstrate the ability to reproduce protein loop geometries in experimentally derived solution structures. Predictions were run on loops drawn from (1)NMR entries in the Protein Databank (PDB), and from (2) the RECOORD database in which NMR entries from the PDB have been standardized and re-refined in explicit solvent. The predicted structures are validated by comparison with experimental distance restraints, a test of structural quality as defined by the WHAT IF structure validation program, root mean square deviation (RMSD) of the predicted loops to the original structural models, and comparison of precision of the original and predicted ensembles. Results show that for the RECOORD ensembles, the predicted loops are consistent with an average of 95%, 91%, and 87% of experimental restraints for the short, medium and long loops respectively. Prediction accuracy is strongly affected by the quality of the original models, with increases in the percentage of experimental restraints violated of 2% for the short loops, and 9% for both the medium and long loops in the PDB derived ensembles. We anticipate the application of our protocol to theoretical modeling of protein structures, such as fold recognition methods; as well as to experimental determination of protein structures, or segments, for which only sparse NMR restraint data is available.     

Construction of the plasmid for expression of ETA-EGFP fusion protein under control of the cytomegalovirus promoter and its effects in HeLa cells

Tumor-targeted vectors encoding toxic protein genes are promising tools for treating malignant tumors. We used the pEGFP-N1 vector to construct a novel plasmid (pCMV-ETA-EGFP) for eukaryotic expression of a truncated Pseudomonas aeruginosa exotoxin A (ETA) that is known to inhibit protein synthesis, and subsequently induce cell death, by inactivation of elongation factor-2. ETA was linked to the enhanced green fluorescent protein (EGFP) gene, and ETA-EGFP gene expression was driven by the cytomegalovirus (CMV) promoter. The time-lapse effects of pCMV-ETA-EGFP expression were examined in transiently transfected HeLa cells. HeLa cells transfected with pCMV-ETA-EGFP or cotransfected with pCMV-ETA-EGFP and рЕGFP-N1 showed lower fluorescence intensity than cells transfected with pEGFP-N1 alone. Analysis of the number of dead cells further confirmed the highly toxic effect of the ETA-EGFP fusion protein on cells transfected with pCMV-ETA-EGFP or cotransfected with pCMV-ETA-EGFP and рЕGFP-N1. ETA-EGFP fusion protein induced apoptotic cell death through the caspase-3 activation. By using the antibody against a marker nucleolar antigen A3 [Grigoryev, A.A., Bulycheva, T.I., Sheval, E.V., Kalinina, I.A., Zatsepina, O.V., 2008. Cytological indicators of the overall suppression of protein synthesis revealed by staining with new monoclonal antibody. Cell Tissue Biol. 2, 191–199], the distribution of which changes when HeLa cells are treated with known translation inhibitors, we obtained evidence to support the idea that protein synthesis is inhibited in transfected cells in situ. ETA-EGFP fusion protein was identified in lysates of transfected cells using anti-GFP-BL antibodies. Collectively, our results indicate that HeLa cells transfected with pCMV-ETA-EGFP synthesize the ETA-EGFP fusion protein that efficiently inhibits protein synthesis, leading to massive cell death by an apoptosis-mediated pathway with a participation of caspase-3. The constructed vector can be used in suicidal gene therapy of cancer and may also be useful for investigating the general effects of translational downregulation in human cancer cells. We also suggest a novel approach for detecting the activity of new vectors in transfected cells, which is based on the redistribution of nucleolar proteins in transfected cells.     

翻译和非翻译马铃薯Y病毒外壳蛋白基因介导的抗病性比较

利用RT－PCR方法克隆获得马铃薯Y病毒烟草叶脉坏死株系（PVY^N）的可翻译和不可翻译外壳蛋白（CP）基因,并分别插入pROKⅡ质粒中获得重组双元表达载体。通过根癌农杆菌（Agrobacterium tumefaciens）介导的基因转化方法,将可翻译和不可翻译的PVY^N-CP基因分别导入烟草栽培品种NC89叶片组织中,得到抗卡那霉素的再生植株,对所得到的抗卡那霉素的再生苗进行PCR检测表明,被导入可翻译和不可翻译CP基因的植株分别占卡那霉素抗性植株的95％和98％。攻毒实验表明,两种类型的转基因烟草对PVY^N的抗病性具有相似性,其表现型为：免疫、抗病和感病。免疫型转基因植株的抗病性不受接种物类型及其剂量的影响。Southern印迹杂交结果显示,目的基因已经整合到烟草基因组中。Northern印迹杂交证明,两种类型的CP基因都已在RNA水平上得到了表达,但细胞内RNA的积累量与转基因植株的抗病强度成负相关。Western印迹杂交表明,在表达不可翻译PVY^N－CP基因的转基因植株内 以CP蛋白,而在导入可翻译的PVY^N-CP基因的植株内检测到了CP蛋白,且CP蛋白含量与抗病性不存在正相关。本研究结果证明,表达可翻译与不可翻译PVY^N-CP基因的转基因烟草对PVY^N的抗病性均为RNA介导的抗病性。     

杆状病毒SpltMNPVSl136基因的克隆、表达及其产物功能

计算机分析斜纹夜蛾核多角体病毒（SpltMNPV)基因组序列,发现第136个读码框基因表达产物具有病毒囊膜蛋白的基本特征,计算机预测的SL136蛋白氨基酸序列N端具有信号肽,C端具有跨膜区,N端区还有一个许多病毒融合蛋白共有的卷曲螺旋结构。通过PCR扩增,我们克隆了Sl136基因并分别构建了原核表达载体pBVSl136及重组病毒表达载体,SDS-PAGE结果表明Sl136基因在大肠杆菌和昆虫细胞中均获得了较高的表达,另外,我们还构建了一个瞬时表达载体pUCSl136。单独转染Sl-zsu-1细胞后,低pH值环境可诱导细胞发生膜融合并形成合胞体,这些实验结果表明,Sl136基因表达的产物是一个病毒膜融合蛋白。     

脑啡肽-干扰素α-m融合蛋白外用治疗单纯疱疹病毒感染

为探讨脑啡肽-干扰素α-m融合蛋白(EI)外用治疗单纯疱疹病毒感染的作用,分别用HSV-1感染兔子角膜、HSV-2感染豚鼠阴道建立动物感染模型.兔子角膜感染24h后用融合蛋白滴眼液治疗,每天3次,每次0.5ml,共14天.豚鼠阴道感染48h后,用融合蛋白涂剂抹外阴病灶,每天3次,每次10mg,共14天.用IFNα-m和生理盐水/赋形剂作为对照.采用记录病损程度分级法进行临床症消减观察,并于治疗前后测定实验动物病灶病毒滴度、HSV抗体滴度及NK细胞活性.结果显示:与IFNα-m相比,EI治疗组实验动物病毒感染症状大幅减轻且病程缩短,动物病灶中病毒滴度下降,抗HSV抗体滴度升高,NK细胞活性增强.说明脑啡肽干扰素融合蛋白具有较强的消除炎症和局部抗病毒作用,可用于治疗HSV感染引起的疾病.     

Modulation of the K(v)4.3 channel by syntaxin 1A

The SNARE protein syntaxin 1A (Syn1A) is known to inhibit delayed rectifier K(+) channels of the K(v)1 and K(v)2 families with heterogeneous effects on their gating properties. In this study, we explored whether Syn1A could directly modulate K(v)4.3, a rapidly inactivating K(v) channel with important roles in neuroendocrine cells and cardiac myocytes. Immunoprecipitation studies in HEK293 cells coexpressing Syn1A and K(v)4.3 revealed a direct interaction with increased trafficking to the plasma membrane without a change in channel synthesis. Paradoxically, Syn1A inhibited K(v)4.3 current density. In particular, Syn1A produced a left-shift in steady-state inactivation of K(v)4.3 without affecting either voltage dependence of activation or gating kinetics, a pattern distinct from other K(v) channels. Combined with our previous reports, our results further verify the notion that the mechanisms involved in Syn1A-K(v) interactions vary significantly between K(v) channels, thus providing a wide scope for Syn1A modulation of exocytosis and membrane excitability.     

Poly (l-lysine) based semi-interpenetrating polymer network as pH-responsive hydrogel for controlled release of a model protein drug streptokinase

With the aim of developing a pH-sensitive controlled drug release system, a poly (L-lysine) (PLL) based cationic semi-interpenetrating polymer network (semi-IPN) has been synthesized. This cationic hydrogel was designed to swell at lower pH and de-swell at higher pH and therefore be applicable for achieving regulated drug release at a specific pH range. In addition to the pH sensitivity, this hydrogel was anticipated to interact with an ionic drug, providing another means to regulate the release rate of ionic drugs. This semi-IPN hydrogel was prepared using a free-radical polymerization method and by crosslinking of the polyethylene glycol (PEG)-methacrylate polymer through the PLL network. The two polymers were penetrated with each other via interpolymer complexation to yield the semi-IPN structures. The PLL hydrogel thus prepared showed dynamic swelling/de-swelling behavior in response to pH change, and such a behavior was influenced by both the concentrations of PLL and PEG-methacrylate. Drug release from this semi-IPN hydrogel was also investigated using a model protein drug, streptokinase. Streptokinase release was found to be dependent on its ionic interaction with the PLL backbones as well as on the swelling of the semi-IPN hydrogel. These results suggest that a PLL semi-IPN hydrogel could potentially be used as a drug delivery platform to modulate drug release by pH-sensitivity and ionic interaction.     

肝癌细胞系差异性表达的糖结合蛋白研究

糖结合蛋白(glycan-binding protein,GBP)在细胞生命周期中扮演着重要角色,如细胞识别、运输、免疫、代谢、增殖分化及细胞间的相互作用等.目前,对GBP的改变对细胞生物过程产生影响的研究甚少.本研究用糖芯片技术对肝癌细胞系Hep G2和正常肝细胞系L02表达的GBP进行研究;糖细胞化学验证确定差异表达GBP在肝癌细胞系中的变化和分布.结果显示,8种糖探针(如SL、LNT和Gal NAc等)和5种糖探针(如Man、Man-9-Glycan,Xyl等)分别对应的GBP在Hep G2细胞中表达上调或下调.糖细胞化学结果显示:Gal NAc识别的GBPs主要表达在Hep G2的胞膜、中央胞质、核周胞质区域,而在L02的相同区域表达减弱;Neu Ac识别的GBPs主要表达在L02的胞膜区及核周胞质区,而在Hep G2细胞的相同区域表达减弱.这些数据为寻找新的肝癌发病机制和抗肿瘤策略提供了有用信息.     

The NADH Dehydrogenase Nde1 Executes Cell Death after Integrating Signals from Metabolism and Proteostasis on the Mitochondrial Surface

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