植物水溶性蔗糖合成酶生物信息学分析初探

用生物信息学方法对已在GenBank上注册的黑麦草、绿竹、菜豆、马铃薯、颤杨等植物水溶性蔗糖合成酶基因的核苷酸序列以及推导的氨基酸序列、组成成分、氨基酸翻译后修饰、导肽、跨膜拓朴结构域、疏水性／亲水性、蛋白质二级结构以及功能结构域等进行分析预测和推断的结果表明,这些植物的水溶性蔗糖合成酶位于线粒体中,是非跨膜的亲水性蛋白,α-螺旋和不规则卷曲是其蛋白质二级结构的主要结构元件,β-转角和延伸链散布于整个蛋白质中,包含2个功能结构域,即蔗糖合成功能域和糖基化合物转移功能域。     

植物蔗糖磷酸合成酶的生物信息学分析

本文采用生物信息学的方法对已在GenBank上注册的拟南芥、紫苜蓿、黑麦草、绿竹、文心兰等植物的蔗糖磷酸合成酶基因的核苷酸序列以及推导的氨基酸序列、组成成分、导肽、跨膜拓朴结构、疏水性／亲水性、蛋白质二级结构及功能域等进行分析预测和推断。结果表明：这些植物的蔗糖磷酸合成酶不存在导肽,为位于细胞质中非跨膜的亲水性不稳定蛋白,α-螺旋和不规则卷曲是其蛋白质二级结构的主要结构元件,β-转角和延伸链散布于整个蛋白质中,包含三个功能结构域。     

生物信息学对番茄LeNHX1基因的研究

应用生物信息学的方法和工具对番茄LeNHX1蛋白质的理化性质、跨膜区域、疏水性/亲水性、二级结构、结构功能域、功能分类和同源性进行分析.结果表明此蛋白为疏水性稳定蛋白,包含一个保守的氨氯吡嗪咪结合位点LFFIYVLPPI区域,相对分子量为59.0 kD,等电点为6.60,存在10个跨膜区域,蛋白质二级结构中的主要构成元件是α-螺旋和不规则卷曲,功能分类和蛋白质同源性分析表明番茄LeNHX1属于液泡膜Na+/H+反向转运蛋白.     

蓝藻磷酸烯醇式丙酮酸羧化酶的生物信息学分析

应用NCBI、Expasy等在线生物信息学网站对蓝藻磷酸烯醇式丙酮酸羧化酶(PEPC)与其他物种进行序列同源比对,分析相同的保守序列及催化活性位点,构建分子进化树;预测跨膜结构、疏水性/亲水性、二级结构、功能域和模体等.结果显示,蓝藻PEPC与高等植物、细菌、真核藻PEPC同源性都比较低(约为33%),但是它们含有两个类似的活性部位和相同的催化活性位点;该蛋白质是非跨膜的亲水性不稳定蛋白,二级结构以a-螺旋和无规则卷曲为主,舍有一个功能结构域,主要的功能是参与氨基酸的合成.     

番茄LeABI3基因的生物信息学分析

对所克隆到的番茄LeABI3基因测序结果进行序列分析,发现得到LeABI3基因的2种转录本.应用生物信息学的方法和工具对LeABI3蛋白质的理化性质、跨膜区域、疏水性/亲水性、二级结构、结构功能域和同源树进行分析,结果表明此蛋白是包含一个保守B3结构功能域的亲水性不稳定蛋白,相对分子量为65.4 kD,等电点为6.54,可能存在2个跨膜区域.蛋白质二级结构中的主要构成元件是α-螺旋和不规则卷曲,蛋白质同源分析发现番茄LeABI3和马铃薯vp1-ABI3类蛋白相似度最高,同源性为89%.     

人转录因子AP4的生物信息学分析

[目的]预测分析人转录因子激活增强子结合蛋白4(activating enhancer binding protein 4,AP4)的性质、结构和功能。[方法]采用生物信息学方法对人AP4蛋白的理化性质、物种间同源性、信号肽与跨膜区、亲水性、蛋白亚细胞定位、蛋白质二/三级结构、三级结构可靠性、蛋白质相互作用等方面进行预测和分析。[结果]人AP4蛋白全长338个氨基酸,理论等电点5.63,相对分子质量38.73 kDa。AP4在进化上较为保守,不含信号肽与跨膜区,属于亲水性蛋白质,94.1%可信度定位于细胞核。二级结构含10个α螺旋区,占全部氨基酸的54.14%,5个β折叠区,占7.99%,其余37.87%的氨基酸处于无规卷曲状态。三维建模结果可靠。预测到10个与AP4存在相互作用的蛋白。[结论]系统预测分析了人AP4蛋白的性质、结构和功能。     

植物萜类合成酶3-羟基-3-甲基戊二酰辅酶A还原酶的生物信息学分析

采用生物信息学的方法和工具对已在GenBank上注册的橡胶、烟草、辣椒、穿心莲等植物的萜类合成酶3-羟基-3-甲基戊二酰辅酶A还原酶的核酸及氨基酸序列进行分析,并对其组成成分、信号肽、跨膜拓朴结构域、疏水性/亲水性、蛋白质二级及三级结构、分子系统进化关系等进行预测和推断。结果表明该类酶基因的全长包括5′、3′非翻译区和一个开放阅读框,无信号肽,是一个跨膜的亲水性蛋白,包括两个功能HMG-CoA结合motif及两个功能NADPH结合motif,α-螺旋和不规则盘绕是蛋白质二级结构最大量的结构元件,β-转角和延伸链散布于整个蛋白质中,蛋白质的功能域在空间布局上折叠成“V”形,“V”形的两臂由螺旋状的N结构域和S结构域构成,中间部分由L结构域构成。     

植物胚胎发育晚期丰富蛋白1组的结构与功能

植物胚胎发育晚期丰富蛋白（late embryogenesis abundant proteins,LEA）是植物胚胎发生后期种子中大量积累的一类蛋白质。根据蛋白质的氨基酸基序和保守结构特点,LEA蛋白一般分为6组,其中第1组LEA蛋白（LEA1）含有高度保守的20氨基酸基序。LEA1蛋白在水溶液中主要呈无规则结构,具高亲水性和热稳定性,与植物抗逆功能密切相关。本文就LEA1蛋白的功能和结构等方面的研究做一综述。     

人转录因子FoxM1B的生物信息学分析

目的:分析预测人转录因子FoxM1B启动子及蛋白结构和功能。方法:运用生物信息学软件对人FoxM1B基因的启动子区域及其蛋白的理化性质、跨膜区、信号肽和亲疏水性进行预测分析;利用软件模拟生成人FoxM1B蛋白质的三级结构图像,了解与其相互作用的蛋白网络。结果:采用生物信息学软件预测出人FoxM1B基因5'侧翼存在转录起始位点及启动子,且启动子(1300~1900bp)的侧翼有1个CpG岛。人FoxM1B蛋白是亲水性蛋白,且不包含跨膜结构域和信号肽;在二级结构中,无规卷曲是其主要折叠方式,模拟生成蛋白质三级结构图像与二级结构预测一致。人FoxM1B蛋白与CCNB1、CCNA2、MYBL2、CDK1和PLK1等蛋白存在相互作用,可能通过这些蛋白参与细胞周期和DNA损伤修复过程。结论:对人FoxM1B基因及其编码蛋白的性质、结构和互作蛋白等进行了预测分析,为后续实验研究提供了依据和线索,奠定了重要的信息基础。     

蛋白质可逆磷酸化调节植物细胞离子跨膜运动研究进展

蛋白激酶和蛋白磷酸酶催化的可逆磷酸化是植物细胞中多种信号转导途径中重要的组成因子.本文对蛋白质可逆磷酸化通过调节多种离子跨膜运动而参与植物细胞激发子信号途径、毒性物质诱导的钙离子内流、盐胁迫适应、气孔运动以及蛋白质可逆磷酸化参与胞外与胞内之间Ca2 状况信息传递,调节花粉管顶端Ca2 离子通道活性进行综述,以揭示蛋白质可逆磷酸化在植物细胞离子跨膜运动中的调控作用,为蛋白质可逆磷酸化调节植物生长发育、响应逆境胁迫等机理的研究提供参考.     

植物类金属硫蛋白半胱氨酸富含区结构的建模

详细了解蛋白质的三级结构信息有助于理解其生物学功能.随着植物基因组研究的进展,已发现了50多个植物类金属硫蛋白(Metallothionein-Like, MT-L)基因.但至今只有少数几个MT-L蛋白得到了纯化,而其结构尚无报道,因此有必要建立分析这类蛋白结构特征的方法.本研究根据已知的哺乳动物MT的结构数据,分析得出了CXC、CXXC模式和金属-硫络合簇结构原子间的距离限制条件,并用距离几何算法计算得出预测蛋白可能的构象;然后通过统计分析筛选出目标函数值显著较小、构象能低的结构作为这些蛋白半胱氨酸富含区的预测结构,由此建成了适合于植物类金属硫蛋白半胱氨酸富含区的结构预测方法.从应用该方法正确地预测出了已知结构的蓝蟹MT的结构来看,该方法是可行的.并用该方法预测了油菜MT-L蛋白的半胱氨酸富含区的结构.     

植物类金属硫蛋白半胱氨酸富含区结构的建模

详细了解蛋白质的三级结构信息有助于理解其生物学功能。随着植物基因组研究的进展 ,已发现了 50多个植物类金属硫蛋白 (Metallothionein_Like ,MT_L)基因。但至今只有少数几个MT_L蛋白得到了纯化 ,而其结构尚无报道 ,因此有必要建立分析这类蛋白结构特征的方法。本研究根据已知的哺乳动物MT的结构数据 ,分析得出了CXC、CXXC模式和金属 硫络合簇结构原子间的距离限制条件 ,并用距离几何算法计算得出预测蛋白可能的构象 ;然后通过统计分析筛选出目标函数值显著较小、构象能低的结构作为这些蛋白半胱氨酸富含区的预测结构 ,由此建成了适合于植物类金属硫蛋白半胱氨酸富含区的结构预测方法。从应用该方法正确地预测出了已知结构的蓝蟹MT的结构来看 ,该方法是可行的。并用该方法预测了油菜MT_L蛋白的半胱氨酸富含区的结构。     

Cross-recognition of two middle T protein epitopes by immunodominant polyoma virus-specific CTL

We recently identified the immunodominant epitope for polyoma virus-specific CTL as the Dk-associated peptide MT389-397 derived from the middle T (MT) viral oncoprotein. Another Dk-restricted peptide corresponding to residues 236-244 of MT was recognized by nearly all MT389-397-reactive CTL clones, but required concentrations at least 2 logs higher to sensitize syngeneic target cells for lysis. Except for identity at the three putative Dk-peptide anchor residues, MT236-244 shares no homology with MT389-397. Using a novel europium-based class I MHC-peptide binding immunoassay, we determined that MT236-244 bound Dk 2-3 logs less well than MT389-397. Infection with a mutant polyoma virus whose MT is truncated just before the MT389-397 epitope or immunization with MT389-397 or MT236-244 peptides elicited CTL that recognized both MT389-397 and MT236-244. Importantly, infection with a polyoma virus lacking MT389-397 and mutated in an MT236-244 Dk anchor position induced polyoma virus-specific CTL recognizing neither MT389-397 nor MT236-244 epitopes. Despite predominant usage of the Vbeta6 gene segment, MT389-397/MT236-244 cross-reactive CTL clones possess diverse complementarity-determining region 3beta domains; this is functionally reflected in their heterogeneous recognition patterns of alanine-monosubstituted MT389-397 peptides. Using Dk/MT389-397 tetramers, we directly visualized MT236-244 peptide-induced TCR down-modulation of virtually all MT389-397-specific CD8+ T cells freshly explanted from polyoma-infected mice, suggesting that a single TCR recognizes both Dk-restricted epitopes. The availability of immunodominant epitope-specific CTL capable of recognizing a second epitope in MT, a viral protein essential for tumorigenesis, may serve to amplify the CTL response to the immunodominant epitope and prevent the emergence of immunodominant epitope-loss viruses and virus-induced tumors.     

Characterization of the role of the "MT-loop": an eight-amino acid insertion specific to progelatinase A (MMP2) activating membrane-type matrix metalloproteinases

Progelatinase A (proGLA) activation is thought to be initiated almost exclusively by the type I transmembrane members of the membrane type matrix metalloproteinase family (MT-MMP): MT1, -2, -3, and -5-MMP (MMP14, -15, -16, and -24). One difference between these enzymes and the other MMP family members is the insertion of eight amino acids between strands betaII and III in the catalytic domain. In MT1-MMP, the best characterized of these enzymes to date, these residues consist of (163)PYAYIREG(170). To investigate the role of this region of MT1-MMP on its catalytic activities, we have made a variety of mutations and deletions in both soluble and membrane-bound forms of the enzyme. Characterization of the activity of the soluble forms toward peptides and fibrinogen revealed that neither mutation nor deletion of residues 163-170 significantly impaired catalytic function, suggesting these residues have little influence on conformation of the active site cleft. Equally none of the mutants showed significant differences in K(I)(app) for the N-terminal inhibitory domain of TIMP2, again indicating that mutation or deletion of resides 163-170 has no major effect on the overall topology of the active site of MT1-MMP. However, characterization of the kinetics of activation of proGLA with and without its gelatin binding region by the mutants generated have shown that efficient activation of proGLA is, at least in part, through an interaction with residues 163-170 of MT1-MMP. The expression, localization, and processing from the 63- to the 60/45-kDa forms of wild-type and key mutant forms of MT1-MMP were also examined by transient transfection in Chinese hamster ovary cells, but no differences were observed. Processing and activation of proGLA was also examined in transiently transfected cells. All the mutants examined were able process proGLA but, as found with the soluble forms, were kinetically impaired when compared with wild-type MT1-MMP.     

Antigenic determinants on rat metallothionein: fine epitope mapping for a murine monoclonal antibody and rabbit polyclonal antisera.

In order to determine the epitope of metallothionein (MT) to a murine monoclonal antibody (MT 189-14-7) which had been produced by immunization with rat MT 2 (Kikuchi et al. (1988) Mol. Immunol. 25, 1033-1036), various lengths of synthetic oligopeptides were tested for their inhibitory activities in competitive radioimmunoassay (RIA). The amino-terminal acetylated pentapeptide, AcMDPNC, exhibited an inhibitory activity comparable to that of native MTs, whereas the acetylated tetrapeptide, AcMDPN, and the deacetylated heptapeptide, MDPNCSC, were much less inhibitory. The results suggest that the major part of the epitope structure of MT to the MT 189-14-7 monoclonal antibody is located within the amino-terminal acetylated pentapeptide, AcMDPNC. The specificities of polyclonal rabbit anti-MT antisera raised against the same immunogen were also determined by using various animal MTs and synthetic peptides as inhibitors in the RIA. Among three antisera tested, two reacted with several amino-terminal oligopeptides similarly to the MT 189-14-7 antibody. The major epitope structures to these polyclonal antibodies were shown to be located within the acetylated tetrapeptide, AcMDPN. Another antiserum contained at least two different populations of antibodies: one consisted of antibodies reactive with the amino-terminal synthetic peptides, while the other was not reactive with them. These results suggest that, in the rabbit also, the amino-terminal region common to various animal MTs can be an epitope to antibodies raised against rat MT, as shown in the mouse. Moreover, the results indicate that the synthetic amino-terminal peptides are useful for determination of the specificity of polyclonal rabbit anti-MT antibodies, which have been widely used for the quantification of MTs.     

Membrane type 4 matrix metalloproteinase (MMP17) has tumor necrosis factor-alpha convertase activity but does not activate pro-MMP2

Membrane type 4 matrix metalloproteinase (MT4-MMP) shows the least sequence homology to the other MT-MMPs, suggesting a distinct function for this protein. We have isolated a complete cDNA corresponding to the mouse homologue which includes the signal peptide and a complete pro-domain, features that were lacking from the human form originally isolated. Mouse MT4-MMP (mMT4-MMP) expressed in COS-7 cells is located at the cell surface but does not show ability to activate pro-MMP2. The pro-catalytic domain was expressed in Escherichia coli as insoluble inclusions and active enzyme recovered after refolding. Activity of the isolated catalytic domain against synthetic peptides commonly used for MMP enzyme assays could be inhibited by TIMP1, -2, and -3. The recombinant mMT4-MMP catalytic domain was also unable to activate pro-MMP2 and was very poor at hydrolyzing components of the extracellular matrix with the exception of fibrinogen and fibrin. mMT4-MMP was able to hydrolyze efficiently a peptide consisting of the pro-tumor necrosis factor alpha (TNFalpha) cleavage site, a glutathione S-transferase-pro-TNFalpha fusion protein, and was found to shed pro-TNFalpha when co-transfected in COS-7 cells. MT4-MMP was detected by Western blot in monocyte/macrophage cell lines which in combination with its fibrinolytic and TNFalpha-converting activity suggests a role in inflammation.     

The propeptide domain of membrane type 1-matrix metalloproteinase acts as an intramolecular chaperone when expressed in trans with the mature sequence in COS-1 cells

It has been assumed that cleavage of the N-terminal propeptide domain of membrane type-1 matrix metalloproteinase (MT1-MMP) is required for enzyme function. We recently demonstrated that the propeptide domain of MT1-MMP is not cleaved and actually is required for function of the membrane-bound enzyme in transfected COS-1 cells (Cao, J., Drews, M., Lee, H. M., Conner, C., Bahou, W. F., and Zucker, S. (1998) J. Biol. Chem. 273, 34745-34752). In this report, we have inserted the cDNA encoding the signal and propeptide sequences of MT1-MMP (MT(1-109)) and the cDNA encoding propeptide-deleted mature MT1-MMP (MT delta pro) in expression vectors that were then transfected into matrix metalloproteinase-deficient COS-1 cells. Co-expression of both the mature sequence and the prosequence of MT1-MMP as independent polypeptides (in trans) in COS-1 cells resulted in reconstitution of MT1-MMP function in terms of facilitating (125)I-labeled tissue inhibitor of metalloproteinase 2 binding to transfected cells and subsequent activation of progelatinase A. Transfection of cells with either cDNA alone resulted in non-functional cells. These results are consistent with the propeptide sequence of MT1-MMP functioning as an intramolecular chaperone involved in protein folding and trafficking to the cell surface.     

AtPNP-A is a systemically mobile natriuretic peptide immunoanalogue with a role in Arabidopsis thaliana cell volume regulation

Cellular and physiological evidence suggests the presence of a novel class of systemically mobile plant molecules that are recognized by antibodies against vertebrate atrial natriuretic peptides (ANPs). In order to characterize the function of these immunoanalogues we have expressed the full-length recombinant (AtPNP-A[1-126]) and demonstrate that this molecule induces osmoticum-dependent H(2)O uptake into protoplasts at nanomolar concentrations and thus affects cell volume. A similar response is also seen with a recombinant that does not contain the signal peptide (AtPNP-A[26-126]) as well as a short domain (AtPNP-A[33-66]) that shows homology to the vertebrate peptide. Taken together, these findings suggest that AtPNP-A has an important and systemic role in plant growth and homeostasis.     

Plant metallothionein domains: functional insight into physiological metal binding and protein folding

Plant metallothioneins (MTs) differ from animal MTs by a peculiar sequence organization consisting of two short cysteine-rich terminal domains linked by a long cysteine-devoid spacer. The role of the plant MT domains in the protein structure and functionality is largely unknown. Here, we investigate the separate domain contribution to the in vivo binding of Zn and Cu and to confer metal tolerance to CUP1-null yeast cells of a plant type 2 MT (QsMT). For this purpose, we obtained three recombinant peptides that, respectively, correspond to the single N-terminal (N25) and C-terminal (C18) cysteine-rich domains of QsMT, and a chimera in which the spacer is replaced with a four-glycine bridge (N25-C18). The metal-peptide preparations recovered from Zn- or Cu-enriched cultures were characterized by ESI-MS, ICP-OES and CD and UV-vis spectroscopy and data compared to full length QsMT. Results are consistent with QsMT giving rise to homometallic Zn- or Cu-MT complexes according to a hairpin model in which the two Cys-rich domains interact to form a cluster. In this model the spacer region does not contribute to the metal coordination. However, our data from Zn-QsMT (but not from Cu-QsMT) support a fold of the spacer involving some interaction with the metal core. On the other hand, results from functional complementation assays in endogenous MT-defective yeast cells suggest that the spacer region may play a role in Cu-QsMT stability or subcellular localization. As a whole, our results provide the first insight into the structure/function relationship of plant MTs using the analysis of the separate domain abilities to bind physiological metals.     

重组蛋白融合信号肽在大肠杆菌周质空间表达的研究进展

重组蛋白在大肠杆菌中表达时,往往面临着形成包涵体的问题,而重组蛋白若是分泌至周质空间则基本解决了这一问题,周质空间的周质蛋白不仅能帮助重组蛋白正确折叠还有利于二硫键的生成。信号肽是一段由15-30个氨基酸组成,被融合在重组蛋白N端的短肽,按照结构、功能的不同可以划分为N区、H区和C区,具有引导重组蛋白转运至细胞周质空间的作用。本文综述了信号肽的结构组成、作用机理和基本分泌途径,讨论了信号肽的高效转运和筛选方法,总结了在大肠杆菌中重组蛋白融合信号肽实现周质表达的新进展,并对未来高效信号肽选择方面的研究进行了探讨。