蛋白质如何"死亡"

2004年以色列科学家阿龙·切哈诺沃、阿夫拉姆·赫什科和美国科学家欧文·罗斯发现——泛素调节的蛋白质降解。该成果发现了蛋白质“死亡”的重要机理, 对人类疾病尤其是癌症的治疗有着十分深远的意义。     

非泛素依赖地降解蛋白质研究进展

如何识别和选择性降解蛋白质是细胞生命过程中非常重要的环节,泛素-蛋白酶体需能降解途径的发现,揭示了蛋白质在细胞内选择性降解的普遍方式,成为研究焦点.然而,很少关注蛋白酶体以非泛素依赖方式降解蛋白质的可能性.近年来,已发现不少蛋白质被蛋白酶体以非泛素依赖方式降解.该途径涉及降解某些短寿命的调节蛋白、错误折叠蛋白、衰老蛋白和氧化蛋白,以及新合成蛋白的"质量控制",并涉及病理过程如癌症、神经退行性疾病,所以具有非常重要的生理和病理作用.总结了近一二十年来发现的一些具有代表性的被蛋白酶体以非泛素依赖方式降解的蛋白质,并重点论述了其作用的分子机制,以期以点带面地展示这一领域的研究概况.     

泛素介导的蛋白质降解系统——从基础研究到临床应用

20世纪60～80年代,大多数生物科研人员都致力于核酸和遗传信息传递的研究。蛋白质降解被认为是非特异的过程,因此没有人感兴趣。泛素修饰的发现使蛋白质降解领域发生革命性的变化,人们逐渐认识到蛋白质降解是一个特异的受严格调控的过程。细胞内蛋白质降解事件的发生会调节许多生命过程,如细胞增殖、分化、衰老和死亡。细胞内蛋白质降解调控异常也会引发多种疾病,包括癌症和神经退行性疾病。人们对细胞内蛋白质降解的研究已经取得一定成果,但是还有很多问题没有解决,全面解读该过程还需要更多的努力和探索。     

蛋白质的选择性降解机制——2004年诺贝尔化学奖部分工作介绍

如何识别和选择性降解蛋白质是细胞生命过程中的重要环节.泛素-蛋白酶体需能降解途径的发现,揭示了蛋白质在细胞内选择性降解的普遍方式.对于需要清除的蛋白质,通过其赖氨酸残基侧链ε-氨基连接多聚泛素链（降解标签）,继而在蛋白酶体中被降解.这种选择性降解机制对于维持蛋白质在细胞内含量的动态平衡起到了关键性作用.     

PI3K信号通路通过Skp2、p27调节肝癌细胞的增殖

探讨磷脂酰肌醇3-激酶(PI3K)信号通路调节肝癌细胞增殖的机制.用LY294002特异性阻断PI3K信号通路后,人肝癌细胞(SMMC-7721)的增殖明显被抑制.RT-PCR及蛋白质印迹结果显示,LY294002增加了p27蛋白的表达,但不影响p27的mRNA表达.在LY294002处理的细胞中转入p27的RNAi质粒以干扰p27蛋白的表达后,肝癌细胞的增殖能力可部分恢复.放线菌酮(Chx)处理实验表明,阻断PI3K信号通路使p27蛋白的半衰期延长,稳定性增加.进一步研究发现,LY294002可抑制介导p27蛋白降解的关键分子Skp2的mRNA表达,还可缩短Skp2蛋白的半衰期,降低Skp2蛋白的稳定性.但在SMMC-7721中分别转染PI3K下游重要靶分子Akt的持续激活和失活突变体,却并不影响p27蛋白的表达.这些结果表明,PI3K信号通路在转录及翻译后水平调节Skp2的表达而影响p27蛋白的降解,从而调节肝癌细胞的增殖,但Akt并没有参与这种调节.     

斜纹夜蛾泛素基因的克隆及表达

泛素介导的蛋白质降解途径对脑内蛋白的选择性降解起着重要作用。设计一对简并引物,从斜纹夜娥(Spodoptera litura)细胞中克隆了泛素基因的编码区,CenBank登录号AF436066。序列分析表明,该编码区的长度为228bp,编码由76个氨基酸组成的、分子质量为8．56kD的蛋白,其等电点为6．56。同源性比较发现,斜纹夜峨泛素基因不仅与其它真核生物的泛素基因在氨基酸水平上具有96％以上的相似性,而且与斜纹夜蛾核多角体病毒(SpltMNPV)泛素基因的同源性为84％。RT—PCR分析发现,泛素基因在所检测的斜纹夜蛾幼虫多种组织,尤其是脂肪体中均有表达。采用构建的原核表达载体pQEUB,在大肠杆菌M15中诱导并高效表达出了带有His—tag的重组融合蛋白,薄层扫描分析得知靶蛋白约占总蛋白的37％。利用Ni—NTA亲和层析胶纯化得到重组融合蛋白,经SDS—PAGE鉴定为单一区带,为进一步研究S．litura泛素在SpltMNPV感染中的作用打下了基础。     

泛素—蛋白酶体途径的组成及其生物学作用

泛素－蛋白酶体途径是近20年来发现的一种高效蛋白分解途径,其生物学作用非常广泛。本文简要介绍泛素－蛋白酶体途径的组成,作用机制,泛素－蛋白酶体途径与骨骼肌蛋白降解,抗原提呈,细胞周期调节,转录因子代谢,临床疾病间的关系,以及在药物开发和临床治疗中的意义。     

人类对DNA的探索

DNA分子双螺旋结构的发现,促使人类破译了遗传密码,并导致了基因工程的迅速崛起,以及人类基因组计划的实施、后基因组时代的到来,对人类和社会的影响是非常深远的,因此与相对论、量子力学一起,被称为人类在20世纪最伟大的三大科学发现。从人类对DNA的探索历程可以感悟科学发展的基本规律。     

化学工业出版社新书

人胚胎干细胞———科学和治疗潜力概论[美]安A.基斯林斯科特C.安德森著章静波等译29.00元2005年7月出版本书主要介绍了与人胚胎干细胞研究相关生物学基础知识、历史事件,以及相关的伦理学问题等,某些章节还描述了一些细胞研究的最新进展。本书有以下特色。(1)突出的信息框:介绍关键性的历史进展,阐明该领域发展的历程和重要的科学资料,从而帮助读者更为充分地理解相关的生物学知识。(2)在各章节中都指出有待发现的重要的科学事实,使读者了解该学科的发展方向。(3)关注技术应用:本书中详细介绍了干细胞疗法可能治疗的疾病及其治疗原理。(4)…     

诺奖精神

2006年诺贝尔奖已经尘埃落定。回顾诺贝尔奖的百年历程,不难发现诺贝尔奖对20世纪科学发展起到了极为重要的作用,正如诺贝尔物理学奖获得者李政道所说:“诺贝尔奖把人类文明提高到了一个新的高度”。诺贝尔奖是根据瑞典人阿尔弗     

Protein trafficking and maturation regulate intramembrane proteolysis

Intramembrane-cleaving proteases (I-CLiPs) are membrane embedded proteolytic enzymes. All substrates identified so far are also membrane proteins, involving a number of critical cellular signaling as well as human diseases. After synthesis and assembly at the endoplasmic reticulum, membrane proteins are exported to the Golgi apparatus and transported to their sites of action. A number of studies have revealed the importance of the intracellular membrane trafficking in i-CLiP-mediated intramembrane proteolysis, not only for limiting the unnecessary encounter between i-CLiPs and their substrate but also for their cleavage site preference. In this review, we will discuss recent advances in our understanding of how each i-CLiP proteolysis is regulated by intracellular vesicle trafficking. This article is part of a Special Issue entitled: Intramembrane Proteases.     

Proteolytic signals in the primary structure of annexins

Annexins are a superfamily of calcium-dependent membrane-associated proteins which interact with phospholipids. The primary structure of Annexins I, III, VII, VIII and XI contain a region enriched in proline, glutamate, serine and threonine (PEST sequences) towards the N-terminal end while annexins II, V and VI possess PEST regions somewhat distal to the N-terminus. These PEST sequences are believed to be the signals for rapid intracellular degradation. Annexin I is known to be cleaved by calpain near its PEST region suggesting that its PEST region might be a possible calpain recognition site. Western blot analysis of annexins V and XI in rat lung homogenates suggest that these proteins are resistant to proteolysis by calpain. Annexin V was found to be stable to intrinsic lung proteases in the presence of either Ca²⁺ or EGTA while annexin XI was found to be partially degraded by intrinsic lung proteases in the presence of EGTA. Eight of the 10 known mammalian annexins also contain a pentapeptide sequence that is biochemically related to the KFERQ motif which is a known signal that targets protein for lysosomal proteolysis. Our data suggest that the annexins may be regulated by limited proteolysis, most likely at their N-terminal end, while most, if not all, of them might be degraded by the lysosomal pathway.     

Molecular mechanisms for the conversion of zymogens to active proteolytic enzymes.

Proteolytic enzymes are synthesized as inactive precursors, or "zymogens," to prevent unwanted protein degradation, and to enable spatial and temporal regulation of proteolytic activity. Upon sorting or appropriate compartmentalization, zymogen conversion to the active enzyme typically involves limited proteolysis and removal of an "activation segment." The sizes of activation segments range from dipeptide units to independently folding domains comprising more than 100 residues. A common form of the activation segment is an N-terminal extension of the mature enzyme, or "prosegment," that sterically blocks the active site, and thereby prevents binding of substrates. In addition to their inhibitory role, prosegments are frequently important for the folding, stability, and/or intracellular sorting of the zymogen. The mechanisms of conversion to active enzymes are diverse in nature, ranging from enzymatic or nonenzymatic cofactors that trigger activation, to a simple change in pH that results in conversion by an autocatalytic mechanism. Recent X-ray crystallographic studies of zymogens and comparisons with their active counterparts have identified the structural changes that accompany conversion. This review will focus upon the structural basis for inhibition by activation segments, as well as the molecular events that lead to the conversion of zymogens to active enzymes.     

Activity-based probes as a tool for functional proteomic analysis of proteases

Traditional proteomics methodology allows global analysis of protein abundance but does not provide information on the regulation of protein activity. Proteases, in particular, are known for their multilayered post-translational activity regulation that can lead to a significant difference between protease abundance levels and their enzyme activity. To address these issues, the field of activity-based proteomics has been established in order to characterize protein activity and monitor the functional regulation of enzymes in complex proteomes. In this review, we present structural features of activity-based probes for proteases and discuss their applications in proteomic profiling of various catalytic classes of proteases.     

Degradation of the auxin response factor ARF1

Auxin-mediated gene expression is largely controlled through a family of DNA-binding proteins known as auxin response factors (ARF). Previous studies on the role of proteolytic regulation in auxin signaling have focused on degradation of their interacting partner, the Aux/IAA proteins. Aux/IAA family members with domain II sequences are rapidly degraded, show auxin-enhanced degradation rates, and interact with the related F-box proteins TIR1 and AFB1-3, which indicates that they are ubiquitylated by a CUL1-dependent E3 ligase. To date, limited data have been generated regarding degradation of ARFs. Here, we focus on the degradation rate of one ARF family member, Arabidopsis thaliana ARF1, and find that the half-lives of N-terminally HA-tagged ARF1 and C-terminally luciferase-tagged ARF1 are both approximately 3–4 h. This half-life appears to be conferred by a component of the middle region (MR), and degradation of the luciferase fusion with the MR is more rapid when the fusion includes an additional nuclear localization signal. ARF1 degradation is proteasome-dependent and rates are not altered in a CUL1 mutant background, suggesting that this ARF is targeted for proteasomal degradation via an alternative set of machinery to that used for Aux/IAA degradation. Consistent with this, exogenous indole acetic acid does not affect the degradation of ARF1. Given increasing evidence that the relative ratio of Aux/IAAs to ARFs rather than the absolute quantity within the cell appears to be the mode through which auxin signaling is modulated, this half-life is likely to be biologically relevant.     

Sequence‐derived structural features driving proteolytic processing

Proteolytic signaling, or regulated proteolysis, is an essential part of many important pathways such as Notch, Wnt, and Hedgehog. How the structure of the cleaved substrate regions influences the efficacy of proteolytic processing remains underexplored. Here, we analyzed the relative importance in proteolysis of various structural features derived from substrate sequences using a dataset of more than 5000 experimentally verified proteolytic events captured in CutDB. Accessibility to the solvent was recognized as an essential property of a proteolytically processed polypeptide chain. Proteolytic events were found nearly uniformly distributed among three types of secondary structure, although with some enrichment in loops. Cleavages in α‐helices were found to be relatively abundant in regions apparently prone to unfolding, while cleavages in β‐structures tended to be located at the periphery of β‐sheets. Application of the same statistical procedures to proteolytic events divided into separate sets according to the catalytic classes of proteases proved consistency of the results and confirmed that the structural mechanisms of proteolysis are universal. The estimated prediction power of sequence‐derived structural features, which turned out to be sufficiently high, presents a rationale for their use in bioinformatic prediction of proteolytic events.     

Intracellular proteolysis: Signals of selective protein degradation

Selective proteolysis is one of the mechanisms for the maintenance of cell homeostasis via rapid degradation of defective polypeptides and certain short-lived regulatory proteins. In prokaryotic cells, high-molecular-mass oligomeric ATP-dependent proteases are responsible for selective protein degradation. In eukaryotes, most polypeptides are attacked by the multicatalytic 26S proteasome, and the degradation of the majority of substrates involves their preliminary modification with the protein ubiquitin. The proteins undergoing the selective proteolysis often contain specific degradation signals necessary for their recognition by the corresponding proteases. This article is dedicated to the 25th Anniversary of the journal Bioorganicheskaya Khimiya     

MgATP binding to the nucleotide-binding domains of the eukaryotic cytoplasmic chaperonin induces conformational changes in the putative substrate-binding domains.

The eukaryotic cytosolic chaperonins are large heterooligomeric complexes with a cylindrical shape, resembling that of the homooligomeric bacterial counterpart, GroEL. In analogy to GroEL, changes in shape of the cytosolic chaperonin have been detected in the presence of MgATP using electron microscopy but, in contrast to the nucleotide-induced conformational changes in GroEL, no details are available about the specific nature of these changes. The present study identifies the structural regions of the cytosolic chaperonin that undergo conformational changes when MgATP binds to the nucleotide binding domains. It is shown that limited proteolysis with trypsin in the absence of MgATP cleaves each of the eight subunits approximately in half, generating two fragments of approximately 30 kDa. Using mass spectrometry (MS) and N-terminal sequence analysis, the cleavage is found to occur in a narrow span of the amino acid sequence, corresponding to the peptide binding regions of GroEL and to the helical protrusion, recently identified in the structure of the substrate binding domain of the archeal group II chaperonin. This proteolytic cleavage is prevented by MgATP but not by ATP in the absence of magnesium, ATP analogs (MgATPyS and MgAMP-PNP) or MgADP. These results suggest that, in analogy to GroEL, binding of MgATP to the nucleotide binding domains of the cytosolic chaperonin induces long range conformational changes in the polypeptide binding domains. It is postulated that despite their different subunit composition and substrate specificity, group I and group II chaperonins may share similar, functionally-important, conformational changes. Additional conformational changes are likely to involve a flexible helix-loop-helix motif, which is characteristic for all group II chaperonins.     

Biological functions and therapeutic opportunities of soluble cytokine receptors

Cytokines control the immune system by regulating the proliferation, differentiation and function of immune cells. They activate their target cells through binding to specific receptors, which either are transmembrane proteins or attached to the cell-surface via a GPI-anchor. Different tissues and individual cell types have unique expression profiles of cytokine receptors, and consequently this expression pattern dictates to which cytokines a given cell can respond. Furthermore, soluble variants of several cytokine receptors exist, which are generated by different molecular mechanisms, namely differential mRNA splicing, proteolytic cleavage of the membrane-tethered precursors, and release on extracellular vesicles. These soluble receptors shape the function of cytokines in different ways: they can serve as antagonistic decoy receptors which compete with their membrane-bound counterparts for the ligand, or they can form functional receptor/cytokine complexes which act as agonists and can even activate cells that would usually not respond to the ligand alone. In this review, we focus on the IL-2 and IL-6 families of cytokines and the so-called Th2 cytokines. We summarize for each cytokine which soluble receptors exist, were they originate from, how they are generated, and what their biological functions are. Furthermore, we give an outlook on how these soluble receptors can be exploited for therapeutic purposes.     

Dynamics and DNA substrate recognition by the catalytic domain of lambda integrase

Bacteriophage lambda integrase (lambda-Int) is the prototypical member of a large family of enzymes that catalyze site-specific DNA recombination via the formation of a Holliday junction intermediate. DNA strand cleavage by lambda-Int is mediated by nucleophilic attack on the scissile phosphate by a conserved tyrosine residue, forming an intermediate with the enzyme covalently attached to the 3'-end of the cleaved strand via a phosphotyrosine linkage. The crystal structure of the catalytic domain of lambda-Int (C170) obtained in the absence of DNA revealed the tyrosine nucleophile at the protein's C terminus to be located on a beta-hairpin far from the other conserved catalytic residues and adjacent to a disordered loop. This observation suggested that a conformational change in the C terminus of the protein was required to generate the active site in cis, or alternatively, that the active site could be completed in trans by donation of the tyrosine nucleophile from a neighboring molecule in the recombining synapse. We used NMR spectroscopy together with limited proteolysis to examine the dynamics of the lambda-Int catalytic domain in the presence and absence of DNA half-site substrates with the goal of characterizing the expected conformational change. Although the C terminus is indeed flexible in the absence of DNA, we find that conformational changes in the tyrosine-containing beta-hairpin are not coupled to DNA binding. To gain structural insights into C170/DNA complexes, we took advantage of mechanistic conservation with Cre and Flp recombinases to model C170 in half-site and tetrameric Holliday junction complexes. Although the models do not reveal the nature of the conformational change required for cis cleavage, they are consistent with much of the available experimental data and provide new insights into the how trans complementation could be accommodated.