计算机辅助的羧肽酶法测定多肽羧端顺序

在初步用计算机辅助的羧肽酶法测定了天花粉蛋白C-端顺序的基础上, 进一步设计了两个计算机程序-DPS程序和CPA程序. 用合成小肽和天然的肽对这两个计算机程序进行模型实验证明, 运用这两个程序能分别满意地从羧肽酶的酶解动力学曲线中获得重要的C-端顺序信息, 并测定了天花粉蛋白分子中未知肽段CB-3的C-端顺序为: -SerAlaSerAlaLeuHserOH, 这一顺序后来已经其他实验结果所证实. 本法不仅使C-端顺序测定延长至七个氨基酸, 而且还基本上解决了多肽或蛋白质含有多种多次重复氨基酸残基的C-端顺序测定.     

天花粉蛋白一级结构的修正及不同产地天花粉蛋白的研究

胰蛋白酶酶解天花粉蛋白, 用高效液相色谱分离酶解肽段, 用顺序仪测定其有关肽段的顺序。用羧肽酶A, B, Y测定了天花粉蛋白C-端和天花粉蛋白溴化氰降解肽CB1的C-端顺序, 修正了我们1985年测定的天花粉蛋白一级结构, 证明天花粉蛋白由246(7)氨基酸残基所组成, 除C-端微观不均一外, 与Collins结果一致。同时比较了芜湖产天花粉蛋白一级结构与平湖产的天花粉蛋白一级结构, 没有发现两者的一级结构有差别。     

天花粉蛋白化学 Ⅳ.天花粉蛋白的基本一级结构

前文报道从我国民间用于引产的中草药天花粉中提取到活性组分结晶天花粉蛋白和它的物理化学性质,N-端氨基酸顺序的测定及其溴化氰降解碎片CBa的顺序分析. 天花粉蛋白是一个由224个氨基酸残基组成的单一肽链的简单蛋白质,其N-末端残基为Asp,C-端顺序经羧肽酶A测定,并结合其水解动力学的计算机拟合为     

栝楼蛋白 2: 栝楼蛋白部分化学结构的初步测定

栝楼蛋白(Trichobitacin)是从栝楼(Trichosanthes kirilowiiMaxim, Cucurbitaceae)中新发现的核糖体失活蛋白, 分子量为27,228; pI为9.6。应用基质辅助的激光解析飞行时间质谱(MALDI-TOF-MS)和快原子轰击质谱法(FAB-MS)分别测定胰蛋白酶酶解栝楼蛋白和天花粉蛋白(Trichosanthin)的混合肽质谱, 通过比较发现了一些分子量相同的肽。由于这两种蛋白质都来源于栝楼块根, 同源性比较强, 所以这些肽序列在两种蛋白质中基本一样; 再结合蛋白N-端自动顺序仪测定栝楼蛋白N-端的结果, 确定了栝楼蛋白N-端38个氨基酸的顺序, 栝楼蛋白经胰蛋白酶酶解后所得肽段用HPLC分离纯化, 再用蛋白质自动顺序仪, DABITC/PITC双偶合手工法和质谱法共确定了栝楼蛋白N-端, C-端等100多个氨基酸残基的序列。     

栝楼蛋白 2: 栝楼蛋白部分化学结构的初步测定

栝楼蛋白(Trichobitacin)是从栝楼(Trichosanthes kirilowiiMaxim, Cucurbitaceae)中新发现的核糖体失活蛋白, 分子量为27,228; pI为9.6。应用基质辅助的激光解析飞行时间质谱(MALDI-TOF-MS)和快原子轰击质谱法(FAB-MS)分别测定胰蛋白酶酶解栝楼蛋白和天花粉蛋白(Trichosanthin)的混合肽质谱, 通过比较发现了一些分子量相同的肽。由于这两种蛋白质都来源于栝楼块根, 同源性比较强, 所以这些肽序列在两种蛋白质中基本一样; 再结合蛋白N-端自动顺序仪测定栝楼蛋白N-端的结果, 确定了栝楼蛋白N-端38个氨基酸的顺序, 栝楼蛋白经胰蛋白酶酶解后所得肽段用HPLC分离纯化, 再用蛋白质自动顺序仪, DABITC/PITC双偶合手工法和质谱法共确定了栝楼蛋白N-端, C-端等100多个氨基酸残基的序列。     

天花粉蛋白的C端测定

天花粉蛋白(trichosanthin)是从葫芦科植物(Culurbitaceae)括楼(trichosantheskerilowii Maxim)的块根中提取的一种植物性蛋白质。该蛋白质有中期妊娠引产、抗早孕和治疗其它有关妇产科疾病的效力。根据已经测定的结果,该蛋白质系由19种约219个氨基酸组成,估计其分子量为24000。本项研究的主要目的是测定天花粉蛋白的C端和C端的部分氨基酸顺序。     

计算机辅助的羧肽酶法测定多肽羧端顺序的研究

作者建立了计算机辅助的羧肽酶法,它能测定蛋白质和多肽的羧端顺序,包括含有重复释放氨基酸的羧端顺序。     

苦瓜子蛋白的分离纯化及真性质研究

从苦瓜种子的粗提物苦瓜子蛋白丙酮分级沉淀干粉中,用CM-Spehadex C-50和SephadexG-75分离得到了两个核糖体失活蛋白,α-苦瓜子蛋白(C-momorcharin,α-MMC和β-苦瓜子蛋白(β-momorcharin,β-MMC),其等电点分别为9.10(α-MMC),9.32(β-MMC).用ESI-MS和MALDI-TOF-MS测定它们的分子量,分别为28625(α-MMC),29076(β- MMC)(+Na,29099);,28795(α-MMC),29074.7(β-MMC).它们都是糖蛋白,其生物活性的分析测定表明,都属于RNA N-糖苷酶,本文重点对β-苦瓜子蛋白的分离纯化及其性质进行详细报道,并对其N-端部分的氨基酸顺序进行了测定.     

天花粉蛋白的化学 Ⅲ.溴化氰降解片段CBa的氨基酸顺序

前文已初步报道了天花粉蛋白的理化性质和N-端的部分氨基酸顺序.结晶天花粉蛋白经琥珀酸酐处理所得的琥珀酰天花粉蛋白,在88％甲酸中经溴化氰降解后的产物通过Sephadex G-75凝胶柱层析,可分得6个峰(见图1).     

八棱丝瓜蛋白1的二级结构及其生物活性

测定了八棱丝瓜蛋白1的N端顺序为Asp-Val-Ser-Phe-Ser-,用CD谱测定了八棱丝瓜蛋白 1的α螺旋,β-折叠和无规卷曲含量分别为37.1%,33.4%,29.5%。实验表明,八棱丝瓜蛋白 1具有RNA N-糖苷酶活性,体外抑制肿瘤细胞生长活性表明其对肿瘤细胞株B16,MGC,Bel的半数抑制浓度分别为1.78×10-7mol/L,2.11×10-7mol/L和4.21×10-7mol/L。并在N端顺序,二级结构和生物活性方面对八棱丝瓜蛋白 1和天花粉蛋白进行了比较。     

C-Terminal sequencing of trichosanthin

Preliminary identification of C-terminus of trichosanthin by chemical and enzymic methods, such as hydrazinolysis, thiohydantoin reaction and carboxypeptidase hydrolysis, showed that there may be the possible presence of more than one terminus, i.e., Met and Ala but complicated by side reactions. A computer-assisted carboxypeptidase method was first introduced by the authors to determine the C-terminal sequence of trichosanthin, and showed that trichosanthin is heterogeneous at its C-terminus and has two C-terminal sequences determined as -Arg-Asn-Asn-Met-OH and -Arg-Asn-Asn-Met-Ala-OH respectively. These results have been later unambiguously confirmed by the results from other experiments through the identification of the free alanine always present in the CNBr degradation products of trichosanthin, and the actual separation of two fragments from the finger prints as well as from the HPLC fractions of the trypsin digest of this protein. All shows that their amino acid sequences, determined by manual DABITC/PITC technique, agree well with those of the two C-terminal sequences determined by the computer-carboxy peptidase method.     

A strategy for rapid and efficient sequencing of Lys-C peptides by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry post-source decay

A modification procedure for Lys-C peptides is described which simplifies the correct assignment of the amino acid sequence. Release of the C-terminal lysine from Lys-C peptides by carboxypeptidase B and subsequent N-terminal acetylation of the resulting peptides leads to predictable shifts of the C- and N-terminal fragment ions in Matrix-assisted laser desorption/ionisation time-of-flight post-source decay mass spectra and facilitates the correct assignment of mostly complete amino acid sequences for oligopeptides. The derived sequences of peptides from unknown proteins were used to search in databases for homologous protein sequences. Our method was applied to an unknown protein isolated from eggs of Drosophila melanogaster, resulting in the identification of a peptidyl prolyl cis-trans-isomerase.     

Applications of gas-liquid chromatography in protein chemistry. Determination of C-terminal sequences on nanomolar amounts of proteins.

A method for the determination of C-terminal amino acids and C-terminal amino acid sequences in nanomolar amounts of proteins is described, based on carboxypeptidase A digestion of the protein, followed by removal of the partially digested protein and quantitative gas-liquid chromatographic determination of the amino acids released after known time intervals. Sequences deduced from the kinetics of release of specific amino acids are compared with the known C-terminal sequences of well-characterized proteins.     

Liquid chromatographic study of the enzymatic degradation of endomorphins, with identification by electrospray ionization mass spectrometry.

The recently discovered native endomorphins play an important role in opioid analgesia, but their metabolic fate in the organism remains relatively little known. This paper describes the application of high-performance liquid chromatography combined with electrospray ionization mass spectrometry to identify the degradation products resulting from the incubation of endomorphins with proteolytic enzymes. The native endomorphin-1, H-Tyr-Pro-Trp-Phe-NH2 (1), and endomorphin-2, H-Tyr-Pro-Phe-Phe-NH2 (2), and an analog of endomorphin-2, H-Tyr-Pro-Phe-Phe-OH (3), were synthetized, and the levels of their resistance against carboxypeptidase A, carboxypeptidase Y, aminopeptidase M and proteinase A were determined. The patterns of peptide metabolites identified by this method indicated that carboxypeptidase Y first hydrolyzes the C-terminal amide group to a carboxy group, and then splits the peptides at the Trp3-Phe4 or Phe3-Phe4 bond. The remaining fragment peptides are stable against the enzymes investigated. Carboxypeptidase A degrades only analog 3 at the Phe3-Phe4 bond. Aminopeptidase M cleaves the peptides at the Pro2-Trp3 or Pro2-Phe3 bond. The C-terminal fragments hydrolyze further, giving amino acids and Phe-NH2-s while the N-terminal part displays a resistance to further aminopeptidase M digestion. Proteinase A exhibits a similar effect to carboxypeptidase Y: the C-terminal amide group is first converted to a carboxy group, and one amino acid is then split off from the C-terminal side.     

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.     

A novel variant of human interferon alpha 1 gene.

A 520-base pair human IFN-alpha gene was isolated by PCR method twice from chromosome DNA of a Chinese (Han Nationality) fetal liver. The nucleotide sequences were determined. These two separately amplified DNA fragments shared the completely identical nucleotide sequence but possessed C and G at positions 410 and 541, respectively, which differ from those of IFN-alpha 1 and IFN-alpha D previously described. Therefore the deduced amino acid sequence would have an Ala at position 114 and a Val at position 158. At all other sites it has the same amino acids as those in IFN-alpha 1 and IFN-alpha D. We recommend that IFN-alpha D gene, IFN-alpha I gene and IFN-alpha I/158V gene found in our laboratory, be named IFN-alpha 1a gene, IFN-alpha 1b gene and IFN-alpha 1c gene.     

Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes

Activation and reaction energies for four model systems capturing the essential physicochemical features of the hydrolysis of the peptide bond have been calculated at various level of theory, including the presumably accurate CCSD(T) calculations. The models studied covered a part of the spectrum encountered in biological systems: the hydrolysis in the absence of metal ions (represented by formamide and Ala–Ala) and the hydrolysis in the presence of one and two zinc(II) ions, mimicking the active sites of mono‐ and dizinc metallopeptidases, respectively (by using thermolysin and glutamate carboxypeptidase II as the model catalytic systems and formamide as the model substrate). The results obtained using CCSD(T)/def2‐TZVP and CCSD(T)/aug‐cc‐pVTZ calculations were used as the benchmark values to which the set of cheaper methods, such as (RI‐)DFT, (RI‐)MP2, and SCS‐MP2, were referenced. It was shown that deviations of 3–5 kcal mol^?1 (translating to 2–3 orders in reaction constants) with respect to the reference CCSD(T) barriers are frequently encountered for many correlated methods and most of studied DFT functionals. It has been concluded that from the set of wave‐function methods, both MP2 and SCS‐MP2 methods can be recommended for smaller models (measured by the mean absolute deviation of the activation barriers over the four systems studied), whereas among the popular DFT functionals, B3LYP and especially M06‐2X are likely to be reasonable choices for calculating the activation barriers of zinc metallopeptidases. Finally, with the model of glutamate carboxypeptidase II, issues related to the convergence of the calculated barriers with the size of the model system used as the representative of the enzyme active site were addressed. The intricacies related to system truncation are demonstrated, and suggest that the correlated wave‐function methods may suffer from problems, such as intramolecular BSSE, which make their usage for the larger system questionable. Altogether, the presented data should contribute to efforts to understand enzymatic catalysis more deeply and to gain control of the accuracy and deficiencies of the available theoretical methods and computational approaches.     

溴化氰裂解结合电喷雾串联质谱测定电泳分离蛋白的C端序列

C端测序是蛋白质及多肽一级结构确认的重要组成部分,也是重组蛋白药物质量控制的重要依据。建立了溴化氰裂解结合电喷雾串联质谱测定蛋白质C端序列的方法,并应用于重组人肿瘤坏死因子受体和纽兰格林的C端测序。首先根据待测蛋白序列进行溴化氰理论裂解,如果C-端肽段理论分子量在500~5000U之间,则将待测样品进行SDS-PAGE分离,考马斯亮兰染色,然后进行胶内溴化氰裂解,最后应用基质辅助激光解吸/电离飞行时间质谱(MALDI-TOF-MS)测定C-端肽段的分子量,电喷雾串联质谱对C端肽段进行测序。应用本方法分别测定了这两个蛋白质C端19个和11个氨基酸残基序列。研究结果表明:本方法灵敏、有效、实用性较强,可适用于部分重组蛋白药物的质量控制和蛋白质的结构确证,是对目前蛋白质C端测序方法的有效补充。     

三七水煎液中还原型谷胱甘肽及腺嘌呤的分离与鉴定

三七经水煎提取,阴、阳离子交换树脂分离以及RP-HPLC分离获得多种含肽类化合物组分,采用游离及酸水解后氨基酸组成及含量对照分析的方法预示了提取液中肽类化合物的存在,经氨基酸组成分析、聚丙烯酰胺薄膜双向层析、羧肽酶C-末端序列分析、质谱测定等方法分析,将YN-3H12组分鉴定为还原型谷胱甘肽,YN-3H11组分鉴定为腺嘌呤,本研究方法可为植物中水溶性肽类化合物等活性成分的研究提供参考。