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.     

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。     

日本三角涡虫热休克蛋白70(DjHSP70)C-端多肽表达及其抗血清制备

首先运用在线生物学软件对日本三角涡虫(Degusia japonica)热休克蛋白70(DjHSP70)氨基酸序列进行亲水区分析,发现该蛋白C-端含有较多亲水性氨基酸,然后以该段多肽序列为基础构建原核表达载体.采用PCR方法扩增450 bp cDNA片段,编码DjHSP70 C-端150个氨基酸多肽.将双酶切的cDNA...     

用有限酶切法分析蛋白质的氨基酸序列

报道了一个通过有限酶切蛋白质产生多肽片段的方法.蛋白质经单向SDS-聚丙烯酰胺凝胶电泳(SDS-PAGE)分离和用考马斯亮蓝短暂染色后,切下所需的蛋白质带,将其放入另一个SDS-PAGE凝胶的样品槽内,在电泳过程中该蛋白质被蛋白酶如蛋白酶V8降解,所产生的多肽片段随之被分离.电泳结束后,将多肽片段电印迹至聚偏二氟乙烯(polyvinylidene difluoride,PVDF)膜上.这些多肽片段从PVDF膜上切下后可以直接被用于分析氨基酸序列.该方法能广泛适用于分析一般蛋白质和N端被修饰蛋白质的氨基酸序列.     

绿色木霉内切几丁质酶cDNA的克隆及其编码蛋白的序列分析

根据已克隆的内切几丁质酶基因序列的同源性比较,设计引物,采用PCR技术从绿色木霉基因组中分离出一个大小为1467bp的特异DNA片段,采用RT．PeR技术从绿色木霉总RNA中分离出大小约1276bp的eDNA片段。序列对比后发现该内切几丁质酶DNA含有三个内含子,大小分别为52bp,69bp,64bp。同源性分析表明其全长eDNA序列和已经报道的内切几丁质酶序列的同源性高达95％以上,预测其编码蛋白的氨基酸序列含424个氨基酸残基,分子量为46kDa,氨基酸序列分析表明该内切几丁质酶164～172位氨基酸是其活性中心,用同源建模法模拟其空间结构模型,为进一步研究其作用机制奠定了良好基础。     

红麻野败型CMS胞质SNP分子标签的发掘

利用同源克隆的方法,克隆了红麻野败型CMS胞质SRAP标记位点Me14上游的侧翼序列,并采用RT-PCR方法研究该位点的表达。结果表明:(1)红麻不育系P3A和保持系P3B的mtDNA在Me14结合位点处存在1个G/A SNP位点;HpaⅡ内切酶可特异性酶切以保持系P3B扩增获得的E1纯化片段,而不育系P3A的E1纯化片段不能被酶切。(2)对红麻的9对不育系/保持系、5个恢复系和F1杂交种在该SNP位点的分析发现,以保持系和恢复系总DNA为模板扩增获得的E1纯化片段均可为HpaⅡ内切酶特异性酶切,而不育系和F1杂交种的E1纯化片段不能被酶切。(3)RT-PCR结果表明,E1片段对应基因在不育系P3A和保持系P3B中的时空表达模式无差异,在GenBank中也没有与E1相匹配的蛋白序列。研究表明,该研究发掘的红麻CMS胞质SNP标记位点处,不育系的mtDNA存在点突变,该标签并非具有嵌合阅读框的不育基因。     

用DREAM技术纠正人工合成基因中的突变

目的：介绍一种简便、有效的定点突变技术。方法：根据突变位点附近的DNA序列推导出氨基酸序列,再以此氨基酸序列进行逆翻译,这样在不改变氨基酸序列的前提下可以得到数目巨大的隐性突变体（silent mutants）,这些突变体中包含大量的限制性内切酶位点,选择合适的酶切位点设计引物用PCR技术扩增两侧DNA片段,然后以相应酶切融合这两个片段即可完成定点突变。结果：用该方法成功地在人工合成的含有缺失的可溶性组织因子基因的472位插入C,T两个碱基,校正了阅读框架,获得了预期的目的基因。结论：该方法简便、有效, 避免了多轮PCR和合成长引物导致突变的可能性,这种改进的PCR 定点诱变技术我们称之为“设计限制酶辅助突变”（Designed Restriction Enzyme Assisted Mutagenesis, DREAM）。此技术简单方便, 诱变的成功率高, 适于实验室常规应用。     

兔防御素(MCP-1)cDNA的克隆与序列分析

从兔脾脏细胞中分离提取总RNA,经反转录PCP(RT-PCR)扩增出兔巨嗜细胞阳离子多肽(MCP-1)cDNA,插入经EcoRI和XbaI双酶切的pUC19中,构建了克隆质粒pUCDEF.进行了限制性酶切鉴定和序列分析,结果在扩增出的cDNA288个碱基中,在前片段中有一个碱基与发表的兔MCP-1cDNA序列不同,即第157位碱基由G变为A,导致编码的氨基酸由丙氨酸变为苏氨酸.该cDNA全长288bp,编码94个氨基酸,由编码信号肽,前片段及成熟肽片段的序列组成.     

一种优化的MALDI-TOF质谱分析多肽C端序列方法

利用基质辅助激光解吸飞行时间 (MALDI TOF)质谱技术 ,测定羧肽酶Y消化蛋白质和多肽 .所产生的缩短肽片段的质量 ,在一张谱图上得到各个不同酶解时间所形成的肽质量梯度 .根据谱图中相邻两肽峰的质量差得到切去氨基酸的信息 ,从而读出C端氨基酸序列 .在pmol水平下对人促肾上腺皮质激素片段 (ACTH 1 3 9) ,人血管紧张肽片段 (angiotensin Ⅰ ,angiotensin Ⅱ )的C端序列进行了测定 .讨论了在不同浓度 ,不同时间 ,不同温度下酶解所得到的序列测定结果 .在优化条件下 ,人ACTH片段得到了C端 2 0个氨基酸残基顺序 ,为目前C端序列分析所得到的最长序列     

rhIL-12二硫键、N-糖基化位点及C端氨基酸序列分析

重组人白细胞介素12（rhIL-12）是一种已经用于治疗肿瘤,寄生虫、病毒性感染及造血障碍等疾病研究的异二聚体糖蛋白。结构确证是质量控制的重要内容,此研究对CHO细胞表达的rhIL-12二硫键配对方式、N-糖基化位点以及C端氨基酸序列进行了分析,使用Trypsin、Chymotrypsin和Glu-C三种酶分别对rhIL-12进行非还原酶解,尽可能地在其所有半胱氨酸残基之间断裂而形成二硫键相连的肽段,然后使用LC-MS/MS对酶解后的肽段样品进行分析,确定了rhIL-12样品中存在和理论配对方式相符的7对二硫键。将rhIL-12二硫键还原后并烷基化修饰保护,分别采用Trypsin,Chymotrypsin和GluC进行酶解,并用LC-MS/MS对酶解后肽段进行了质谱肽图及C端氨基酸序列分析,确定了rhIL-12 p35亚基C端氨基酸序列的8个氨基酸、p40亚基C端氨基酸序列的15个氨基酸。对rhIL-12样品还原及烷基化后用Trypsin变性酶解,所得肽段在H₂O及H₂¹⁸O水中分别用PNGase F糖苷酶处理酶切产物。并通过二级质谱分析脱糖后糖肽段分子量变化,从而确定了rhIL-12的3个N糖基化修饰位点,分别为p35亚基的71位和85位以及p40亚基的200位。通过建立酶解结合二级质谱鉴定的方法,证明了新药rhIL-12的二硫键位点、C端氨基酸序列和糖基化位点与理论一致。     

Identification of the penicillin-binding active site of penicillin-binding protein 2 of Escherichia coli

We determined the active site of penicillin-binding protein (PBP) 2 of Escherichia coli. A water-soluble form of PBP 2, which was constructed by site-directed mutagenesis, was purified by affinity chromatography, labeled with dansyl-penicillin, and then digested with a combination of proteases. The amino acid composition of the labeled chymotryptic peptide purified by HPLC was identical with that of the amino acid sequence, Ala-Thr-Gln-Gly-Val-Tyr-Pro-Pro-Ala-Ser330-Thr-Val-Lys-Pro (residues 321-334) of PBP 2, which was deduced from the nucleotide sequence of the pbpA gene encoding PBP 2. This amino acid sequence was verified by sequencing the labeled tryptic peptide containing the labeled chymotryptic peptide region. A mutant PBP 2 (thiol-PBP 2), constructed by site-directed mutagenesis to replace Ser330 with Cys, lacked the penicillin-binding activity. These findings provided evidence that Ser330 near the middle of the primary structure of PBP 2 is the penicillin-binding active-site residue, as predicted previously on the basis of the sequence homology. Around this active site, the sequence Ser-Xaa-Xaa-Lys was observed, which is conserved in the active-site regions of all E. coli PBPs so far studied, class A and class C beta-lactamases, and D-Ala carboxypeptidases. The COOH-terminal amino acid of PBP 2 was identified as His633.     

Specific modification of the condensation domain of fatty acid synthase and the determination of the primary structure of the modified active site peptides

Fatty acid synthase from the uropygial gland of goose was inactivated by iodoacetamide with a second-order rate constant of 1.3 M-1 S-1 at pH 6.0 and 25 degrees C. Of the seven component activities of the synthase, only the condensation activity was significantly inhibited by iodoacetamide modification. Since preincubation of the enzyme with acetyl-CoA, but not with malonyl-CoA, protected the enzyme from inactivation by iodoacetamide, it is suggested that iodoacetamide probably modified the primer-binding thiol group at the condensation active site. Determination of the stoichiometry of modification was done using [1-14C]iodoacetamide that was purified by high-performance liquid chromatography. Graphical analysis of the data showed that binding of 1.2 carboxamidomethyl groups per subunit of fatty acid synthase would result in complete inhibition of the enzyme activity, suggesting that there is one condensation domain per subunit of fatty acid synthase. Analysis of the tryptic peptide map of the enzyme that was modified with [1-14C]iodoacetamide in the presence and absence of acetyl-CoA revealed that acetyl-CoA prevented the labeling of a major radioactive peptide and a minor radioactive peptide. These two peptides were purified by high-performance liquid chromatography. Amino acid analysis of these two peptides revealed that the major radioactive peptide contained S-carboxymethylcysteine while the minor radioactive peptide did not. However, the latter peptide contained beta-alanine, suggesting that this peptide was from the acyl carrier protein segment of fatty acid synthase and that the iodoacetamide treatment resulted in modification of the pantetheine thiol, although to a lower extent than the primer-binding thiol. The sequence of the primer-binding active site peptide from the condensation domain was H2N-Gly-Pro-Ser-Leu-Ser-Ile-Asp- Thr-Ala-Cys(carboxamidomethyl)-X-Ser-Ser-Leu-Met-Ala-Leu-Glu-Asn-A la-Tyr-Lys- COOH, the first reported sequence of the condensation active site from a vertebrate fatty acid synthase. The acyl carrier protein segment showed extensive sequence homology with the acyl carrier protein of Escherichia coli, particularly in the vicinity of the phosphopantetheine attachment, and the sequence was H2N-Asp-Val-Ser-Ser-Leu- Asn-Ala-Asp-Ser-Thr-Leu-Ala-Asp-Leu-Gly-Leu-Asp-Ser(4'-phosphopanteth ein e) -Leu-Met-Gly-Val-Glu-Val-Arg-COOH.     

Primary structure of a base non-specific ribonuclease from Rhizopus niveus

The primary structure of a base non-specific ribonuclease from Rhizopus niveus (RNase Rh) was determined by nucleotide sequence analysis of the DNA fragment encoding RNase Rh gene including signal peptide sequence, and amino acid sequence analysis of the peptide obtained from RNase Rh and RNase Rh' (a protease-modified RNase Rh created during the course of purification). The sequence determined was: MKAVLALATLIGSTLASSCSSTA LSCSNSANSDTCCSPEYGLVVLNMQWAPGYGPANAFTLHGLWPDKCSGAYAPSGGCDSN RASSSIASVIKSKDSSLYNSMLTYWPSNQGNNNVFWSHEWSKHGTCVSTYDPDCYDNYE EGEDIVDYFQKAMDLRSQYNVYKAFSSNGITPGGTYTATEMQSAIESYFGAKAKIDCSSG TLSDVALYFYVRGRDTYVITDALSTGSCSGDVEYPTK (the sequence of signal peptide is underlined). The sequence indicates that the homology with the sequence of RNase T2 from A. oryzae with the same base specificity is about 42% and that the sequences around the two histidine residues which are supposed to be involved in the active site are fairly conserved.     

Active site of human liver aldehyde dehydrogenase

Bromoacetophenone (2-bromo-1-phenylethanone) functions as an affinity reagent for human aldehyde dehydrogenase (EC 1.2.1.3) and has been found specifically to label a unique tryptic peptide in the enzyme. Amino-terminal sequence analysis of the labeled peptide after purification by two different procedures revealed the following sequence: Val-Thr-Leu-Glu-Leu-Gly-Gly-Lys. Radioactivity was found to be associated with the glutamate residue, which was identified as Glu-268 by reference to the known amino acid sequence. This paper constitutes the first identification of an active site of aldehyde dehydrogenase.     

Identification of an alpha(3)beta(1) integrin recognition sequence in thrombospondin-1.

A synthetic peptide containing amino acid residues 190-201 of thrombospondin-1 (TSP1) promoted adhesion of MDA-MB-435 breast carcinoma cells when immobilized and inhibited adhesion of the same cells to TSP1 when added in solution. Adhesion to this peptide was enhanced by a beta(1) integrin-activating antibody, Mn(2+), and insulin-like growth factor I and was inhibited by an alpha(3)beta(1) integrin function-blocking antibody. The soluble peptide inhibited adhesion of cells to the immobilized TSP1 peptide or spreading on intact TSP1 but at the same concentrations did not inhibit attachment or spreading on type IV collagen or fibronectin. Substitution of several residues in the TSP1 peptide with Ala residues abolished or diminished the inhibitory activity of the peptide in solution, but only substitution of Arg-198 completely inactivated the adhesive activity of the immobilized peptide. The essential residues for activity of the peptide as a soluble inhibitor are Asn-196, Val-197, and Arg-198, but flanking residues enhance the inhibitory activity of this core sequence, either by altering the conformation of the active sequence or by interacting with the integrin. This functional sequence is conserved in all known mammalian TSP1 sequences and in TSP1 from Xenopus laevis. The TSP1 peptide also inhibited adhesion of MDA-MB-435 cells to the laminin-1 peptide GD6, which contains a potential integrin-recognition sequence Asn-Leu-Arg and is derived from a similar position in a pentraxin module. Adhesion studies using recombinant TSP1 fragments also localized beta1 integrin-dependent adhesion to residues 175-242 of this region, which contain the active sequence.     

The amino acid sequence of an active site peptide from the H,K-ATPase of gastric mucosa

The gastric H,K-ATPase is an active transport protein that is responsible for the maintenance of a large pH gradient across the secretory canaliculus of the mammalian parietal cell. Acid secretion across these epithelial cell membranes is coupled to the potassium-stimulated hydrolysis of ATP catalyzed by H,K-ATPase, but the mechanism of coupling between ion transport and ATP hydrolysis is unknown. In order to investigate the enzymatic mechanism of this coupling, a peptide derived from the ATP binding site of H,K-ATPase has been purified and its amino acid sequence has been determined. The peptide was identified by the incorporation of a fluorescent probe, fluorescein 5'-isothiocyanate (FITC), into the active site before trypsin digestion of the protein. The labeling of the enzyme by FITC was associated with the irreversible inhibition of enzymatic activity, and both the labeling of the tryptic peptide and inhibition of activity were prevented when the reaction was performed in the presence of ATP. At 100% inhibition of activity, 3.5 +/- 1.6 nmol of FITC were incorporated per mg of protein. The amino acid sequence of the active site peptide is His-Val-Leu-Val-Met-Lys-Gly-Ala-Pro-Glu-Gln-Leu-Ser-Ile-Arg, and FITC reacts with the lysine. This sequence is very similar to sequences of fluorescein-labeled peptides from the ATP binding sites of Na,K-ATPase and Ca2+-ATPase, and suggests that the active site structures of these ion transport ATPases are similar.     

Identification of the active site in penicillin-binding protein 3 of Escherichia coli.

We report the sequence of the active site tryptic peptide of penicillin-binding protein 3 from Escherichia coli. Purified penicillin-binding protein 3 was labeled with [14C]penicillin G and digested with trypsin, and the resulting radioactive peptides were isolated by a combination of gel filtration and high-pressure liquid chromatography. The major radioactive peak from high-pressure liquid chromatography was sequenced, and the peptide Thr-Ile-Thr-Asp-Val-Phe-Glu-Pro-Gly-Ser-Thr-Val-Lys, which comprises residues 298 to 310 in the amino acid sequence, was identified. This sequence is compared with the active site sequences from other penicillin-binding proteins and beta-lactamases.     

Genetic locus,primary structure,and chemical synthesis of human immunodeficiency virys protease

The genetic locus and primary structure of the human immunodeficiency virus (HIV) protease was determined by comparing the data of protein analyses with the published data of the gene analysis. The complete sequence of HIV-1 and HIV-2 protease was synthesized by solid-phase peptide synthesis. The synthetic protease was capable of accurately cleaving synthetic peptide substrates corresponding to known cleavage sites in gag polyproteins of HIV-1, HIV-2, and murine leukemia virus. The chemical synthesis of protease confirms the DNA sequence and provides a means of rapidly producing active protease in substantial quantities for biochemical and physical studies.     

Active site sequence of hepatic fructose-2,6-bisphosphatase. Homology in primary structure with phosphoglycerate mutase

The reaction mechanism of rat hepatic fructose-2,6-bisphosphatase involves the formation of a phosphohistidine intermediate. In order to determine the sequence around the active site histidine, the enzyme was incubated with [2-32P]fructose 2,6-bisphosphate, denatured, and treated with trypsin or endoproteinase Lys-C. The resultant labeled 32P-phosphopeptides were purified by gel filtration, anion exchange chromatography, and reverse phase high pressure liquid chromatography. The sequence of the tryptic peptide was determined to be HGESELNLR, while the partial sequence of the endoproteinase Lys-C peptide was IFDVGTRYMVNRVQDHVQSRTAYYLMNIHVTPRSIYLRHGESEL. The active site sequence was compared with the active site sequence of other enzymes that catalyze phospho group transfer via a phosphohistidine intermediate. Active site sequences of phosphoglycerate mutase and bisphosphoglycerate synthase were highly homologous with the active site of fructose-2,6-bisphosphatase implying a structural similarity and a common evolutionary origin.     

Purification and sequencing of the active site tryptic peptide from penicillin-binding protein 1b of Escherichia coli

This paper reports the sequence of the active site peptide of penicillin-binding protein 1b from Escherichia coli. Purified penicillin-binding protein 1b was labeled with [14C]penicillin G, digested with trypsin, and partially purified by gel filtration. Upon further purification by high-pressure liquid chromatography, two radioactive peaks were observed, and the major peak, representing over 75% of the applied radioactivity, was submitted to amino acid analysis and sequencing. The sequence Ser-Ile-Gly-Ser-Leu-Ala-Lys was obtained. The active site nucleophile was identified by digesting the purified peptide with aminopeptidase M and separating the radioactive products on high-pressure liquid chromatography. Amino acid analysis confirmed that the serine residue in the middle of the sequence was covalently bonded to the [14C]penicilloyl moiety. A comparison of this sequence to active site sequences of other penicillin-binding proteins and beta-lactamases is presented.