丝组二肽——现代蛋白酶分子进化过程中的原始雏形

系统阐述了我们实验室近十五年来对丝组二肽的生物活性的研究.丝组二肽是目前报道的具有多种切割活性的最小活性肽,它不仅能够切割DNA,而且可以切割蛋白质及羧酸酯.丝组二肽是迷你的磷酸酯酶和蛋白水解酶,是现代蛋白酶分子进化过程中的原始雏形.     

具有生物活性的人带3蛋白胞质片段融合蛋白的克隆、表达与纯化

用PCR法从质粒pHB3中扩增了人红细胞带3蛋白胞质片段(CDB3)基因.PCR产物经限制性内切酶切割后与多克隆位点处带有编码6个组氨酸序列的高效表达载体pET28b连接,构建为重组子pCDBHistag.重组子经酶切及序列测定后在大肠杆菌BL21(DE3)中获得高效表达,可溶性目的蛋白占菌体总蛋白的40%左右.C端带有6个连续组氨酸的带3蛋白胞质片段作为融合蛋白不仅可以降低宿主菌蛋白酶对其水解程度,而且简化了目的蛋白的纯化过程.经一步螯合Ni²⁺的亲和层析获得了电泳纯的带3蛋白胞质片段融合蛋白.活性测定结果表明,带3蛋白胞质片段融合蛋白能够抑制醛缩酶(Aldolase)活性的70%,与文献报道的人红细胞内带3蛋白胞质片段具有相同的功能.     

中国蛇岛蝮蛇毒蛋白的电泳结合串联质谱法分析

采用十二烷基硫酸钠聚丙烯酰胺凝胶电泳(SDS-PAGE)对中国辽宁蛇岛蝮(Gloydius shedaoensis)蛇毒(GSSV)进行分离,染色结果显示该蛇毒中含有多种相对分子质量为12 ～85 ku的蛋白组分.凝胶上切割的蛋白带经胶内二硫苏糖醇(DTT)还原和碘乙酰胺(IAM)修饰后进行胰蛋白酶水解,所得肽段采用高效液相色谱-电喷雾串联质谱(HPLC-nESI MS/MS)进行分析,蛋白鉴定采用Sequest Bioworks软件搜索NCBInr数据库完成.从GSSV中鉴定出超过25种蛋白组分,主要包括:酸性磷脂酶A2、碱性磷脂酶A2、神经生长因子、突触前神经毒素、出血因子、类凝血酶、丝氨酸蛋白酶、糖原合酶、金属蛋白酶、成熟酶、L-氨基酸氧化酶、纤溶酶源激活物、外源凝集素、富含半胱氨酸分泌酶、去整合素、纤连蛋白结合蛋白、纤维蛋白原凝固抑制因子A、血管凋亡诱导蛋白1、氨甲酰基磷酸合成酶、吡喃糖-2-氧化酶以及ablomin,catrin,mucrofirase,pallabin,salmosin和triflin的同源蛋白.     

一个能分泌出哺乳动物细胞的HBV表面抗原大蛋白

本文用定向突变方法缺失了人乙型肝炎病毒表面抗原氨端位于preS1区的54个碱基对(编码氨基酸2—19).该基因在猴肾细胞株COS-M6中表达的产物(S301蛋白)和野生型表面抗原大蛋白不同.它不但能被分泌出细胞,而且对表面抗原主蛋白分泌的抑制作用大大减弱,提示了缺失区域中含有一个阻止大蛋白分泌的滞留顺序.S301蛋白的分泌依赖于主蛋白的表达,而且它们的分泌有同步性.和野生型表面抗原大蛋白一样,S301蛋白在COS细胞中合成后能转移至内质网膜,并被糖基化.它对热稳定,对蛋白酶不敏感,并保留了大蛋白和主蛋白的抗原性.由于S301蛋白具有易分泌、稳定性好、抗原性和大蛋白相同等特点,它很可能成为新一代的防治肝炎的基因工程疫苗.     

膀胱癌分子标志物基质金属蛋白酶1的可溶性表达和尿液中的活性分析

通过分离人胚胎肾细胞(HEK293)中基质金属蛋白酶1(MMPl)基因序列,利用基因工程技术在大肠杆菌中表达并纯化了包涵体复性的MMP1;采用融合表达硫氧还蛋白(Thioredoxin,TrxA)的方法获得了可溶性的MMPl-TrxA复合蛋白,在TrxA蛋白和MMP1活性中心之间引入了一个肠激酶切割位点,通过酶切作用获得可溶性MMP1.明胶酶谱分析法对体外表达的MMP1和体内(尿液中)MMP1进行了分析比较.结果表明,TrxA蛋白能够显著提高MMP1的可溶性,且可溶性MMP1的明胶降解活性是复性的MMP1降解活性的1.54倍,与尿液中的MMP1的明胶酶降解活性相当.因此,明胶酶谱法是一种有效的、高灵敏的MMP1检测方法,所表达的可溶性MMP1为小分子探针筛选提供了更可靠的分子靶点.     

催化RNA切割反应的苏糖核酸酶的表征及在切割microRNA中的应用

对一条催化RNA切割反应的苏糖核酸(TNA)酶6-29进行了系统的生物化学表征，探究了TNA酶6-29对RNA底物的序列要求，测定了TNA酶6-29催化反应的酶学常数，并进一步开发了TNA酶6-29在切割microRNA中的应用.研究结果表明，TNA酶6-29能够耐受底物结合臂和切割位点的多种变化，具有良好的底物序列通用性; TNA酶6-29能够在镁离子和锰离子等多种金属离子的存在下发挥催化活性，并且能够催化多个底物分子发生切割反应，具有酶的典型特征.基于TNA酶6-29良好的普适性，进一步展示了TNA酶6-29可以切割不同序列microRNA分子.本文结果表明，具有催化活性的TNA是一种有潜力的分子工具，有望进一步应用于疾病诊疗领域.     

颗粒性甲烷单加氧酶分离纯化方法的研究进展

颗粒性甲烷单加氧酶(pMMO)是甲烷氧化菌的特征酶之一,在生物催化方面具有广泛的应用前景,但由于其内膜蛋白的性质以及纯化过程中的不稳定性,使其生物化学性质、金属活性位点等方面仍存在许多未知和争议.着重总结了颗粒性甲烷单加氧酶的分离纯化方法,并对其活性以及与甲烷氧化菌素-Cu(methanobactin-Cu)和其他物质之间的作用关系进行了概述,以促进颗粒性甲烷单加氧酶的深入研究和应用.     

丝氨酸蛋白酶抑制剂超家族的一个新成员——痘苗病毒(天坛株)基因组HindⅢK片段编码的K1蛋白

本文测定了位于痘苗病毒(天坛株)基因组的Hind Ⅲ K片段左端,由1893个碱基所组成的开放读码框架K1(ORF K1)的核苷酸排列顺序,并利用微机对ORFK1所编码K1蛋白的序列进行了研究。结果发现,K1蛋白与丝氨酸蛋白酶抑制剂超家族的成员在蛋白质一级结构上有着显著的同源性,通过点阵分析和序列同源排列,证明K1蛋白是丝氨酸蛋白酶抑制剂超家族的一个新成员,它可能具有与丝氨酸蛋白酶抑制剂超家族其他成员相似的活性中心及其他特征序列。这一发现对于研究痘苗病毒的进化地位及所编码蛋白的功能均有一定意义。     

五配位磷化合物与生物化学

综述了五配位磷化合物与生物化学的关系, 发现当a-氨基酸的氨基接上磷酰基团以后, 化学性质发生了许多奇特的现象, 在室温下可发生自身活化现象而成肽、成酯、磷上酯交换及N→O磷酰基转位; 丝氨酸和苏氨酸与核苷缀合以后, 在弱碱性条件下能够对不同的碱基进行识别; 磷酰化组氨酸和丝组二肽可以在中性条件下切割核酸、蛋白、酯. 发现上述现象的发生都经历了一个五配位磷中间体, 认为五配位磷中间体是决定它们活性的结构因素.     

基于CRISPR/Cas的生物传感平台在分子诊断中的应用

簇状规则间隔短回文重复序列(CRISPR)和CRISPR相关蛋白(Cas)不仅在基因工程领域炙手可热,而且正发展成为核酸精准检测领域的新利器.得益于Cas蛋白对核酸序列的特异性识别以及部分Cas蛋白的附属切割活性,Ⅱ类CRISPR/Cas系统在体外诊断及现场即时检测领域独具优势.该综述简要介绍了CRISPR/Cas系统...     

丝组二肽所含基团在其切割DNA反应中的作用

近 2 0年来 ,人工核酸切割试剂的研究一直是化学、生物化学和分子生物学中最为活跃的前沿领域之一[1,2 ] .人工核酸切割试剂可以在足迹技术和核酸高级结构的研究中用作高分辨率的化学探针 ,还可以用于合成定点切割试剂[3] .后者又被称为人工工具酶 ,是一种非常重要的分子生物学工具 ,在疾病的基因治疗、反义 PCR技术等领域中都具有重要的应用 .人工核酸切割试剂的切割机理主要有自由基机理和磷酸酯水解机理两大类 .相对于自由基机理 ,水解机理具有许多优点 ,使得水解型切割试剂具有更为广泛的应用 .对于 DNA,目前文献报道的水解型人工切…     

具有DNA切割功能的新型多聚酰胺/丝组缀合物

为得到具有核酸切割功能的人工核酸酶, 设计合成了一种新型多聚酰胺/丝组缀合物, 并研究了其DNA切割活性. 合成的目标化合物在pH=6.0的BR缓冲溶液中对pBR322 DNA切割活性的初步实验结果表明, 于37 ℃保温6 h后, pBR322 DNA基本上被完全从Form Ⅰ切割为Form Ⅱ, 保温36 h后, pBR322 DNA几乎被切割完全.     

Application of Combinatorial Procedures in the Search for Serine-Protease-Like Activity with Focus on the Acyl Transfer Step

Recursive deconvolution of a 729-membered peptide library has identified three active sequences, in which both Ser and His are present in one of the two tripeptidic chains generated on a steroidal scaffold (see structural formula), for the cleavage of an activated p-nitrophenyl ester. This combinatorial approach aims at searching for serine-protease-like activity.     

Site-specifically Hydrolytic Cleavage of Oxidized Insulin B Chain With Cu(II) Ion

Selectively chemical cleavage of peptides and proteins is one of the most important reactions in both chemical and biochemical processes. Over the past decade, the interaction of palladium(II) complexes with methionine, cysteine and histidine-containing peptides and proteins and the hydrolytic cleavage of the corresponding amide bond by Pd(II) complexes have been extensively studied1-13. However, reports concerning the directly selective hydrolysis of peptides and proteins with other simple …     

Metal compound-mediated hydrolytic cleavage of oxidized insulin B chain:Regioselectivity and influence of peptide secondary structure

The interaction of oxidized insulin B chain(B)with cis-[Pd-(en)Cl2](en=ethylenediamine),cis-[Pd-(dtco-3-OH)Cl2](dtco-3-OH=dithiacyclooctan-3-ol)and CuCl2 was studied by electrospray inass spectrometry.It is discovered that the binding of Pd(Ⅱ)complexes and the sites of cleavage are highly dependent on the secondary structure and local environment of B.The hydrolytic cleavage of denatured B by Pd(Ⅱ)complexes was monitored by HPLC.The reaction is regioselective and follows first order kinetics with half-life of 4.8 days at 40℃.Two amide bonds,i.e.at Leu6-Cys7 and at Gly8-Ser9,which are close to the two potential Pd(Ⅱ)binding sites His5 and His10,are selectively cleaved.In the case of Cu(Ⅱ)ion as promoter,only one cleavage site was observed which is located at Gly8-Ser9 bond.These results provide improved understanding on the design of artificial metallopeptidase.     

Characterization of amino acids in silk sericin protein from Gonometa rufobrunnae by MEKC with phenyl isothiocyanate derivatization

An MEKC method was developed for the separation and characterization of phenyl-isothiocyanate (PITC)-labeled amino acids derived from Gonometa rufobrunnae silkworm after microdialysis sample cleanup. The influence of the buffer and SDS concentration on the resolution of the amino acids was investigated. A buffer system consisting of 25 mM phosphate, 10 mM borate buffer at pH 9.00, and 70 mM SDS showed the best results, with 13 PITC-amino acid derivatives being resolved out of 15 possible amino acids that were under study. Microdialysis sampling demonstrated its efficiency as a sample cleanup technique. Sericin protein from G. rufobrunnae was found to be characterized by at least 11 positively identified amino acids. These included His, Tyr, Ser, Ala, Phe, Lys, Gly, Arg, Cys, Glu, and Asp. Leu/Met and Val/Thr were coeluting pairs and hence could not be positively confirmed.     

Structure and function of vanadium haloperoxidases

A quantum mechanics/molecular mechanics study of the resting state of the vanadium dependent chloroperoxidase from fungi Curvularia inaequalis and of the early intermediates of the halide oxidation is reported. The investigation of different protonation states indicates that the enzyme likely consists of an anionic H2VO4- vanadate moiety where one hydroxo group is in axial position. The calculations suggest that the hydrogen peroxide binding may not involve an initial protonation of the vanadate cofactor. A low free energy reactive path is found where the hydrogen peroxide directly attacks the axial hydroxo group, resulting in the formation of an hydrogen peroxide intermediate. This intermediate is promptly protonated to yield a peroxo species. The free energy barrier for the formation of the peroxo species does not depend significantly upon the protonation state of the cofactor. The most likely protonation states of the peroxo cofactor are neutral forms HVO2(O2) with a hydroxo group either H-bonded to Ser402 or coordinated to Arg360. The peroxo cofactor is also coordinated to an axial water molecule, which could be important for the stability of the peroxovanadate/His496 adduct. Our calculations strongly suggest that the halide oxidation may take place with the preliminary formation of a peroxovanadate/halogen adduct. Subsequently, the halogen reacts with the peroxo moiety yielding a hypohalogen vanadate. The most reactive protonation state of peroxovanadate is the neutral HVO2(O2) with the hydroxo group H-bonded to Ser402. The important role of Lys353 in determining the catalytic activity is also confirmed.     

The inorganic perspective of nerve growth factor: interactions of Cu2+ and Zn2+ with the N-terminus fragment of nerve growth factor encompassing the recognition domain of the TrkA receptor

There is a significant overlap between brain areas with Zn(2+) and Cu(2+) pathological dys-homeostasis and those in which the nerve growth factor (NGF) performs its biological role. The protein NGF is necessary for the development and maintenance of the sympathetic and sensory nervous systems. Its flexible N-terminal region has been shown to be a critical domain for TrkA receptor binding and activation. Computational analyses show that Zn(2+) and Cu(2+) form pentacoordinate complexes involving both the His4 and His8 residues of the N-terminal domain of one monomeric unit and the His84 and Asp105 residues of the other monomeric unit of the NGF active dimer. To date, neither experimental data on the coordination features have been reported, nor has one of the hypotheses according to which Zn(2+) and Cu(2+) may have different binding environments or the Ser1 α-amino group could be involved in coordination been supported. The peptide fragment, encompassing the 1-14 sequence of the human NGF amino-terminal domain (NGF(1-14)), blocked at the C terminus, was synthesised and its Cu(2+) and Zn(2+) complexes characterized by means of potentiometric and spectroscopic (UV/Vis, CD, NMR, and EPR) techniques. The N-terminus-acetylated form of NGF(1-14) was also investigated to evaluate the involvement of the Ser1 α-amino group in metal-ion coordination. Our results demonstrate that the amino group is the first anchoring site for Cu(2+) and is involved in Zn(2+) coordination at physiological pH. Finally, a synergic proliferative activity of both NGF(1-14) and the whole protein on SHSY5Y neuroblastoma cell line was found after treatment in the presence of Cu(2+). This effect was not observed after treatment with the N-acetylated peptide fragment, demonstrating a functional involvement of the N-terminal amino group in metal binding and peptide activity.     

Fluorogenic peptide sequences--transformation of short peptides into fluorophores under ambient photooxidative conditions

Long-lived proteins are susceptible to nonenzymatic chemical reactions and the evolution of fluorescence; however, little is known about the sequence-dependence of fluorogenesis. We synthesized a library of over half a million octapeptides and exposed it to light and air in pH 7.4 buffer to identify fluorogenic peptides that evolve under mild oxidative conditions. The bead-based peptide library was composed of the general sequence H(2)N-Ala-(Xxx)(6)-Ala-resin, where Xxx was one of nine representative amino acids: Asp, Gly, His, Leu, Lys, Pro, Ser, Trp, and Tyr. Next, we selected five highly fluorescent beads from the library and subjected them to microsequencing, revealing the sequence of the unreacted peptide. All five of the fluorogenic sequences were ionic; lacked Tyr, His, and Leu; and most of the sequences contained only one Trp. We then synthesized the five soluble peptides corresponding to the fluorogenic peptide sequences and exposed them to photooxidative conditions. In general, the soluble peptides reacted slowly, generating nonfluorescent monooxygenated and dioxygenated products. However, one peptide (H(2)N-AlaLysProTrpGlyGlyAspAla-CONH(2)) evolved into a highly fluorescent photoproduct as well as a nonfluorescent monooxygenated photoproduct. The fluorescent photoproduct consisted of a 2-carboxy-quinolin-4-yl moiety fused to the N-terminus of GlyGlyAspAla. The formation of this photoproduct requires cleavage of the peptide backbone and a dramatic reorganization of tryptophan. This work demonstrates that sequencing unreacted peptide on beads can reveal sequences with unique nonenzymatic reactivity. The study also confirms that peptide fluorogenesis is dependent on sequence and not merely on the presence of tryptophan. The potential importance of fluorogenic peptide sequences is two-fold. First, fluorogenic sequences that arise through mutation could prove to be hot spots for human aging. Second, fluorogenic sequences, particularly those compatible with intracellular conditions, may serve as fluorescent tags for proteins or as fluorescent biomaterials.     

Regioselective cleavage of myoglobin with copper(II) compounds at neutral pH

Selective hydrolytic cleavage of myoglobin was studied with CuCl2, Cu(ClO4)2, Cu(AC)2, and binuclear Cu(II) complexes of 3,6,9,16,19,22-hexaaza-6,19-bis (2-hydroxyethyl)-tricyclo- [22,2,2,2(11,14)]-triaconta-1,11,13,24,27,29-hexaene (1) and 3,6,9,16,19,22-hexaaza-tricyclo-[22,2,2,2(11,14)]-triaconta- 1,11,13,24,27,29-hexaene (2). The sites of cleavage were precisely determined by LC-ESIMS and further confirmed by an MS/MS method through fragmentation from both the N-terminal and C-terminal. The peptide bonds of Gln91-Ser92 and Ala94-Thr95 were remarkably cleaved by Cu(II) anchored to the side chain of the His93 residue. The data presented in this study show that Cu(II)-mediated cleavage of myoglobin is able to proceed at neutral pH, more selectively than Pd(II)-mediated cleavage, and buffer solution of phosphate and NH4HCO3 accelerates the cleavage reaction.