酪氨酸酶、漆酶和谷氨酰胺转氨酶催化交联蛋白质的比较分析

蛋白质交联在食品加工、组织工程、酶工程和药物传递等领域具有广泛用途。以酪蛋白和牛血清白蛋白(BSA)为模式蛋白,考察酪氨酸酶、漆酶和谷氨酰胺转氨酶催化蛋白质交联的底物特异性及交联规律,揭示酶对底物蛋白质结构及反应条件的要求。采用十二烷基磺酸钠-聚丙烯酰胺凝胶电泳(SDS-PAGE)分析酶催化蛋白质交联规律,激光粒度分布仪测量交联产物粒径。结果表明：酪氨酸酶、漆酶和谷氨酰胺转氨酶对底物的特异性有共同特征,即均可以催化结构松散的蛋白质分子(酪蛋白)交联,但不能催化结构紧密的蛋白质分子(BSA)交联;还原剂二硫苏糖醇(DTT)的加入能促进酶催化BSA交联反应;DTT对酪氨酸酶和谷氨酰胺转氨酶催化酪蛋白交联无影响,但抑制漆酶对酪蛋白的交联。     

蛋白质交联的研究进展

蛋白质共价交联不但存在于一些生理过程 ,还与一些神经性疾病的发病机理相关。本文综述国内外 3种观点 ,阐述蛋白质由功能体 /单体转变成交联的二聚体 /多聚体的分子机理     

蛋白质相互作用热点残基的预测北大核心CSCD

氨基酸突变扫描实验揭示了在蛋白质相互作用的结合过程中大部分的结合自由能是由极少数热点残基贡献的,通常定义结合自由能变化△△G≥2.0 kcal/mol的蛋白质残基为热点残基。热点残基对蛋白质相互作用具有重要意义。因此,如何有效进行热点残基的预测,仍然是一个研究课题。综合蛋白质氨基酸理化属性的加权疏水性、加权残基接触数、结构属性溶剂可接近面积和残基突出指数等特征,提出利用机器学习支持向量机算法来预测热点残基的方法。所提方法在丙氨酸热力学数据库数据和结合界面数据库选定的数据集上有很好的效果。在一定程度上对以后的研究发展有所帮助。     

体内甲醛交联及染色质免疫沉淀--研究DNA和蛋白质作用的新方法

甲醛交联及染色质免疫沉淀作用研究体内DNA和蛋白质相互作用的一种新方法,在染色质结构研究中获得了广泛的应用。该方法利用甲醛固定活细胞中的DNA与蛋白质,通过免疫沉淀分离复合物,从而分析蛋白质及其体内的DNA结合序列。     

氨酰tRNA合成酶作用机制及其应用北大核心CSCD

氨酰tRNA合成酶(aminoacyl-tRNA synthetases,aaRSs)通过催化氨基酸与相应tRNA的氨酰化以保证遗传信息翻译的准确性,在生物体内具有重要作用。近年来,随着对aaRS催化机制理解的不断加深,aaRS的应用逐渐成为研究热点。在细菌中,aaRS活性被抑制后会导致其生命活动发生紊乱,根据aaRS在人体与病原菌内不同的催化特点设计针对病原体的特异性aaRS抑制剂,将有助于开发以aaRS为靶标的新型抗生素。另外,通过突变aaRS可以在蛋白质序列中定点掺入非天然氨基酸,扩展蛋白质工程。本文简述了aaRS的分类、结构与功能的特点,并在此基础上综述了aaRS在研发新型抑制剂,设计改造特殊蛋白质等方面的应用。     

胃粘膜非典型增生中微环境蛋白质的相互作用北大核心CSCD

微环境在胃癌发病过程中发挥重要作用。了解胃粘膜早期癌变的分子机制,对防治胃癌具有十分重要的意义。为了解胃粘膜非典型增生过程中,微环境中蛋白质的相互作用及调节机制,采用激光捕获显微切割(laser capture microdissection,LCM)技术,纯化正常胃粘膜组织(normal gastric mucosa tissue,NGM)和胃粘膜非典型增生(gastric mucosal atypical hyperplasia,GMAH)间质,通过同位素标记定量蛋白质组学技术分析,鉴定NGM和GMAH间质的差异表达蛋白质。利用生物信息学软件,分析NGM和GMAH间质差异表达蛋白质的相互作用及其联系。共鉴定出165个GMAH间质差异表达蛋白质,其中GMAH组织中表达上调者99个,下调者66个。它们涉及一些与肿瘤相关的信号通路,如p53信号通路、MAPK信号通路、细胞周期与凋亡等信号通路,且与细胞生长、增殖、凋亡和体液免疫应答等生物学过程有关。这些差异表达蛋白质,在STRING网络中呈现相互作用,两两间相互联系。本文的研究提示,胃粘膜非典型增生微环境中存在S100A6和SOD3等蛋白质间的相互作用,它们通过影响p53信号通路、MAPK信号通路、细胞周期与凋亡等信号通路,在胃癌发病过程中发挥作用。     

蛋白质谷氨酰胺酶的发酵及初步分离和应用研究

研究了不同发酵条件对于产吲哚金黄杆菌（Chryseobacterium indologenes）生产蛋白质谷氨酰胺酶能力的影响,酶的分离和初步的应用。通过考察种子的生长曲线,发酵的温度、转速、摇瓶装液量,碳源和氮源,得出最大产酶能力的发酵条件为：30℃,200r/min,装液量25ml/250ml,蔗糖为碳源,多聚蛋白胨为氮源,发酵10~12h。初步分离研究表明在4倍超滤浓缩和4倍乙醇沉淀条件下,酶活力回收率均为最高,分别为84.99%和76.07%。该酶与酪蛋白37℃温育2h时,酪蛋白的脱酰胺度为41.03%,到24h后,脱酰胺度不再增加,并且酪蛋白的溶解性也有所增加。     

细菌漆酶的研究及应用进展北大核心CSCD

漆酶作为一种绿色环保的多酚氧化酶类,目前被广泛地应用于染料降解、造纸等领域。细菌漆酶与真菌漆酶相比,有更好的热稳定性和更宽的最适pH范围。因此,在工业应用方面更具优势与潜力。综述细菌漆酶的来源、分布、分子结构等基本信息,以及目前细菌漆酶发酵生产水平,并对固定化细菌漆酶进行总结。此外,对细菌漆酶在染料废水、电化学应用及造纸等工业生产方面的应用作简要的介绍。     

自噬的相关分子机制北大核心CSCD

细胞自噬是真核生物中高度保守的一类生物学途径,它通过降解细胞浆内不同组分,维持细胞自身平衡并帮助细胞在应激情况下生存。自噬在生物体生长发育、免疫防御、肿瘤抑制及神经退行性疾病中都有重大的意义。哺乳动物细胞中,自噬过程主要由自噬相关蛋白(Atg)所形成的一系列复合物所调控,这些蛋白质分别在自噬的启动、自噬泡的形成、延伸及成熟和降解过程中发挥重要的作用。在此,本文针对一些重要的自噬相关蛋白质对近年来自噬分子机制的研究进展做一总结。     

蛋白质-蛋白质、蛋白质-核酸相互作用研究方法及在人肠道病毒A71型研究中的应用北大核心CSCD

研究蛋白质-蛋白质相互作用的方法主要有酵母双杂交、噬菌体展示、免疫共沉淀、谷光苷肽巯基转移酶沉淀、细胞内共定位、亲和印迹、病毒铺覆蛋白结合技术、表面等离子共振、荧光共振能量转移等技术。检测蛋白质-核酸相互作用的方法主要包括酵母单杂交、染色质免疫沉淀、电泳迁移率实验、DNA-蛋白质印迹、报告基因、免疫共沉淀、谷光苷肽巯基转移酶沉淀、噬菌体展示等技术。在我们实验室对人肠道病毒A71型(EV-A71)的研究中经常会用到这些方法,但在该研究领域尚未有中文综述发表,因此本文对EV-A71研究中这些方法的应用进行了综述,该综述对蛋白质-蛋白质、蛋白质-核酸在其他病毒研究中的应用同样具有重要启示。     

Chemical cross-linking and mass spectrometry for protein structural modeling

The growth of gene and protein sequence information is currently so rapid that three-dimensional structural information is lacking for the overwhelming majority of known proteins. In this review, efforts towards rapid and sensitive methods for protein structural characterization are described, complementing existing technologies. Based on chemical cross-linking and offering the analytical speed and sensitivity of mass spectrometry these methodologies are thought to contribute valuable tools towards future high throughput protein structure elucidation.     

Covalent cross-linking of proteins without chemical reagents

A facile method for the formation of zero-length covalent cross-links between protein molecules in the lyophilized state without the use of chemical reagents has been developed. The cross-linking process is performed by simply sealing lyophilized protein under vacuum in a glass vessel and heating at 85 degrees C for 24 h. Under these conditions, approximately one-third of the total protein present becomes cross-linked, and dimer is the major product. Chemical and mass spectroscopic evidence obtained shows that zero-length cross-links are formed as a result of the condensation of interacting ammonium and carboxylate groups to form amide bonds between adjacent molecules. For the protein examined in the most detail, RNase A, the cross-linked dimer has only one amide cross-link and retains the enzymatic activity of the monomer. The in vacuo cross-linking procedure appears to be general in its applicability because five different proteins tested gave substantial cross-linking, and co-lyophilization of lysozyme and RNase A also gave a heterogeneous covalently cross-linked dimer.     

大肠杆菌二氢叶酸还原酶基因folA的克隆、表达纯化及分子间交联

利用PCR技术从大肠杆菌DH5α中获取二氢叶酸还原酶(DHFR)基因folA。用限制性内切酶BamHI与PstI将该片段插入到克隆载体pUC18上,DNA测序鉴定目的基因。而后再将该基因亚克隆到表达载体pTrcHisC上,IPTG诱导表达重组蛋白。在非变性条件下,用TALON金属亲和层析树脂纯化含组氨酸标记的重组DHFR。纯化产物在热诱导条件下行SDSPAGE分析,除23000大小的单体外,还出现了交联的二聚体和多聚体;而当反应体系中含有还原剂β-巯基乙醇时,二聚体和多聚体都被减弱。推断蛋白质在热诱导条件下二级结构发生改变而产生交联,并且有二硫键的参与。     

Formation of 5-carbomethoxyvaleramidine during hydrolysis of the protein cross-linking agent dimethyl adipimidate

Imidoesters have been used in biological studies to measure interresidue distances of proteins and macromolecular complexes, and in hematology as antisickling agents. Treatment of human red blood cells with¹⁴C-labeled dimethyl adipimidate (DMA), a bifunctional imidoester with antisickling properties, was followed by gradual loss of radioactivity from the treated cells. The radioactive compound released was isolated by thin-layer chromatography and identified by high-resolution mass spectrometry and by carbon-13 nuclear magnetic resonance, ultraviolet, and infrared spectroscopy as 5-carbomethyoxyvaleramidine, which was also shown to be the major product of DMA hydrolysis in vitro at physiologic pH in phosphate buffer. High-resolution mass spectrometry studies indicated that this product is formed via cyclization to a reactive intermediate (7-methoxy-2-imino-3,4,5,6-tetrahydro-2H-azepine) followed by hydrolysis. The intermediate exhibited strong UV absorbance, maximal at 232 nm. Such an intermediate would be capable of participating in cross-linking reactions which would have smaller dimensions than those observed with the imidoester in its extended form. The hydrolysis product, an unreactive species, should have no toxic effects on individuals receiving infusions of DMA-treated red cells.     

Quantitative evaluation of the lengths of homobifunctional protein cross-linking reagents used as molecular rulers

Homobifunctional chemical cross-linking reagents are important tools for functional and structural characterization of proteins. Accurate measures of the lengths of these molecules currently are not available, despite their widespread use. Stochastic dynamics calculations now provide quantitative measures of the lengths, and length dispersions, of 32 widely used molecular rulers. Significant differences from published data have been found.     

The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks

During the last 15 years, chemical cross-linking combined with mass spectrometry (MS) and computational modeling has advanced from investigating 3D-structures of isolated proteins to deciphering protein interaction networks. In this article, the author discusses the advent, the development and the current status of the chemical cross-linking/MS strategy in the context of recent technological developments. A direct way to probe in vivo protein–protein interactions is by site-specific incorporation of genetically encoded photo-reactive amino acids or by non-directed incorporation of photo-reactive amino acids. As the chemical cross-linking/MS approach allows the capture of transient and weak interactions, it has the potential to become a routine technique for unraveling protein interaction networks in their natural cellular environment.     

共价交联捕获聚酮合成中的酮基还原酶和酰基载体蛋白结构域的瞬时复合物

【背景】在模块化聚酮合成酶(polyketidesynthase,PKS)的催化过程中,催化结构域与同源酰基载体蛋白(acyl-carrierprotein,ACP)之间的蛋白质-蛋白质相互作用起重要作用,但这种瞬时可逆的相互作用难以捕捉分析。【目的】获得ACP和酮基还原酶(ketoreductase,KR)相互作用的蛋白复合物。【方法】在KR和ACP之间的Linker上插入烟草蚀纹病毒(tobacco etch virus,TEV)蛋白酶切位点,通过双功能马来酰亚胺试剂BMH将KR和ACP共价交联,随后TEV酶切检测交联结果。调整反应条件,使交联效率最大化。根据KR-ACP交联复合物与体系内其他蛋白标签和分子量的差异,通过亲和层析和凝胶过滤等纯化手段,获得纯度较高的KR-ACP稳定交联复合物。【结果】单独表达的KR和ACP结构域交联不成功,融合表达的KR+ACP双结构域可以有效交联,结合使用亲和层析和凝胶过滤等纯化手段成功获得纯度较高的复合物。该策略可运用于多个KR和ACP的共价交联。【结论】建立了捕获并纯化KR和ACP瞬时相互作用复合物的有效方法,为后期晶体结构的解析、KR与ACP相互作用机理的揭示及参与相互作用关键氨基酸的鉴定提供了实验基础。     

Effects of the calcium-mediated enzymatic cross-linking of membrane proteins on cellular deformability

Summary Excess calcium binding affects the shape and dynamics of cellular deformation of human erythrocytes. It may be hypothesized that incorporation of calcium may modify cellular deformability by processes which include specific cross-linking of membrane proteins with resultant changes in cell shape and deformability. Since previous studies indicate that accumulation of calcium ions causes development of -glutamyl--lysine bridges in membrane proteins, under control of a membrane transamidating enzyme which specifically requires calcium ions for activation, experiments were devised to examine the relationship between cross-linking and deformability and to determine the effects of specific inhibitor of membrane protein cross-linking on the calcium-dependent modification of erythrocyte to the echinocytic shape. The elastic shear modulus of the membrane was not significantly affected by calcium-induced cross-linking, indicating that induced shape change, not altered elasticity, causes the observed reduction in cellular deformability. These findings support the interpretation that Ca⁺⁺-induced and transamidase-catalyzed cross-linking of membrane proteins contributes to fixation of altered cellular shape and decreased cellular deformability.     

Chemical cross-linking of the chloroplast localized small heat-shock protein, Hsp21, and the model substrate citrate synthase

The molecular mechanism whereby the small heat-shock protein (sHsp) chaperones interact with and prevent aggregation of other proteins is not fully understood. We have characterized the sHsp-substrate protein interaction at normal and increased temperatures utilizing a model substrate protein, citrate synthase (CS), widely used in chaperone assays, and a dodecameric plant sHsp, Hsp21, by chemical cross-linking with 3,3'-Dithiobis[sulfosuccinimidylpropionate] (DTSSP) and mass spectrometric peptide mapping. In the absence of CS, the cross-linker captured Hsp21 in dodecameric form, even at increased temperature (47 degrees C). In the presence of equimolar amounts of CS, no Hsp21 dodecamer was captured, indicating a substrate-induced Hsp21 dodecamer dissociation by equimolar amounts of CS. Cross-linked Hsp21-Hsp21 dipeptides indicated an exposure of the Hsp21 C-terminal tails and substrate-binding sites normally covered by the C terminus. Cross-linked Hsp21-CS dipeptides mapped to several sites on the surface of the CS dimer, indicating that there are numerous weak and short-lived interactions between Hsp21 and CS, even at normal temperatures. The N-terminal arms especially interacted with a motif in the CS dimer, which is absent in thermostable forms of CS. The cross-linking data suggest that the presence of substrate rather than temperature influences the conformation of Hsp21.     

High-specific-activity probes and a high-resolution in-gel photo cross-linking assay for protein-DNA complexes

Photochemical cross-linking has been widely employed to identify proteins interacting with specific sites on DNA. Identification of bound proteins usually relies on transfer of a radiolabel from the DNA to the protein by cross-linking. We set out to fine-map a small viral replication preinitiation complex composed of two protein dimers bound to DNA, the bovine papillomavirus E1E2-ori complex. Here we describe a simple method for generating high-specific-activity probes with a phenyl-azide photoactivatible cross-linking group positioned immediately adjacent to a labeled nucleotide. The method is based on the selective destruction of one 5'-phosphorylated strand of a polymerase chain reaction product with lambda exonuclease and reconstitution of the probe with a phosphorothioate-substituted oligonucleotide, an [alpha-(32)P]dNTP, and thermophilic enzymes. We also developed a high-resolution in-gel cross-linking assay to probe defined protein-DNA complexes. With these methods we have obtained structural information for the papillomavirus E1E2-ori preinitiation complex that would otherwise have been hard to obtain. These approaches should be widely applicable to the study of protein-DNA complexes.