蛋白激酶与植物逆境信号传递途径

蛋白质的可逆磷酸化是细胞信号识别与转导的重要环节,蛋白激酶主要催化蛋白质的磷酸化作用,植物中已发现并分离了大量蛋白激酶及其基因,它们介导了植物激素和胞外环境信号等引起的多种生理生化反应。文章着重介绍分裂原激活蛋白激酶（MAPK）、钙依赖而钙调素不依赖的蛋白激酶（CDPK）、受体蛋白激酶（RPK）、核糖体蛋白激酶和转录调控蛋白激酶等多种蛋白激酶在植物逆境信号识别与转导中的作用。     

蛋白激酶D的生物学功能研究进展

蛋白激酶D(protein kinase D,PKD)属于钙/钙调素依赖性蛋白激酶家族中的丝/苏氨酸蛋白激酶家族,与其它蛋白激酶家族不同,蛋白激酶D的结构相对保守,但在很多方面都有重要作用。PKD对于细胞的增殖、凋亡有调节作用,在心血管、内分泌以及中枢神经系统中也有重要的生物学功能。本文就蛋白激酶D以上几方面的一些研究进展进行综述。     

植物和小麦蛋白激酶的研究现状

蛋白激酶是酶中的一个大家族,在诸如发育、自交不亲和、雄性不育、抗逆和抗病反应中起重要作用。植物,尤其是小麦的蛋白激酶研究远远落后于人类和动物。为了促进小麦蛋白激酶的研究,本文对植物和小麦蛋白激酶的研究现状进行了综述。     

蛋白激酶研究进展：Ⅰ.结构和分类

蛋白激酶含有２５０～３００个氨基酸残基构成的催化功能域,包括１２个功能亚域．这些氨基酸序列折叠成为一个核心催化结构．根据蛋白激酶功能域氨基酸序列比较分析可以找出各蛋白激酶在进化上的亲缘关系,这是蛋白激酶的分类基础．蛋白激酶可分为二大类,一类是丝氨酸／苏氨酸蛋白激酶,另一类是酪氨酸蛋白激酶．丝氨酸／苏氨酸蛋白激酶在进化上出现较早,可分为几个组,每个组又分为许多家族．酪氨酸蛋白激酶在进化上出现较晚,亲缘关系较紧密,同属于一个组,该组也分为许多家族．最近发现的许多双底物特异蛋白激酶,分散在丝氨酸／苏氨酸蛋白激酶的不同家族中．     

酪氨酸蛋白激酶的分离、鉴定及基本特性

自1979年发现动物细胞内存在有能使酪氨酸磷酸化的蛋白激酶以来,对酪氨酸蛋白激酶的研究工作有了很大进展,特别是发现癌细胞的增殖与酪氨酸蛋白激酶有关。本文对该蛋白激酶的分离、鉴定及基本特性作一综述。     

信号传导途径新热点：双重特异性蛋白激酶家族

信号传导途径新热点：双重特异性蛋白激酶家族按照传统,蛋白激酶分为两类,即丝氨酸／苏氨酸蛋白激酶与酪氨酸蛋白激酶。近来发现还存在着第三类蛋白激酶──双重特异性蛋白激酶（ｄｕａｌｓｐｅｃｉｆｉｃｉｔｙｋｉｎａｓｅ,ＤＳＫ）,它们在信号传导途径与细胞的生长...     

蛋白激酶CK2的研究进展

蛋白激酶CK2是一种真核细胞中普遍存在的信使非依赖性丝／苏氨酸蛋白激酶。近年来,对蛋白激酶CK2的研究也取得了一些重要进展,尤其是蛋白激酶CK2的结构及其作用底物,蛋白激酶CK2与肿瘤及细胞凋亡的关系,越来越引起人们的关注。     

苹果和葡萄果实发育过程中蛋白激酶特性的比较研究

在苹果 (MalusdomesticaL .Borkh .cv .RedStarking)和葡萄 (VitisviniferaL .×V .lubruscaL .cv .Kyoho)的不同发育阶段均检测到蛋白激酶活性 ,它们可被Ca2 强烈激活 ,表明依赖钙的蛋白激酶是苹果和葡萄果实中一类非常重要的蛋白激酶。钙调素 (CaM)对苹果和葡萄果实蛋白激酶没有激活作用 ,同时CaM拮抗剂calmidazolium、W7及三氟乙酸 (TFA)均可不同程度地抑制其活性 ,表明依赖钙的蛋白激酶中可能有含类似钙调素结构域的蛋白激酶(CDPK)的存在。在苹果和葡萄果实发育中 ,依赖钙的蛋白激酶无论在其活性变化还是特性上都存在着显著差异 :苹果果实发育的不同阶段依赖钙的蛋白激酶活性无明显变化 ,而葡萄果实在发育的第Ⅱ期蛋白激酶活性大大高于第Ⅰ、Ⅲ期 ;苹果果实依赖钙的蛋白激酶可被Mn2 强烈激活并对热敏感 ,而葡萄果实依赖钙的蛋白激酶却不受Mn2 及热处理的影响 ;此外 ,葡萄果实蛋白激酶活性不受磷脂酰丝氨酸 (PS)的影响 ,而苹果果实蛋白激酶可被PS激活 ,表明苹果果实中还可能有钙和磷脂激活的蛋白激酶即PKC的存在。苹果和葡萄果实发育中蛋白激酶种类、特性及其活性变化的不同 ,暗示了这两种果实发育调控的差异 ,也意味着苹果和葡萄果实发育调控可能与蛋白激酶密切相关。     

植物逆境胁迫相关蛋白激酶的研究进展

干旱、高盐、高温和低温等非生物胁迫及各种病虫害等生物胁迫严重影响植物的生长发育和作物产量.蛋白激酶主要通过激活不同的磷酸化途径介导外界环境信号的感知和传递,调控下游抗逆基因的转录表达,启动相应的生理生化等适应性反应来降低或消除危害.该文对近年来国内外有关与非生物胁迫和生物胁迫信号传导相关的受体蛋白激酶、促分裂原活化蛋白激酶、钙依赖而钙调素不依赖的蛋白激酶、蔗糖不发酵相关蛋白激酶和其它胁迫相关的植物蛋白激酶的研究进展进行综述,探索蛋白激酶介导的不同磷酸化途径应对逆境胁迫的信号传递网络,为进一步了解植物逆境分子应答机制提供依据.     

蛋白激酶在微血管通透性中的作用

微血管内皮细胞层是一层半选择通透性屏障,可以调节血液中的液体、溶质和血浆蛋白进入组织间隙。在炎症刺激作用下,可通过旁细胞途径和跨细胞途径引起内皮通透性上升。旁细胞通路主要由内皮细胞间的紧密连接、黏附连接和细胞与外基质的黏着斑组成。炎症介质,如脂多糖和肿瘤坏死因子α可激活多种蛋白激酶。活化的蛋白激酶主要包括Rho相关的卷曲蛋白激酶、肌球蛋白轻链激酶、蛋白激酶C、酪氨酸激酶和丝裂原活化蛋白激酶等,参与引发内皮屏障生化和结构改变,旁细胞通路开放,导致通透性上升。该文对上述蛋白激酶在微血管通透性中作用机制的研究进展进行综述。     

Protein microarrays and their applications

In recent years, the importance of proteomic works, such as protein expression, detection and identification, has grown in the fields of proteomic and diagnostic research. This is because complete genome sequences of humans, and other organisms, progress as cellular processing and controlling are performed by proteins as well as DNA or RNA. However, conventional protein analyses are time-consuming; therefore, high throughput protein analysis methods, which allow fast, direct and quantitative detection, are needed. These are so-called protein microarrays or protein chips, which have been developed to fulfill the need for high-throughput protein analyses. Although protein arrays are still in their infancy, technical development in immobilizing proteins in their native conformation on arrays, and the development of more sensitive detection methods, will facilitate the rapid deployment of protein arrays as high-throughput protein assay tools in proteomics and diagnostics. This review summarizes the basic technologies that are needed in the fabrication of protein arrays and their recent applications.     

Biochemical basis of the temperature-inducible constitutive protease activity of the RecA441 protein of Escherichia coli

We compared the biochemical properties of the RecA441 protein to those of the wild-type RecA protein in an effort to account for the constitutive protease activity observed in recA441 strains. The two RecA proteins have similar properties in the absence of single-stranded DNA binding protein (SSB protein), and the differences that do exist shed little light on the temperature-inducible phenotype observed in recA441 strains. In contrast, several biochemical differences are apparent when the two proteins are compared in the presence of SSB protein, and these are conducive to a hypothesis that explains the temperature-sensitive behavior observed in these strains. We find that both the single-stranded DNA (ssDNA)-dependent ATPase and LexA-protease activities of RecA441 protein are more resistant to inhibition by SSB protein than are the activities of the wild-type protein. Additionally, the RecA441 protein is more capable of using ssDNA that has been precoated with SSB protein as a substrate for ATPase and protease activities, implying that RecA441 protein is more proficient at displacing SSB protein from ssDNA. The enhanced SSB protein displacement ability of the RecA441 protein is dependent on elevated temperature. These observations are consistent with the hypothesis that the RecA441 protein competes more efficiently with SSB protein for limited ssDNA sites and can be activated to cleave repressors at elevated temperature by displacing SSB protein from the limited ssDNA that occurs naturally in Escherichia coli. Neither the ssDNA binding characteristics of the RecA441 protein nor the rate at which it transfers from one DNA molecule to another provides an explanation for its enhanced activities, leading us to conclude that kinetics of RecA441 protein association with DNA may be responsible for the properties of the RecA441 protein.     

Protein accumulation in aleurone cells,sub-aleurone cells and the center starch endosperm of cereals

There are mainly three endosperm storage tissues in the cereal endosperm: aleurone cells, sub-aleurone cells and the center starch endosperm. The protein accumulation is very different in the three endosperm storage tissues. The aleurone cells accumulate protein in aleurone granules. The sub-aleurone cells and the center starch endosperm accumulate protein in endoplasmic reticulum-derived protein bodies and vacuolar protein bodies. Proteins are deposited in different patterns within different endosperm storage tissues probably because of the special storage properties of these tissues. There are several special genes and other molecular factors to mediate the protein accumulation in these tissues. Different proteins have distinct functions in the protein body formation and the protein interactions determine protein body assembly. There are both cooperation and competition relationships between protein, starch and lipid in the cereal endosperm. This paper reviews the latest investigations on protein accumulation in aleurone cells, sub-aleurone cells and the center starch endosperm. Useful information will be supplied for future investigations on the cereal endosperm development.     

Solvent interaction analysis as a proteomic approach to structure-based biomarker discovery and clinical diagnostics

Proteins have several measurable features in biological fluids that may change under pathological conditions. The current disease biomarker discovery is mostly based on protein concentration in the sample as the measurable feature. Changes in protein structures, such as post-translational modifications and in protein–partner interactions are known to accompany pathological processes. Changes in glycosylation profiles are well-established for many plasma proteins in various types of cancer and other diseases. The solvent interaction analysis method is based on protein partitioning in aqueous two-phase systems and is highly sensitive to changes in protein structure and protein–protein- and protein–partner interactions while independent of the protein concentration in the biological sample. It provides quantitative index: partition coefficient representing changes in protein structure and interactions with partners. The fundamentals of the method are presented with multiple examples of applications of the method to discover and monitor structural protein biomarkers as disease-specific diagnostic indicators.     

Diversity of protein inclusion bodies and identification of mosquitocidal protein in Bacillus thuringiensis subsp. israelensis

Bacillus thuringiensis subsp. israelensis produces, during sporulation, protein inclusion bodies of wide ranging sizes, all of which are toxic to mosquitoes. Two proteins are present in the smallest protein bodies (less than 0.2 micron dia.), but the number of proteins increases with increasing size of protein bodies. The largest bodies (greater than 1.5 micron dia.) contain seven proteins. All of the proteins are synthesized at different times during sporulation and are added to developing protein bodies in a stepwise manner. The protein component responsible for mosquitocidal activity is a 65,000-dalton protein, that is present in all of the protein bodies.     

Construction of protein binding sites in scaffold structures

We have developed a strategy for grafting a protein-protein interface based on the known crystal structure of a native ligand and receptor proteins in a complex. The key interaction residues at the ligand protein binding interface are transferred onto a scaffold protein so that the mutated scaffold protein will bind the receptor protein in the same manner as the ligand protein. First, our method identifies key residues and atoms in the ligand protein, which strongly interact with the receptor protein. Second, this method searches the scaffold protein for combinations of candidate residues, among which the distance between any two candidate residues is similar to that between relevant key interaction residues in the ligand protein. These candidate residues are mutated to key interaction residues in the ligand protein respectively. The scaffold protein is superposed onto the ligand protein based upon the coordinates of corresponding atoms, which are assumed to strongly interact with the receptor protein. Complementarity between scaffold and receptor proteins is evaluated. Scaffold proteins with a low superposing rms difference and high complementary score are accepted for further analysis. Then, the relative position of the scaffold protein is adjusted so that the interfaces between the scaffold and receptor proteins have a reasonable packing density. Other mutations are also considered to reduce the desolvation energy or bad steric contacts. Finally, the scaffold protein is cominimized with the receptor protein and evaluated. To test the method, the binding interface of barstar, the inhibitor of barnase, was grafted onto small proteins. Four scaffold proteins with high complementary scores are accepted.     

Protein complex prediction: A survey

Protein complexes are one of the most important functional units for deriving biological processes within the cell. Experimental methods have provided valuable data to infer protein complexes. However, these methods have inherent limitations. Considering these limitations, many computational methods have been proposed to predict protein complexes, in the last decade. Almost all of these in-silico methods predict protein complexes from the ever-increasing protein–protein interaction (PPI) data. These computational approaches usually use the PPI data in the format of a huge protein–protein interaction network (PPIN) as input and output various sub-networks of the given PPIN as the predicted protein complexes. Some of these methods have already reached a promising efficiency in protein complex detection. Nonetheless, there are challenges in prediction of other types of protein complexes, specially sparse and small ones. New methods should further incorporate the knowledge of biological properties of proteins to improve the performance. Additionally, there are several challenges that should be considered more effectively in designing the new complex prediction algorithms in the future. This article not only reviews the history of computational protein complex prediction but also provides new insight for improvement of new methodologies. In this article, most important computational methods for protein complex prediction are evaluated and compared. In addition, some of the challenges in the reconstruction of the protein complexes are discussed. Finally, various tools for protein complex prediction and PPIN analysis as well as the current high-throughput databases are reviewed.     

Conformational changes in bacteriophage P22 scaffolding protein induced by interaction with coat protein

Many prokaryotic and eukaryotic double-stranded DNA viruses use a scaffolding protein to assemble their capsid. Assembly of the double-stranded DNA bacteriophage P22 procapsids requires the interaction of 415 molecules of coat protein and 60-300 molecules of scaffolding protein. Although the 303-amino-acid scaffolding protein is essential for proper assembly of procapsids, little is known about its structure beyond an NMR structure of the extreme C-terminus, which is known to interact with coat protein. Deletion mutagenesis indicates that other regions of scaffolding protein are involved in interactions with coat protein and other capsid proteins. Single-cysteine and double-cysteine variants of scaffolding protein were generated for use in fluorescence resonance energy transfer and cross-linking experiments designed to probe the conformation of scaffolding protein in solution and within procapsids. We showed that the N-terminus and the C-terminus are proximate in solution, and that the middle of the protein is near the N-terminus but not accessible to the C-terminus. In procapsids, the N-terminus was no longer accessible to the C-terminus, indicating that there is a conformational change in scaffolding protein upon assembly. In addition, our data are consistent with a model where scaffolding protein dimers are positioned parallel with one another with the associated C-termini.     

Regulation of protein accumulation in cultured cells.

1. A technique is described whereby protein synthesis, protein breakdown and net protein accumulation are measured separately in monolayer cultures of mammalian cells. All rates are expressed as microgram of protein per 18 h incubation. 2. Under most incubation conditions with either L6 rat myoblasts or T47D human breast carcinoma cells the rates of protein accumulation, determined directly, agreed with the rates obtained by subtracting protein breakdown from protein synthesis. 3. Foetal calf serum, human and bovine colostrum, human milk and insulin increased protein accumulation in both cell lines, mainly as a consequence of effects on protein synthesis. 4. NH4Cl, in addition to inhibiting protein breakdown in both cell lines in the presence and in the absence of serum, stimulated protein synthesis in L6 myoblasts. 5. Leupeptin slightly inhibited protein breakdown without affecting protein-synthesis rates. 6. Cycloheximide almost completely inhibited protein synthesis, but restricted the net loss of cell proteins under most conditions because protein-breakdown rates were also decreased. 7. The assumptions, limitations and potential application of this technique for evaluating changes in protein turnover are described.     

Cyclic Nucleotide-Dependent Protein Kinases and Some Major Substrates in the Rat Cerebellum After Neonatal X-Irradiation

The levels of cAMP-dependent protein kinase (type I), or cGMP-dependent protein kinase, or protein I, and of a 23,000 MW substrate for the cGMP-dependent protein kinase were measured in cerebella from normal rats and in the cerebella from rats in which a selective loss of interneurons in the cerebellar cortex had been produced by X-irradiation. A decrease was observed in the concentrations of cAMP-dependent protein kinase and of protein I, whereas an increase was observed in the concentrations of cGMP-dependent protein kinase and of the 23,000 MW substrate. The data, taken together with the results of other studies, support the interpretation that cAMP-dependent protein kinase and protein I are distributed throughout the cerebellum, but that cGMP-dependent protein kinase and the 23,000 MW substrate are highly concentrated in Purkinje cells.