牙龈卟啉单胞菌血凝素2氯化血红素结合位点多肽对牙龈卟啉单胞菌生长抑制作用

目的探讨牙龈卟啉单胞菌血凝素2（Porphyromonas gingivalis hemagglutinin-2,PgHA-2）的氯化血红素结合位点多肽对牙龈卟啉单胞菌（Porphyromonasgingivalis,Pg）摄取氯化血红素生长的影响。方法合成多肽DHYAVMISK（肽1）,DEYAVMISK（肽2,肽1中第2位氨基酸突变为谷氨酸）,ALHPDHYLI（肽3,HA-2结合位点不相关多肽）。将肽l、肽2、肽3分别与氯化血红素琼脂糖珠预孵育,加入Pg重组血凝素2（Porphyromonas gingivalis recombinant HA-2,PgrHA-2）,收集与氯化血红素结合的PgrHA-2,SDS—PAGE电泳,分析多肽对PgrHA-2与氯化血红素结合的抑制作用。肽1、肽2、肽3与氯化血红素预孵育后,加入到CDC液体培养基中培养Pg,测定菌液A600值,分析多肽对Pg生长的抑制作用。结果肽1浓度依赖性抑制PgrHA-2与氯化血红素结合,而肽2和肽3对PgrHA-2与氯化血红素的结合无抑制作用。在24、48和72h时间点,肽1组的A600值较肽2、肽3和PBS组明显降低（P〈0．05）。结论本研究表明PgHA-2氯化血红素结合位点多肽DHYAVMISK与Pg竞争结合氯化血红素,抑制Pg的生长,为开发新的牙周病防治方法奠定基础。     

牙龈卟啉单胞菌血凝素2与氯化血红素结合位点分析

目的 通过竞争性ELISA方法明确牙龈卟啉单胞菌血凝素2(Porphyromonas gingivalis hemagglutinin-2,Pg HA-2)与氯化血红素结合的多肽位点,为牙周病保护性抗体的制备奠定基础.方法 人工合成疑为Pg HA-2氯化血红素结合位点的多肽片段,制备抗Pg HA-2单克隆抗体(MAb QB),通过间接竞争性ELISA,进一步分析血红素特异性结合位点.结果 Pg HA-2氯化血红素结合位点的氨基酸序列为DGFPGDHYAVMISK.MAb QB可以抑制Pg HA-2与氯化血红素结合.结论 明确了Pg HA-2氯化血红素结合位点的氨基酸序列,确定了Pg HA-2氯化血红素结合位点的位置.为今后Pg HA-2氯化血红素结合位点的鉴定、功能结构区分析和多肽疫苗的制备奠定基础.     

抗牙龈卟啉单胞菌血凝素2单克隆抗体的制备

目的制备抗牙龈卟啉单胞菌(Porphyromonas gingivalis,Pg)血凝素2(hemagglutinin-2,HA-2)的单克隆抗体(monoclonal antibody,mAb)。方法用重组HA-2(recombinant HA-2,rHA-2)免疫BALB/C小鼠,取其脾细胞与小鼠骨髓瘤细胞SP2/0融合,间接ELISA方法筛选杂交瘤细胞.用ELISA方法测效价。结果获得1株能够高效识别rHA-2的mAb,命名为4F11。此单克隆抗体的免疫球蛋白亚类为IgG1,效价达1?106。结论成功制备了重组牙龈卟啉单胞菌血凝素2的单克隆抗体mAb.将进一步用于牙龈卟啉单胞菌的诊断,并为牙周疾病的治疗研究奠定基础。     

牙龈卟啉单胞菌分子生物学研究进展

牙龈卟啉单胞菌已公认为是牙周炎的致病菌,它的一些表面结构诸如细胞外囊泡,菌毛,外膜蛋白,凝集素介导该菌对牙周组织粘附、定植,或作为毒性因子破坏牙周组织,随着分子生物学技术的发展,已对这些结构进行了分子克隆,本文拟就牙龈卟啉单胞菌(Porphyromonasgingivalis)简称Pg)分子生物学进展作一简要综述。1　菌毛基因的分子克隆牙龈卟啉单胞菌菌毛作为该菌表面结构之一介导了该菌对牙周组织的粘附和定植。已纯化了41kda菌毛亚单位蛋白,并克隆了菌毛蛋白基因[1]。使用寡核苷酸M1和M2作为引物,采用PCR从9株Pg菌株中扩增了1.3kb的DNA片段,E…     

多肽内切酶鉴定牙龈卟啉单胞菌血凝素2结合位点

目的利用多肽内切酶分析牙龈卟啉单胞菌凝血素2(Porphyromonas gingivalishemagglutinin-2,PgHA-2)与氯化血红素结合位点的氨基酸序列。方法Endoproteinase Lys-C多肽内切酶水解获得与氯化血红素结合的功能性的多肽片段,质谱技术鉴定多肽片段的氨基酸序列。结果质谱鉴定与氯化血红素结合的多肽片段的氨基酸序列为YAVNDGFPGDHYAVMISK。结论进一步明确了HA-2与氯化血红素结合位点的氨基酸序列,为牙周病的预防和治疗方法的改进奠定基础。     

牙龈卟啉单胞菌蛋白酶及疫苗的研究进展

牙龈卟啉单胞菌 (P g) ,革兰阴性厌氧菌 ,是人类牙周炎的主要致病菌[1] 。动物实验表明它在小鼠、大鼠和灵长类动物的龈下定植与牙周炎的发生和进展相关。P g可以调整真核细胞信号转导途径 ,为了满足新陈代谢的需要 ,P g基因表达的调节可以控制在转录水平。证据表明 ,P g的感染会导致严重的全身系统疾病如心血管疾病和分娩早产儿。P g含有大量毒性因子[2 ] ,如菌毛 ,血凝素[3 ] ,脂多糖等 ,其中Arg、Lys样半胱氨酸蛋白酶在牙周致病作用中占据了一个重要地位 ,他们通过激活宿主前体酶 ,例如 :血纤维蛋白酶原 ,或通过暴露细胞隐位及改变血…     

牙龈卟啉单胞菌HA2基因和白细胞介素IL-15基因重组质粒的构建

构建抗牙龈卟啉单胞菌的牙周炎基因疫苗p VAX1-HA2、pVAX1-HA2/IL-15,体外检测其在293T细胞的表达。以HA2基因(牙龈卟啉单胞菌牙龈素—血凝素基因编码区的核心功能区)为目的基因与IL-15基因为免疫佐剂构建真核表达质粒,用Lip2000介导瞬时转染293T细胞,RT-PCR检测目的基因mRNA水平及酶联免疫吸附试验检测IL-15蛋白表达水平。重组质粒p VAX1-HA2、pVAX1-HA2/IL-15经酶切及DNA测序鉴定构建正确,转染的293T细胞能够检测到目的基因的表达,也可以检测到IL-15蛋白的表达。说明我们成功构建了真核共表达质粒pVAX1-HA2和p VAX1-HA2/IL-15,为下一步研制抗牙龈卟啉单胞菌DNA疫苗奠定了基础。     

牙龈卟啉单胞菌相关致病因子的研究进展

牙龈卟啉单胞菌是一种生长于口腔内的革兰阴性厌氧茵.它能够利用脂多糖、荚膜多糖、菌毛、牙龈蛋白酶等一系列致病因子,侵袭局部牙周组织并逃避宿主的免疫防御机制,是诱发牙周炎的重要因素之一,引起了学者们的广泛关注.因此,探讨牙龈卟啉单胞菌的致病因子对于牙周炎的防治具有重要意义.     

牙龈卟啉单胞菌编码基因重注释研究

为了确保牙龈卟啉单胞菌生物大分子信息的准确性,对NCBI数据库中的3株牙龈卟啉单胞菌的注释信息进行研究。首先,准备好蛋白质编码与非编码序列正负样本,用基于Z曲线理论的Fisher判别法对正负样本集进行训练,确定一个判断ORF编码或非编码的阈值t0,由阈值作为判别条件来识别所有的ORFs,判断基因片段是否具有编码蛋白质的功能,由此阈值为判别标准排除掉3株牙龈卟啉单胞菌基因组中错误的基因注释信息。然后,用Prodigal基因预测软件对牙龈卟啉单胞菌进行基因预测,基因预测结果与原始功能已知基因进行比对,挑选出具有不同5’终端的ORFs,将这些具有不同5’终端的ORFs与功能已知的基因片段进行比对,找到重叠率小于20%的候选基因。最后,对这些候选基因用Blast进行序列比对找到满足条件的新基因,并为这些新基因添加功能注释信息。基于以上方法共排除了117个非编码的开放式阅读框,并找到了30个NCBI数据库中缺失的编码蛋白质的新基因。     

牙龈卟啉单胞菌酪氨酸激酶致病性的分子机制

目的 探讨牙龈卟啉单胞菌（Porphyromonas gingivalis,P. gingivalis）酪氨酸激酶（Ptk1)致病性的分子机制。方法 采用重组PCR技术构建P. gingivalis野生菌株ATCC 33277的Ptk1单基因缺失的突变菌株（ΔPtk1）,通过Real-time PCR技术检测并比较参与调控P. gingivalis（野生型P. gingivalis ATCC 33277与突变型ΔPtk1）细胞外多糖（extracellular polysaccharides,EPS）合成的转录因子SinR的表达情况,同时采用激光共聚焦显微镜观察Ptk1缺失的突变菌株与野生型菌株EPS的形成情况,最后通过ELISA试剂盒检测并比较Ptk1缺失的突变菌株与野生型菌株白细胞介素-1β(IL-1β)表达情况。结果 与野生菌株P. gingivalis ATCC 33277比较,Ptk1单基因缺失的突变菌株转录因子SinR的表达量没有显著变化（t=–1.572,P>0.05）;ELISA检测发现,Ptk1单基因缺失的突变菌株IL-1β的表达量较野生型菌株显著下降,差异有统...     

Defective intestinal amino acid absorption in Ace2 null mice

Mutations in the main intestinal and kidney luminal neutral amino acid transporter B(0)AT1 (Slc6a19) lead to Hartnup disorder, a condition that is characterized by neutral aminoaciduria and in some cases pellagra-like symptoms. These latter symptoms caused by low-niacin are thought to result from defective intestinal absorption of its precursor l-tryptophan. Since Ace2 is necessary for intestinal B(0)AT1 expression, we tested the impact of intestinal B(0)AT1 absence in ace2 null mice. Their weight gain following weaning was decreased, and Na(+)-dependent uptake of B(0)AT1 substrates measured in everted intestinal rings was defective. Additionally, high-affinity Na(+)-dependent transport of l-proline, presumably via SIT1 (Slc6a20), was absent, whereas glucose uptake via SGLT1 (Slc5a1) was not affected. Measurements of small intestine luminal amino acid content following gavage showed that more l-tryptophan than other B(0)AT1 substrates reach the ileum in wild-type mice, which is in line with its known lower apparent affinity. In ace2 null mice, the absorption defect was confirmed by a severalfold increase of l-tryptophan and of other neutral amino acids reaching the ileum lumen. Furthermore, plasma and muscle levels of glycine and l-tryptophan were significantly decreased in ace2 null mice, with other neutral amino acids displaying a similar trend. A low-protein/low-niacin diet challenge led to differential changes in plasma amino acid levels in both wild-type and ace2 null mice, but only in ace2 null mice to a stop in weight gain. Despite the combination of low-niacin with a low-protein diet, plasma niacin concentrations remained normal in ace2 null mice and no pellagra symptoms, such as photosensitive skin rash or ataxia, were observed. In summary, mice lacking Ace2-dependent intestinal amino acid transport display no total niacin deficiency nor clear pellagra symptoms, even under a low-protein and low-niacin diet, despite gross amino acid homeostasis alterations.     

Predicting DNA-binding sites of proteins from amino acid sequence

Background  

Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residues involved in protein-DNA interactions.     

Prediction of RNA binding sites in proteins from amino acid sequence

RNA-protein interactions are vitally important in a wide range of biological processes, including regulation of gene expression, protein synthesis, and replication and assembly of many viruses. We have developed a computational tool for predicting which amino acids of an RNA binding protein participate in RNA-protein interactions, using only the protein sequence as input. RNABindR was developed using machine learning on a validated nonredundant data set of interfaces from known RNA-protein complexes in the Protein Data Bank. It generates a classifier that captures primary sequence signals sufficient for predicting which amino acids in a given protein are located in the RNA-protein interface. In leave-one-out cross-validation experiments, RNABindR identifies interface residues with >85% overall accuracy. It can be calibrated by the user to obtain either high specificity or high sensitivity for interface residues. RNABindR, implementing a Naive Bayes classifier, performs as well as a more complex neural network classifier (to our knowledge, the only previously published sequence-based method for RNA binding site prediction) and offers the advantages of speed, simplicity and interpretability of results. RNABindR predictions on the human telomerase protein hTERT are in good agreement with experimental data. The availability of computational tools for predicting which residues in an RNA binding protein are likely to contact RNA should facilitate design of experiments to directly test RNA binding function and contribute to our understanding of the diversity, mechanisms, and regulation of RNA-protein complexes in biological systems. (RNABindR is available as a Web tool from http://bindr.gdcb.iastate.edu.).     

Natural human interferon-gamma. Complete amino acid sequence and determination of sites of glycosylation

Fresh human peripheral blood lymphocytes were induced with desacetylthymosin -alpha 1 and staphylococcal enterotoxin B. The induced gamma interferon (or IFN-gamma, immune interferon, type II interferon) was purified to homogeneity utilizing controlled-pore glass, concanavalin A-Sepharose, Bio-Gel P100, or Sephacryl S-200, and reversed phase high performance liquid chromatography. This procedure resulted in two active species with apparent Mr = 20,000 and 25,000 as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Both species were found to have identical amino acid sequences with a pyroglutamate residue as NH2-terminus. In both cases six different COOH termini were found. They are, at least qualitatively, identical in both species. There are two possible Asn-X-Ser/Thr glycosylation sites. Both carry carbohydrates in the Mr = 25,000 species whereas in the Mr = 20,000 species only one site is glycosylated. This likely explains the difference in apparent molecular weight between the two species and the expected molecular weight based upon the amino acid sequence.     

Identification of possible adenine nucleotide-binding sites in nitrogenase Fe- and MoFe-proteins by amino acid sequence comparison

Published amino acid sequences for nitrogenase component polypeptides were compared with those of other proteins which also bind adenine nucleotides. Three sequences which might contribute to an adenine nucleotide-binding domain were found for the Fe-protein component of nitrogenase. The beta-subunit of the MoFe-protein (nifK gene product) contains a sequence which is similar to other proteins which exhibit ATPase activity. No similarities were observed for the alpha-subunit of this component. The findings are discussed in relation to the experimental data on adenine nucleotide binding and the proposed role of ATP in the enzyme mechanism.