抗癌晶体蛋白Parasporin-2空间结构的研究

通过同源建模得到了抗癌晶体蛋白Parasporin-2(Cry46Aa1)活性区的初始三维结构,利用分子动力学方法对初始三维结构进行优化。为了评估模型的好坏,利用Ramachandran plot和结构匹配等方法对模型进行评价。结果显示,所得的Parasporin-2空间模型良好。比较了Cry46Aa1与Cry46Ab1这两种高度同源的抗癌晶体蛋白的空间结构,找出了其空间结构上的不同之处。通过大分子对接程序Hex4.5,模拟了Parasporin-2与受体GPI-瞄固蛋白(CD59)的相互作用。结果显示,Parasporin-2中参与对接的活性位点位于两个α-螺旋下方的凹槽内,而CD59中的四个loop倾向于插入该凹槽内。研究结果为Parasporin-2的抗癌机制研究及其理性改造奠定了基础。     

Ⅱ型抗癌晶体蛋白抗肝癌作用的关键芳香族氨基酸

为探讨Ⅱ型抗癌晶体蛋白(Parasporin-2)上与抗肝癌作用相关的关键氨基酸,利用5-BU对Parasporin-2活性区编码DNA(P2Y)进行PCR诱变,之后在大肠杆菌中表达,产物纯化后经MTT法检测其对肝癌细胞系和正常肝细胞系的作用。获得的9个突变体其抗肝癌活性差异极大,其中P2M1和P2M8对两种肝癌细胞系SMMC7721和Bel7402均有较强的细胞毒杀作用而不影响正常肝细胞系Chang-liver。比较了P2M1、P2M8和P2Y的二级结构与三级结构,发现二级结构上的变化如β折叠变长或α螺旋增加影响着Ⅱ型抗癌晶体蛋白的抗肝癌活性。基于突变体间氨基酸序列比对、突变体与受体间分子对接以及模拟突变等研究的结果表明,位点52、56、58和208上的氨基酸残基特别是芳香族氨基酸在Parasporin-2与受体间的互作中可能起着重要作用。     

基于联合残基力场的蛋白质能量优化

简述了蛋白质结构预测中存在的问题,主要介绍了蛋白质分子力场的一种模型即联合残基力场,然后利用这种模型对一种多肽和葡萄球菌蛋白的部分段进行试验,使它们的能量不同程度的得到了最小化,其中前者的初始能量为-71.50461kcal/mol,最小化后为-73.32767kcal/mol.     

白色念珠菌羊毛甾醇14α-去甲基化酶三维结构分子模型研究

基于四种原核细胞色素Ｐ４５０晶体蛋白Ｐ４５０ＢＭ３、Ｐ４５０ｃａｍ、Ｐ４５０ｔｅｒｐ、Ｐ４５０ｅｒｙＦ模建白色念珠菌羊毛甾醇１４α－去甲基化酶三维结构。序列匹配采用四种晶体结构比较结果基础之上提出的细胞色素Ｐ４５０超家族蛋白基于结构知识的序列匹配方法。以Ｐ４５０ＢＭ３晶体结构坐标模建目标蛋白结构保守区主链结构,结构保守区侧链构象来源于四种晶体蛋白与模建蛋白对应残基同源性得分最高残基构象。模建结果用分子力学和分子动力学进行结构优化,模建结果蛋白采用Ｐｒｏｆｉｌｅ－３Ｄ图、Ｒａｍａｃｈａｎｄｒａｎ图和疏水图分析确证结构的合理性。并根据模型推测与血红素辅基相互作用的残基、与氧化还原偶联蛋白作用和参与电子传递的残基、底物进出通道和活性位点的残基。这些研究结果为定点突变研究、抗多肽抗体结合实验等提供理论依据,为高效低毒抗真菌药物合理设计提供靶标。     

苏云金芽胞杆菌抗癌晶体蛋白的研究进展

抗癌晶体蛋白(parasporins,PS)是由没有杀虫活性的苏云金芽胞杆菌产生的一种晶体蛋白,在经过蛋白酶酶解后产生的活性多肽对来自人类不同组织的癌细胞具有特异性细胞毒性,而对正常细胞具有较低毒性或不具有毒性,是一种具有很大潜力的微生物抗癌蛋白。就最近几年苏云金芽胞杆菌中已发现的抗癌晶体蛋白的种类、结构特征、细胞活性谱和杀虫机制进行简要概述。     

α-葡萄糖苷酶三维结构的同源模建与分子设计

目的:该文预测了来源于嗜热脂肪芽孢杆菌(Bacillus stearothermophilus)ATCC 12016编码α-葡萄糖苷酶序列的三维结构,设计突变位点,构建突变体模型,并对预测三维结构与突变体进行了评估与分析.方法:分析了α-葡萄糖苷酶的核酸序列与蛋白序列,确定了α-葡萄糖苷酶蛋白序列的同源性与保守区特征;利用来源于蜡状芽胞杆菌(Bacillus cereus)ATCC 7064寡聚-1,6-葡萄糖苷酶三维蛋白结构作为模板,同时基于同源模建方法对α-葡萄糖苷酶序列的三维结构与突变突变体模型进行了结构预测.结果:对预测的三维结构与突变体进行评估与分析,表明预测与设计的结构达到合理化标准.结论:基于以上研究结果,构建α-葡萄糖苷酶的三维结构模型是合理的,为蛋白质工程应用建立了理论研究平台.     

白桦4CL蛋白结构分析及同源建模

利用生物信息学方法分析白桦4CL蛋白的氨基酸组成、等电点、疏水/亲水区、跨膜区及二级结构等蛋白质性质;并同拟南芥、水稻和毛白杨的4CL蛋白进行对比,进行同源性分析;利用生物信息学软件对其空间结构进行了模拟,得到了可靠的分子生物学模型,并根据模型对白桦4CL蛋白功能进行预测,为今后测定白桦4CL蛋白生物学功能奠定了理论基础。     

大鼠βB2—晶体蛋白的克隆,高效表达及纯化

β－晶体蛋白是含量最高的一组晶状体结构蛋白。它的正常结构对维持晶状体的高折射系数和透明至关重要,而其结构的改变与白内障的形成密切相关。为了获得大量纯的βＢ２－晶体蛋白并用定点突变的方法研究其聚合的机制,建立了大鼠βＢ２－晶体蛋白的细菌表达系统及纯化方法。用ＲＴ－ＰＣＲ的方法克隆了β－晶体蛋白中含量最高的βＢ２－晶体蛋白的ｃＤＮＡ。用苯啶酮酸诱导ｒｅｃＡ启动子后,蛋白质在大肠杆菌中得到了高效表达。β     

转人工合成GFM CryIA基因烟草表现明显杀虫活性

为了使来自原核生物的苏云金芽孢杆菌的杀虫晶体蛋白（ＩＣＰ）基因能够在高等植物中得到很好的表达,对编码这种杀虫晶体蛋白基因的核苷酸顺序进行了必要而又合理的修饰和改造：不改变杀虫晶体蛋白基因的氨基酸编码顺序,将杀虫晶体蛋白基因的密码子更换成植物基因组中常用的优化密码子,同时更换掉Ｂｔ杀虫晶体蛋白结构基因中的不稳定元件,人工全合成了长度为１８２４ｂｐ的杀虫晶体蛋白基因－ＧＦＭ ＣｒｙＩＡ基因。为了检测合     

苏云金芽孢杆菌Cry1Ac杀虫晶体蛋白及其分子设计

cry1Ac编码的杀虫晶体蛋白是苏云金芽孢杆菌(Bt)产生的多种杀虫晶体蛋白中对鳞翅目昆虫有很高毒性的蛋白.第一个Cry1Ac杀虫晶体蛋白最早在库斯塔克亚种HD73中以伴胞晶体形式分离获得,其编码区为3 534 bp,编码蛋白分子量为133 kD,含1 178个氨基酸,等电点为4.84.自此以来,Cry1Ac杀虫晶体蛋白结构、功能以及应用研究一直是Bt杀虫晶体蛋白研究的重要方向.本文介绍了苏云金芽孢杆菌中应用最广泛的Cry1Ac杀虫晶体蛋白家族的结构、功能及其基因分类,并进一步就基于苏云金芽孢杆菌Cry1Ac杀虫晶体蛋白的基因工程研究做了分析,提出了持续利用BtCry1Ac杀虫晶体蛋白的一些见解.     

Parasporin-1, a novel cytotoxic protein from Bacillus thuringiensis, induces Ca2+ influx and a sustained elevation of the cytoplasmic Ca2+ concentration in toxin-sensitive cells

Parasporin-1 is a novel non-insecticidal inclusion protein from Bacillus thuringiensis that is cytotoxic to specific mammalian cells. In this study, we investigated the effects of parasporin-1 on toxin-sensitive cell lines to elucidate the cytotoxic mechanism of parasporin-1. Parasporin-1 is not a membrane pore-forming toxin as evidenced by measurements of lactate dehydrogenase release, propidium iodide penetration, and membrane potential in parasporin-1-treated cells. Parasporin-1 decreased the level of cellular protein and DNA synthesis in parasporin-1-sensitive HeLa cells. The earliest change observed in cells treated with this toxin was a rapid elevation of the intracellular free-Ca(2+) concentration; increases in the intracellular Ca(2+) levels were observed 1-3 min following parasporin-1 treatment. Using four different cell lines, we found that the degree of cellular sensitivity to parasporin-1 was positively correlated with the size of the increase in the intracellular Ca(2+) concentration. The toxin-induced elevation of the intracellular Ca(2+) concentration was markedly decreased in low-Ca(2+) buffer and was not observed in Ca(2+)-free buffer. Accordingly, the cytotoxicity of parasporin-1 decreased in the low-Ca(2+) buffer and was restored by the addition of Ca(2+) to the extracellular medium. Suramin, which inhibits trimeric G-protein signaling, suppressed both the Ca(2+) influx and the cytotoxicity of parasporin-1. In parasporin-1-treated HeLa cells, degradation of pro-caspase-3 and poly(ADP-ribose) polymerase was observed. Furthermore, synthetic caspase inhibitors blocked the cytotoxic activity of parasporin-1. These results indicate that parasporin-1 activates apoptotic signaling in these cells as a result of the increased Ca(2+) level and that the Ca(2+) influx is the first step in the pathway that underlies parasporin-1 toxicity.     

Cytocidal actions of parasporin-2, an anti-tumor crystal toxin from Bacillus thuringiensis

Parasporin-2, a new crystal protein derived from noninsecticidal and nonhemolytic Bacillus thuringiensis, recognizes and kills human liver and colon cancer cells as well as some classes of human cultured cells. Here we report that a potent proteinase K-resistant parasporin-2 toxin shows specific binding to and a variety of cytocidal effects against human hepatocyte cancer cells. Cleavage of the N-terminal region of parasporin-2 was essential for the toxin activity, whereas C-terminal digestion was required for rapid cell injury. Protease-activated parasporin-2 induced remarkable morphological alterations, cell blebbing, cytoskeletal alterations, and mitochondrial and endoplasmic reticulum fragmentation. The plasma membrane permeability was increased immediately after the toxin treatment and most of the cytoplasmic proteins leaked from the cells, whereas mitochondrial and endoplasmic reticulum proteins remained in the intoxicated cells. Parasporin-2 selectively bound to cancer cells in slices of liver tumor tissues and susceptible human cultured cells and became localized in the plasma membrane until the cells were damaged. Thus, parasporin-2 acts as a cytolysin that permeabilizes the plasma membrane with target cell specificity and subsequently induces cell decay.     

Mode of action of parasporin-4, a cytocidal protein from Bacillus thuringiensis

Parasporin-4 (PS4) is a cytotoxic protein produced by Bacillus thuringiensis strain A1470. It exhibits specific cytotoxicity against human cancer cell lines, CACO-2, Sawano, and MOLT-4 cells, in particular. When cells were administrated with PS4, cell swelling and nuclear shrinkage were induced, and, the ballooned cells burst within 24 h. PSI-BLAST search showed that the protein shared homology not only with B. thuringiensis Cry toxins but also with aerolysin-type β-pore-forming toxins. Circular dichroism measurements suggested that PS4 was a β-sheet-rich protein. PS4 aggregated into oligomers on the plasma membrane of PS4-susceptible CACO-2 cells, but not on that of PS4-resistant HeLa cells. Leakage of lactate dehydrogenase and influx of extracellular FITC-dextrans were observed only in susceptible cells. The activation of effectors caspase 3 and/or 7 was not observed in PS4-treated CACO-2 cells. It was shown that cytotoxicity of the PS4 against CACO-2 cells was exhibited when treated by cyclodextrin which induces cholesterol depletion. These results suggest that PS4 is a unique β-pore-forming toxin with a cholesterol-independent activity.     

Packaging double-helical DNA into viral capsids

DNA packaging in bacteriophage P4 has been examined using a molecular mechanics model with a reduced representation containing one pseudoatom per turn of the double helix. The model is a discretized version of an elastic continuum model. The DNA is inserted piecewise into the model capsid, with the structure being reoptimized after each piece is inserted. Various optimization protocols were investigated, and it was found that molecular dynamics at a very low temperature (0.3 K) produces the optimal packaged structure. This structure is a concentric spool, rather than the coaxial spool that has been commonly accepted for so many years. This geometry, which was originally suggested by Hall and Schellman in 1982 (Biopolymers Vol. 21, pp. 2011-2031), produces a lower overall elastic energy than coaxial spooling.     

Computational investigations of structural changes resulting from point mutations in a collagen-like peptide

The results of 0.5-1.0 ns molecular dynamics simulations of the collagen-like peptides [(POG)4(POA)(POG)4]3 and [(POG)9]3 (POG: proline-hydroxyproline-glycine) are presented. All simulations were performed using the AMBER-94 molecular mechanical force field with a shell of TIP3P waters surrounding the peptides. The initial geometries for the collagen-like peptides included an x-ray crystallographic structure, a computer-generated structure, a [(POG)9]3 structure modeled from the x-ray structure, and the x-ray structure with crystallographic waters replaced with a shell of modeled TIP3P waters. We examined the molecular dynamics peptide residue rms deviation fluctuations, dihedral angles, molecular and chain end-to-end distances, helical parameters, and peptide-peptide and peptide-solvent hydrogen-bonding patterns. Our molecular dynamics simulations of [(POG)4(POA)(POG)4]3 show average structures and internal coordinates similar to the x-ray crystallographic structure. Our results demonstrate that molecular dynamics can be used to reproduce the experimental structures of collagen-like peptides. We have demonstrated the feasibility of using the AMBER-94 molecular mechanical force field, which was parameterized to model nucleic acids and globular proteins, for fibril proteins. We provide a new interpretation of peptide-solvent hydrogen bonding and a peptide-peptide hydrogen bonding pattern not previously reported in x-ray studies. Last, we report on the differences; in particular with respect to main-chain dihedral angles and hydrogen bonding, between the native and mutant collagen-like peptides.     

Homology model of 1alpha,25-dihydroxyvitamin D3 24-hydroxylase cytochrome P450 24A1 (CYP24A1): active site architecture and ligand binding

Homology models of cytochrome P450 24A1 (CYP24A1) were constructed using three human P450 structures, CYP2C8, CYP2C9 and CYP3A4 as templates for the model building. Using molecular operating environment (MOE) software the lowest energy CYP24A1 model was then assessed for stereochemical quality and side chain environment. Further active site optimisation of the CYP24A1 model built using the CYP3A4 template was performed by molecular dynamics to generate a final CYP24A1 model. The natural substrate, 1,25-dihydroxyvitamin D(3) (calcitriol) and the CYP24 inhibitor (R)-N-(2-(1H-imidazol-1-yl)-2-phenylethyl)-4'-chlorobiphenyl-4-carboxamide ((R)-VID-400) were docked into the model allowing further validation of the active site architecture. Using the docking studies structurally and functionally important residues were identified with subsequent characterisation of secondary structure.     

Computational study,synthesis and evaluation of active peptides derived from Parasporin-2 and spike protein from Alphacoronavirus against colorectal cancer cells

Parasporin-2Aa1 (PS2Aa1) is a toxic protein of 37 KDa (30 kDa, activated form produced by proteolysis) that was shown to be cytotoxic against specific human cancer cells, although its mechanism of action has not been elucidated yet. In order to study the role of some native peptide fragments of proteins on anticancer activity, here we investigated the cytotoxic effect of peptide fragments from domain-1 of PS2Aa1 and one of the loops present in the binding region of the virus spike protein from Alphacoronavirus (HCoV-229E), the latter according to scientific reports, who showed interaction with the human APN (h-APN) receptor, evidence corroborated through computational simulations, and thus being possible active against colon cancer cells. Peptides namely P264-G274, Loop1-PS2Aa, and Loop2-PS2Aa were synthesized using the Fmoc solid-phase synthesis and characterized by mass spectrometry (MS). Additionally, one region from loop 1 of HCoV-229E, Loop1-HCoV-229E, was also synthesized and characterized. The A4W-GGN5 anticancer peptide and 5-fluorouracil (5-FU) were taken as a control in all experiments. Circular dichroism revealed an α-helix structure for the peptides derived from PS2Aa1 (P264-G274, Loop1-PS2Aa, and Loop2-PS2Aa) and β-laminar structure for the peptide derived from Alphacoronavirus spike protein Loop1-HCoV-229E. Peptides showed a hemolysis percentage of less than 20% at 100 µM concentration. Besides, peptides exhibited stronger anticancer activity against SW480 and SW620 cells after exposure for 48 h. Likewise, these compounds showed significantly lower toxicity against normal cells CHO-K1. The results suggest that native peptide fragments from Ps2Aa1 may be optimized as a novel potential cancer-therapeutic agents.     

Modeling and docking of the three-dimensional structure of the human melanocortin 4 receptor

A three-dimensional structure of the human melanocortin 4 receptor (hMC4R) is constructed in this study using a computer-aided molecular modeling approach. Human melanocortin 4 receptor is a G Protein-Coupled Receptor (GPCR). We structurally aligned transmembrane helices with bovine rhodopsin transmembrane domains, simulated both intracellular and extracellular loop domains on homologous loop regions in other proteins of known 3D structure and modeled the C terminus on the corresponding part of bovine rhodopsin. Then tandem minimization and dynamics calculations were run to refine the crude structure. The simulative model was tested by docking with a triplet peptide (RFF) ligand. It was found that the ligand is located among transmembrane regions TM3, TM4, TM5, and TM6 of hMC4R. In consistence with mutational and biochemical data, binding site is mainly formed as a hydrophobic and negatively charged pocket. The model constructed here might provide a structural framework for making rational predictions in relevant fields.     

Homology modelling of a sensor histidine kinase from Aeromonas hydrophila

Aeromonas hydrophila has been implicated in extra-intestinal infection and diarrhoea in humans. Targetting unique effectors of bacterial pathogens is considered a powerful strategy for drug design against bacterial variations to drug resistance. The two-component bacterial system involving sensor histidine kinase (SHK) and its response regulators is considered a lucrative target for drug design. This is the first report describing a three-dimensional (3D) structure for SHK of A. hydrophila. The model was constructed by homology modelling using the X-ray structure of PleD—a response regulator—in conjunction with cdiGMP (PDB code 1W25) and HemAT sensor domain (PDB code 1OR4)—a globin coupled sensor. A combination of homology modelling methodology and molecular dynamics (MD) simulations was applied to obtain a reasonable structure to understand the dynamic behaviour of SHK. Homology modelling was performed using MODELLER9v2 software. The structure was relaxed to eliminate bad atomic contacts. The final model obtained by molecular mechanics and dynamics methods was assessed using PROCHECK and VERIFY 3D graph, which confirmed that the final refined model is reliable. Until complete biochemical and structural data of SHK are determined by experimental means, this model can serve as a valuable reference for characterising the protein and could be explored for drug targetting by design of suitable inhibitors.     

Trophoblast-specific knockdown of CSPG4 expression causes pregnancy complications with poor placentation in mice

The multifunctional molecule chondroitin sulfate proteoglycan 4 (CSPG4/NG2) plays key roles in organogenesis and tumorigenesis. However, its roles in placentation remain unclear. In this study, CSPG4 expression in human and mouse placentas was investigated through immunohistochemistry (IHC), qPCR and western blotting. The theoretical structure and function of CSPG4 were assessed using bioinformatic tools, and the functions of CSPG4 in fetal and placental development were investigated using a mouse model established by trophoblast-specific CSPG4 knockdown and a trophoblast cell line with CSPG4 knockout by lentivirus infection. The results showed that CSPG4 was mainly located in trophoblasts in both human placentas and mouse placentas, with a higher level in preeclampsia (PE) placentas than in healthy control placentas. Furthermore, there was a trend of increasing expression in mouse placentas during pregnancy. The 3D structure of CSPG4 was visualized using an M model composed of two chains, and the structure implied that CSPG4 was a multifunctional molecule containing multiple pockets with multiligand binding sites and enzyme active sites. Trophoblast-specific CSPG4 knockdown caused frequent fetal loss, and viable fetal development was restricted by poor placentation, with mice placentas having reduced weight and width. The proliferation and invasion of CSPG4-knockout trophoblasts were significantly inhibited, and as such, the molecular signaling of AKT and ERK phosphorylation was inhibited, and the expression of MMP2 and MMP9 was reduced. In summary, CSPG4 deficiency inhibited trophoblast proliferation and invasion, which was associated with AKT, ERK and MMP signaling. CSPG4 deficiency also caused pregnancy complications with poor placentation in mice.