革兰氏阴性菌膜间质蛋白酶DegP研究进展

膜间质蛋白酶(DegP),是一种广泛存在于真核生物和原核生物细胞中的蛋白。DegP同时具有酶活性和分子伴侣活性,并通过多聚体构成胶囊状结构执行其分子伴侣功能。DegP的酶活性依赖酶切位点与PDZ1结构域双重识别方式识别底物,这种识别模式被称为"分子量尺"。在革兰氏阴性菌中,DegP主要位于膜间质,通过分子伴侣活性与酶活性帮助保护错误折叠蛋白或降解变性蛋白。DegP也参与外膜蛋白的转运,是DegP胞内活性的研究重点。DegP也可以被分泌到胞外,帮助宿主对抗恶劣环境,并参与调节生物被膜的形成。本文将从DegP的结构与活性、胞内功能与胞外功能三大方面对DegP的研究进展进行总结,为革兰氏阴性菌周质中蛋白质质量控制与DegP体外功能的进一步研究提供参考。     

与老年痴呆形成相关的β淀粉样多肽构象变化机理研究取得进展

中国科学院上海生命科学研究院药物研究所科学家在老年痴呆形成相关的β淀粉样多肽构象变化机理研究方面取得重要进展,2005年4月12日,研究结果发表在国际权威期刊《美国科学院院刊》(PNAS)上。     

大肠杆菌DsbA蛋白的氧化还原性质和构象变化

DsbA蛋白是大肠杆菌周质空间内的巯基 /二硫键氧化酶 ,主要催化底物蛋白质二硫键的形成。利用定点突变结合色氨酸类似物标记技术 ,研究了DsbA蛋白的氧化还原性质和构象变化。结果显示 :(1 )DsbA蛋白的还原态比氧化态的结构更加稳定 ,说明DsbA的强氧化性来源于氧化态构象的紧张状态 ;(2 )DsbA氧化和还原态间特殊的荧光变化主要来源于Trp76在不同状态间微观环境的差异 ;(3 )色氨酸类似物标记不会对DsbA蛋白的结构和功能产生明显的影响 ,利用1 9F NMR进一步证实了DsbA氧化还原状态间的构象变化 ,而且这种变化主要影响Trp76的局部环境 ,而对Trp1 2 6的局部环境没有太大的影响     

整合素的构象变化与亲和力调控

整合素(integrin)是由α、β两个亚单位通过非共价键连接而组成的异源二聚体。每种α、β亚单位都是含有多种结构域的大分子量Ⅰ型穿膜糖蛋白。它在细胞与细胞间、细胞与基质间相互作用的过程中发挥着十分关键的作用。整合素多种结构域的空间排列决定了其构象特征,而整合素的不同构象状态与其亲和力呈高度相关。对αVβ133整合素晶体结构的解析使我们对整合素的结构与功能有了更进一步的理解。     

寡聚结构变化与DegP蛋白酶的激活

种类繁多的蛋白质所发挥的各种功能对于生命现象是至关重要的,然而蛋白质的结构却总是受到体内外各种因素的干扰甚至破坏。因此,生物体为了维持蛋白质的活性构象,蛋白质质量控制（protein quality control）机制是必不可少的,而这种机制一旦失效将导致各种与蛋白质折叠相关的严重疾病,例如帕金森病（Parkinson’s disease）和阿尔茨海默病（Alzheimer’s disefse）等。分子伴侣和蛋白酶是参与蛋白质质量控制的主要两类蛋白质分子,它们能够结合错误折叠的底物蛋白并辅助其重新折叠或将其降解。DegP蛋白（又称为HtrA）是存在于大肠杆菌的膜间质中的一种热休克蛋白,对于大肠杆菌在高温下的存活是必需的。它的独特之处在于它同时具有分子伴侣和蛋白酶两种活性,因此DegP是研究蛋白质质量控制机制的一种典型样品。DegP同源蛋白（统称为HtrA蛋白家族）几乎存在于所有的生物种类中,它们的功能可能是参与细胞的胁迫反应。     

pH值及Na＋诱导α-辅肌动蛋白构象变化

用ＦＴＩＲ研究了不同浓度ＮａＣｌ溶液中α－辅肌动蛋白二级结构的变化。实验结果发现,在不同ＮａＣｌ浓度下,α－辅肌动蛋白至少具有三种不同的构象：低盐（３０－９０ｍｍｏｌ／ＬＮａＣｌ）,中盐（１５０ｍｍｏｌ／Ｌ－２５０ｍｍｏｌ／ＬＮａＣｌ）与高盐（３００－５００ｍｍｏｌ／ＬＮａＣｌ）构象。在低盐溶液中,α－辅肌动蛋白含有较高比例的α－螺旋结构（３３－３４％）,随着溶液中钠盐浓度的升高部分α－螺旋结构转变为β－转角或β－折叠结构。此外还研究了ｐＨ诱导α－辅肌动蛋白构象的变化,定量分析结果表明在ｐＨ７．０和中盐条件下（α－辅肌动蛋白交联Ｆ－ａｃｔｉｎ成束的活性最高）,α－辅肌动蛋白β－转角结构含量最高,而α－螺旋结构含量较低。由此可见,β－转角结构在α－辅肌动蛋白交联肌动蛋白成束中可能具有重要的功能。     

乳铁多肽,一种具有潜在抗菌能力的活性多肽

乳铁多肽(1actoferricin,Lfcin)是具有广谱杀菌,抑真菌,抑病毒,抑杀肿瘤细胞等作用的一类活性多肽,是乳铁蛋白(lactoferrin,Lf)经蛋白酶水解而产生的。该主要介绍Lfcin的来源、结构特征、生物学功能及机制等方面的研究进展。     

多糖分子链构象变化与生物活性关系研究进展

多糖因具有增强免疫、抗肿瘤、抗氧化等功能活性而倍受关注。本文在多糖研究文献统计分析的基础上,综述了多糖分子侧链、分子质量,分子修饰、溶液、金属离子、温度、pH和物理场作用等内外因素对多糖分子链构象的影响,分析了主链柔韧性、螺旋构象与多糖活性的关系,并对多糖构象及其与活性关系研究中的科学问题、发展方向和重点进行了总结与展望。     

多肽酰胺化酶的结构与功能

C端酰胺化是许多神经内分泌多肽重要的翻译后加工过程,是在酰胺化酶的催化下分两步进行的,PHM和PAL分别催化这两步反应.PHM由两个结构相似的结构域组成,每个结构域均为九链β折叠组成的三明治样结构,分别由三个His或两个His和一个Met螯合一个Cu组成活性中心.在一个反应周期中,两个Cu分别独立地与抗坏血酸和分子氧发生单电子传递的氧化还原反应,最后完成多肽底物的α-碳的羟化反应.     

新型抗肿瘤转移多肽-三聚β肽(β３)在大肠杆菌中的表达及其抗粘附作用

自行设计了抗肿瘤转移多肽－三聚β肽（β3）,人工合成了β3的基因片段,构建了β3的表达质粒pET-His-β3,在大肠杆菌BL21(DE3)plysS中表达。在用IPTG诱导15h后可见明显的His-β3融合蛋白的表达,表达产物约占细胞总蛋白的4％,占细胞总不溶性蛋白的10％。每升pET-His-β3/BL21(DE3)plysS细菌培养液用金属螯合琼脂糖凝胶6B FF分离后可回收纯度为92.2%的β3产物约20mg。所表达出的β3肽对人肝癌细胞株SMMC-7721细胞及人肝癌高转移细胞株HCCLM6细胞与纤连蛋白（fibronectin, FN）粘附具有特异的抑制作用,呈现剂量效应相关关系和时间效应相关关系,抑制作用强于β肽（β1）、3倍浓度的β1（3×β1）和GRGDS。研究结果表明：pET-His-β3/BL21(DE3)plysS是β3适合的表达系统;表达的β3肽具有特异的抗肿瘤细胞粘附作用。     

戊型肝炎病毒衣壳蛋白中和表位间的构象诱导

重组蛋白NE2包含了戊型肝炎病毒(HEV)衣壳蛋白(pORF2)的aa394～606片段.在NE2上已鉴定出了2个HEV中和表位,并获得了3个识别中和表位的单克隆抗体(MAb)8C11、13D8和8H3.这3个MAb间的交叉阻断ELISA实验发现,8C11和13D8可以彼此完全阻断,8H3对8C11和13D8均不能阻断,而8C11非但不能阻断8H3,反而显著增强了8H3与抗原的结合.用生物传感器进行的抗体与抗原结合的动力学分析也证实了这一现象.这些结果提示,在NE2上8H3表位区域受到抗原上某些结构的掩盖,而8C11与NE2的结合引起了抗原空间结构的改变,导致了掩盖8H3表位的结构的去除和8H3表位的充分暴露.免疫捕获RT-PCR发现,8C11同样可以显著增强8H3对天然HEV病毒的捕获能力,提示这种结合诱导的衣壳蛋白空间构象改变在天然HEV病毒颗粒上同样存在.     

Large Conformational Changes of Insertion 3 in Human Glycyl-tRNA Synthetase (hGlyRS) during Catalysis

Glycyl-tRNA synthetase (GlyRS) is the enzyme that covalently links glycine to cognate tRNA for translation. It is of great research interest because of its nonconserved quaternary structures, unique species-specific aminoacylation properties, and noncanonical functions in neurological diseases, but none of these is fully understood. We report two crystal structures of human GlyRS variants, in the free form and in complex with tRNA^Gly respectively, and reveal new aspects of the glycylation mechanism. We discover that insertion 3 differs considerably in conformation in catalysis and that it acts like a “switch” and fully opens to allow tRNA to bind in a cross-subunit fashion. The flexibility of the protein is supported by molecular dynamics simulation, as well as enzymatic activity assays. The biophysical and biochemical studies suggest that human GlyRS may utilize its flexibility for both the traditional function (regulate tRNA binding) and alternative functions (roles in diseases).     

Osmoregulation of the HtrA (DegP) protease of Escherichia coli: an Hha-H-NS complex represses HtrA expression at low osmolarity

The HtrA protein of Escherichia coli is a heat-shock inducible periplasmic protease, essential for bacterial survival at high temperatures. Expression of htrA gene depends on the alternative factor sigmaE and on the two-component regulatory system Cpx. These regulators systems respond, among others factors, to overproduction of misfolded proteins in the periplasm or to high level synthesis of various extracytoplasmic proteins. We describe in this report the osmoregulation of the expression of htrA gene. Low osmolarity conditions result in htrA repression. We report, as well, the role of the nucleoid associated proteins H-NS and Hha in the repression of htrA expression at low osmolarity.     

The LA Loop as an Important Regulatory Element of the HtrA (DegP) Protease from Escherichia coli: STRUCTURAL AND FUNCTIONAL STUDIES*

Bacterial HtrAs are serine proteases engaged in extracytoplasmic protein quality control and are required for the virulence of several pathogenic species. The proteolytic activity of HtrA (DegP) from Escherichia coli, a model prokaryotic HtrA, is stimulated by stressful conditions; the regulation of this process is mediated by the LA, LD, L1, L2, and L3 loops. The precise mechanism of action of the LA loop is not known due to a lack of data concerning its three-dimensional structure as well as its mode of interaction with other regulatory elements. To address these issues we generated a theoretical model of the three-dimensional structure of the LA loop as per the resting state of HtrA and subsequently verified its correctness experimentally. We identified intra- and intersubunit contacts that formed with the LA loops; these played an important role in maintaining HtrA in its inactive conformation. The most significant proved to be the hydrophobic interactions connecting the LA loops of the hexamer and polar contacts between the LA′ (the LA loop on an opposite subunit) and L1 loops on opposite subunits. Disturbance of these interactions caused the stimulation of HtrA proteolytic activity. We also demonstrated that LA loops contribute to the preservation of the integrity of the HtrA oligomer and to the stability of the monomer. The model presented in this work explains the regulatory role of the LA loop well; it should also be applicable to numerous Enterobacteriaceae pathogenic species as the amino acid sequences of the members of this bacterial family are highly conserved.     

Antibody Responses Raised against a Conformational V3 Loop Peptide of HIV-1

The amino acid sequence of the principal neutralizing determinant (PND) of 224 cases of human immunodeficiency virus type 1 (HIV-1) was determined and the most frequently occurring sequence was used as a peptide antigen for studying virus-specific antibody responses. In our present study, a linear peptide of the most frequent PND was first synthesized and then oxidized to create a disulfide-bridged loop conformation. Then, in order to construct a macromolecular structure for the purpose of increasing anti-genicity, the synthetic peptide was conjugated to a core peptide. We compared the immunogenicity of the disulfide-bridged loop PND peptide antigen (AG4) and the linear PND peptide antigen (AG5). After immunizing rabbits 5 and 6 times with both peptides, the results obtained using ELISA revealed that AG4 (conformational-loop type) was more capable of inducing a high titer of antigen-specific antibodies than was AG5 (linear type). Despite an amino acid sequence homology of 72%, a 1:8 dilution of serum raised against AG4 inhibited 81.9% of HIV-1_IIIB-mediated cell fusion, suggesting that conformational V3 loop peptide is able to elicit an antibody response which is strongly HIV-1-specific.     

Identification of the Escherichia coli sohB gene, a multicopy suppressor of the HtrA (DegP) null phenotype.

We cloned and sequenced the sohB gene of Escherichia coli. The temperature-sensitive phenotype of bacteria that carry a Tn10 insertion in the htrA (degP) gene is relieved when the sohB gene is present in the cell on a multicopy plasmid (30 to 50 copies per cell). The htrA gene encodes a periplasmic protease required for bacterial viability only at high temperature, i.e., above 39 degrees C. The sohB gene maps to 28 min on the E. coli chromosome, precisely between the topA and btuR genes. The gene encodes a 39,000-Mr precursor protein which is processed to a 37,000-Mr mature form. Sequencing of a DNA fragment containing the gene revealed an open reading frame which could encode a protein of Mr 39,474 with a predicted signal sequence cleavage site between amino acids 22 and 23. Cleavage at this site would reduce the size of the processed protein to 37,474 Mr. The predicted protein encoded by the open reading frame has homology with the inner membrane enzyme protease IV of E. coli, which digests cleaved signal peptides. Therefore, it is possible that the sohB gene encodes a previously undiscovered periplasmic protease in E. coli that, when overexpressed, can partially compensate for the missing HtrA protein function.     

The HtrA (DegP) protein, essential for Escherichia coli survival at high temperatures, is an endopeptidase.

As a preliminary step in the understanding of the function of the Escherichia coli HtrA (DegP) protein, which is indispensable for bacterial survival only at elevated temperatures, the protein was purified and partially characterized. The HtrA protein was purified from cells carrying the htrA gene cloned into a multicopy plasmid, resulting in its overproduction. The sequence of the 13 N-terminal amino acids of the purified HtrA protein was determined and was identical to the one predicted for the mature HtrA protein by the DNA sequence of the cloned gene. Moreover, the N-terminal sequence showed that the 48-kilodalton HtrA protein is derived by cleavage of the first 26 amino acids of the pre-HtrA precursor polypeptide and that the point of cleavage follows a typical target sequence recognized by the leader peptidase enzyme. The HtrA protein was shown to be a specific endopeptidase which was inhibited by diisopropylfluorophosphate, suggesting that HtrA is a serine protease.     

Peptide selectivity between the PDZ domains of human pregnancy‐related serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) can be reshaped by different halogen probes

The human HtrA family of serine proteases (HtrA1, HtrA2, HtrA3, and HtrA4) are the key enzymes associated with pregnancy and closely related to the development and progression of many pathological events. Previously, it was found that halogen substitution at the indole moiety of peptide Trp‐1 residue can form a geometrically satisfactory halogen bond with the Drosophila discs large, zona occludens‐1 (PDZ) domain of HtrA proteases. Here, we attempt to systematically investigate the effect of substitution with 4 halogen types and 2 indole positions on the binding affinity and specificity of peptide ligands to the 4 HtrA PDZ domains. The complex structures, interaction energies, halogen‐bonding strength, and binding affinity of domain‐peptide systems were modeled, analyzed, and measured via computational modeling and fluorescence‐based assay. It is revealed that there is a compromise between the local rearrangement of halogen bond involving different halogen atoms and the global optimization of domain‐peptide interaction; the substitution position is fundamentally important for peptide‐binding affinity, while the halogen type can effectively shift peptide selectivity between the 4 domains. The HtrA1‐PDZ and HtrA4‐PDZ as well as HtrA2‐PDZ and HtrA3‐PDZ respond similarly to different halogen substitutions of peptide; –Br substitution at R2‐position and –I substitution at R4‐position are most effective in improving peptide selectivity for HtrA1‐PDZ/HtrA4‐PDZ and HtrA2‐PDZ/HtrA3‐PDZ, respectively; –F substitution would not address substantial effect on peptide selectivity for all the 4 domains. Consequently, the binding affinities of a native peptide ligand DSRIWWV^–COOH as well as its 4 R2‐halogenated counterparts were determined as 1.9, 1.4, 0.5, 0.27, and 0.92 μM, which are basically consistent with computational analysis. This study would help to rationally design selective peptide inhibitors of HtrA family members by using different halogen substitutions.     

Temperature Dependent Protease Activity and Structural Properties of Human HtrA2 Protease

Human HtrA2 belongs to a new class of oligomeric serine protease, members of which are found in most organisms. Mature HtrA2 is released from mitochondria into the cytosol in response to apoptotic stimuli. In this report, the effect of temperature on proteolytic activity of HtrA2 and related structural properties were investigated. In the range from 25 to 55 degrees C, the proteolytic activity of HtrA2 rapidly increased with temperature, and it drastically decreased at and over 60 degrees C. Structural analysis using far-UV CD spectroscopy and gel filtration revealed no significant change in the secondary structure of HtrA2 from 25 to 70 degrees C, or in the oligomeric size between 25 and 55 degrees C. However, a significant change at the tertiary level, as examined using near-UV CD, was observed for HtrA2 in the range from 25 to 60 degrees C. Differential scanning calorimetry indicated that HtrA2 exhibits a thermal transition beginning at around 61 degrees C. The fluorescence intensity of ANS interacting with HtrA2 decreased with increasing temperature. HtrA2 was found to be able to complement DegP function at 44 degrees C, indicating that HtrA2 could have protective functions in mitochondria.