寿命调控同源蛋白Sch9与S6K1的结构与功能分析

芽殖酵母Sch9与哺乳动物S6K1是保守的寿命调控同源蛋白,利用生物信息学手段比较分析了Sch9与S6K1的理化性质、亚细胞定位、信号肽和跨膜区、空间结构、蛋白质相互作用网络、序列同源性及进化关系,以期对Sch9与S6K1的结构功能的深入研究提供线索和基础。结果表明Sch9为酸性稳定性亲水蛋白,而S6K1为酸性不稳定的亲水蛋白,均无信号肽和跨膜区域,两者定位于细胞核的可能性最大。Sch9与S6K1的主要二级结构均为无规卷曲,在进化上相当保守,Sch9属于C2超家族和PKc_like超家族,S6K1属于PKc_like超家族。Sch9相互作用蛋白主要有Cyr1、Tor1、Tor2、Pkh1/2,而S6K1相互作用蛋白主要有PIK3CA、RHEB、Rps6、RPTOR、mTOR,显示两者的相互作用蛋白保守性也较强。同时,分析显示Sch9与S6K1均具有利于蛋白间相互作用的结构特点,为进一步深入研究Sch9与S6K1的分子功能及调控机制提供了一定的理论参考。     

mTOR信号通路与调节

哺乳动物雷帕霉素靶蛋白mTOR是一种非典型丝氨酸／苏氨酸蛋白激酶,可整合细胞外信号,磷酸化下游靶蛋白核糖体p70S6激酶,如S6K1及4E—BP1,影响转录与翻译,从而参与调控细胞生长、增殖等过程。近年来研究发现,调控mTOR通路可以干预某些疾病的病理过程。mTOR研究的新发现,可望为今后相关疾病的治疗提供新的靶点。     

心肌肌钙蛋白Ⅰ的磷酸化与非磷酸化调节

由于心肌肌钙蛋白复合体Ⅰ亚基(Troponin Ⅰ,TnⅠ)特殊的分子结构,使其在心肌收缩过程中起"分子开关"的重要作用.心肌TnⅠ具有6个磷酸化位点,第23/24位丝氨酸残基可被蛋白激酶A(PKA)、蛋白激酶D(PKD)和蛋白激酶G(PKG)磷酸化,发挥正性肌力作用;第43/45位丝氨酸残基以及第144位酪氨酸残基可被蛋白激酶C(PKC)磷酸化,可能主要起负性肌力作用;蛋白激活激酶(PAK)磷酸化第149位丝氨酸残基后的作用尚待探明.另外,经蛋白水解酶calpain降解含磷酸化位点的片段,产生去磷酸化作用;亦可通过降解一些特定片段来改变TnⅠ空间构象,引起非磷酸化调节作用.     

3-磷酸肌醇依赖性蛋白激酶-1激活AGC家族激酶的机制研究进展

3磷酸肌醇依赖性蛋白激酶1(3phosphoinositidedependentproteinkinase1,PDK1PDPK1)是蛋白激酶B(proteinkinaseB,PKBCAKT)的上游激酶,通过与3,4,5三磷酸磷脂酰肌醇[PtdIns(3,4,5)P3]作用激活相邻的PKB分子.同时,PDK1被称为AGC激酶的掌管者(master),能够激活包含PKB在内的一系列的AGC激酶家族成员.PDK1磷酸化这些激酶的保守区域Tloop区,使它们充分激活,从而调节细胞代谢,生长,扩散,生存,抗凋亡等诸多生理过程.本文就PDK1调节AGC激酶的活性,与功能上命名的PDK2的关系,PDK1分子自身的调节,PH结构域对自身活性及AGC激酶活性的影响,PDK1定位以及作为一个新药物靶标等方面做了综述.     

酵母PAP1与PHO85激酶复合物对YLR190w的磷酸化

酵母基因Pho85编码一个依赖于细胞周期蛋白 (cyclin)的蛋白激酶 (CDK) ,参与多种调控途径。PHO85功能的多效性归于其相关的细胞周期因子 ,现已经鉴定了 10个与PHO85相关的细胞周期因子 (PCL)。为了筛选PAP1 PHO85激酶复合物的特异底物 ,以PAP1为靶分子 ,利用酵母双杂交 (two hybrid)系统从酵母cDNA文库中克隆到一个与PAP1相互作用的蛋白质因子的基因 ,Ylr190w。Ylr190w编码 491个氨基酸的多肽链。体外翻译的YLR190w与纯化的融合蛋白GST PAP1可以被谷胱甘肽亲和柱共同吸附 ,这表明PAP1与YLR190w在体外也可以结合。用免疫沉淀获得的PAP1 PHO85复合物可以磷酸化在大肠杆菌中表达GST YLR190w ;并受到无机磷浓度影响 :高磷条件时磷酸化程度高 ,低磷条件时磷酸化程度低。它能与酵母细胞内YAF9结合 ,YAF9是人具有转录调控活性蛋白质因子AF9的酵母同源物。YLR190w与YAF9的相互作用受到磷条件影响 ,突变YLR190w蛋白S/TP位点的S和T后 ,它们的相互作用明显减弱 ,且不再受到磷条件影响     

酵母细胞分裂周期突变株中磷酸化蛋白的变化

最近对酵母细胞腺苷酸环化酶和依赖于cAMP的蛋白激酶基因的分子生物学研究,说明磷酸化蛋白在细胞周期中有重要作用。本文用聚丙烯酰胺凝胶电泳研究了酵母细胞分裂周期突变株中蛋白质的磷酸化。依赖cAMP的突变株AM18生长在无cAMP的培基中时,发生了几种磷酸化蛋白的变化,最明显的是分子量为72K Da的蛋白的积聚。细胞分裂周期温度敏感突变株cdc35生长在高于允许温度对,以及野生株生长在稳定期时,也出现类似现象。在这三种情况下,72K Da磷酸化蛋白同时还具有相同的pI值(pI=4.7),磷酸化都发生在苏氨酸残基上,用蛋白酶部分水解法证明它们有相似的肽谱。这些结果说明它们为同一蛋白。     

mTOR信号通路的生物学功能

哺乳动物的雷帕霉素靶(mammalian target of rapamycin,mTOR)是一种非典型丝氨酸/苏氨酸蛋白激酶,可整合细胞外信号,磷酸化下游靶蛋白核糖体p70S6激酶,如S6K1及4E-BP1,影响基因转录与蛋白质翻译,从而参与调控细胞生长、增殖等过程。mTOR的生物学功能的多样性,使其成为当今生物学研究的焦点之一。mTOR与蛋白质合成、免疫、细胞运动及代谢、细胞凋亡及自噬等均有联系。     

β肾上腺素受体的结构与功能域

β肾上腺素受体具有视紫红质样结构,包括由膜两侧亲水环相互联结7个疏水性跨膜α螺旋结构,N端无信号序列而含有2个N-糖基化位点,C端富含丝氨酸和苏氨酸残基.7个跨膜结构构成配基结合位点.β受体细胞膜内侧环状序列形成两亲α螺旋结构,与G蛋白相互作用.C端及第3个内侧环的丝氨酸及苏氨酸残基构成受体磷酸化位点,参与受体功能调控.     

大熊猫核糖体蛋白S11亚基基因(RPS11)cDNA的克隆及序列分析

RPS11是核糖体小亚基40S的组成部分,由RPS11基因所编码,属于核糖体蛋白S17p家族,主要存在于真核生物中.为了解大熊猫核糖体蛋白亚基RPS11基因的结构特点及其与已报道的人和其他哺乳动物核糖体蛋白亚基RPS11 基因的异同,本研究根据已报道的部分哺乳动物核糖体蛋白S11亚基基因(RPS11)的相关信息设计引物,运用RT-PCR 技术从大熊猫的肌肉组织总RNA中成功克隆了核糖体蛋白亚基RPS11基因,并进行了测序和序列分析.结果表明:大熊猫RPS11亚基基因的开放阅读框(ORF)长为477 bp,编码158 个氨基酸的蛋白质,该蛋白的相对分子量为18.4275 kDa,pI为10.96.拓扑预测显示该蛋白含有14个功能位点:即2 个N-糖基化位点,6个蛋白激酶C磷酸化位点,4个酪蛋白激酶Ⅱ磷酸化位点,1个酪氨酸激酶磷酸化位点和1个核糖体蛋白S17 signature位点.进一步分析发现,大熊猫RPS11基因与已报道的部分哺乳动物的表达序列及其编码的氨基酸序列都具有很高的相似性.本研究结果为丰富和完善哺乳动物RPS11基因资源库提供了基础资料.     

mTOR/4E-BP1参与诺考达唑诱导的Dami细胞多倍体化调控

目的:多倍性是物种形成的重要机制,决定一些重要器官细胞产生的数量和功能,而且与某些病理过程(如恶性肿瘤)的发生有密切关系.我们通过建立相对同步化的多倍体细胞模型,已经证实mTOR/S6K1参与多倍体细胞周期的调控.本课题主要研究mTOR下游的另一个重要信号分子4E-BP1是否也参与细胞的倍体化调控.方法:诺考达唑诱导Dami细胞建立相对同步化的多倍体细胞模型,Western-blot分析多倍体细胞模型中mTOR/4E-BP1通路信号分子表达和磷酸化修饰位点的变化,流式细胞仪双荧光分析4E-BP1不同结构域磷酸化位点修饰与细胞周期各时相的关系.结果:诺考达唑诱导的Dami细胞可作为相对同步化的多倍体细胞周期模型,在二倍体和多倍体细胞周期中,mTOR表达增加及第2448位丝氨酸位点磷酸化发生在G1期进入S期,4E-BP1的第37,46位苏氨酸和第65位丝氨酸位点磷酸化发生在G2/M期.结论:mTOR/4E-BP1通路参与多倍体细胞周期的调控.     

Yeast 3-phosphoinositide-dependent protein kinase-1 (PDK1) orthologs Pkh1-3 differentially regulate phosphorylation of protein kinase A (PKA) and the protein kinase B (PKB)/S6K ortholog Sch9

Pkh1, -2, and -3 are the yeast orthologs of mammalian 3-phosphoinositide-dependent protein kinase-1 (PDK1). Although essential for viability, their functioning remains poorly understood. Sch9, the yeast protein kinase B and/or S6K ortholog, has been identified as one of their targets. We now have shown that in vitro interaction of Pkh1 and Sch9 depends on the hydrophobic PDK1-interacting fragment pocket in Pkh1 and requires the complementary hydrophobic motif in Sch9. We demonstrated that Pkh1 phosphorylates Sch9 both in vitro and in vivo on its PDK1 site and that this phosphorylation is essential for a wild type cell size. In vivo phosphorylation on this site disappeared during nitrogen deprivation and rapidly increased again upon nitrogen resupplementation. In addition, we have shown here for the first time that the PDK1 site in protein kinase A is phosphorylated by Pkh1 in vitro, that this phosphorylation is Pkh-dependent in vivo and occurs during or shortly after synthesis of the protein kinase A catalytic subunits. Mutagenesis of the PDK1 site in Tpk1 abolished binding of the regulatory subunit and cAMP dependence. As opposed to PDK1 site phosphorylation of Sch9, phosphorylation of the PDK1 site in Tpk1 was not regulated by nitrogen availability. These results bring new insight into the control and prevalence of PDK1 site phosphorylation in yeast by Pkh protein kinases.     

Hydrophobic motif phosphorylation is not required for activation loop phosphorylation of p70 ribosomal protein S6 kinase 1 (S6K1)

p70 ribosomal protein S6 kinase 1 (S6K1) is regulated by multiple phosphorylation events. Three of these sites are highly conserved among AGC kinases (cAMP dependent Protein Kinase, cGMP dependent Protein Kinase, and Protein Kinase C subfamily): the activation loop in the kinase domain, and two C-terminal sites, the turn motif and the hydrophobic motif. The common dogma has been that phosphorylation of the hydrophobic motif primes S6K1 for the phosphorylation at the activation loop by phosphoinositide-dependent protein kinase 1 (PDK1). Here, we show that the turn motif is, in fact, phosphorylated first, the activation loop second, and the hydrophobic motif is third. Specifically, biochemical analyses of a construct of S6K1 lacking the C-terminal autoinhibitory domain as well as full-length S6K1, reveals that S6K1 is constitutively phosphorylated at the turn motif when expressed in insect cells and becomes phosphorylated in vitro by purified PDK1 at the activation loop. Only the species phosphorylated at the activation loop by PDK1 gets phosphorylated at the hydrophobic motif by mammalian target of rapamycin (mTOR) in vitro. These data are consistent with a previous model in which constitutive phosphorylation of the turn motif provides the key priming step in the phosphorylation of S6K1. The data provide evidence for regulation of S6K1, where hydrophobic motif phosphorylation is not required for PDK1 to phosphorylate S6K1 at the activation loop, but instead activation loop phosphorylation of S6K1 is required for mTOR to phosphorylate the hydrophobic motif of S6K1.     

Vacuolar Localization via the N-terminal Domain of Sch9 is Required for TORC1-dependent Phosphorylation and Downstream Signal Transduction

The budding yeast Sch9 kinase (functional orthologue of the mammalian S6 kinase) is a major effector of the Target of Rapamycin Complex 1 (TORC1) complex in the regulation of cell growth in response to nutrient availability and stress. Sch9 is partially localized at the vacuolar surface, where it is phosphorylated by TORC1. The recruitment of Sch9 on the vacuole is mediated by direct interaction between phospholipids of the vacuolar membrane and the region of Sch9 encompassing amino acid residues 1-390, which contains a C2 domain. Since many C2 domains mediate phospholipid binding, it had been suggested that the C2 domain of Sch9 mediates its vacuolar recruitment. However, the in vivo requirement of the C2 domain for Sch9 localization had not been demonstrated, and the phenotypic consequences of Sch9 delocalization remained unknown. Here, by examining cellular localization, phosphorylation state and growth phenotypes of Sch9 truncation mutants, we show that deletion of the N-terminal domain of Sch9 (aa 1-182), but not the C2 domain (aa 183-399), impairs vacuolar localization and TORC1-dependent phosphorylation of Sch9, while causing growth defects similar to those observed in sch9Δ cells. These defects can be reversed either via artificial tethering of the protein to the vacuole, or by introducing phosphomimetic mutations at the TORC1 target sites, suggesting that Sch9 localization on the vacuole is needed for the TORC1-dependent activation of the kinase. Our study uncovers a key role for the N-terminal domain of Sch9 and provides new mechanistic insight into the regulation of a major TORC1 signaling branch.     

Expression, purification, and characterization of a structurally disordered and functional C-terminal autoinhibitory domain (AID) of the 70 kDa 40S ribosomal protein S6 kinase-1 (S6K1)

S6K1 is a member of the AGC subfamily of serine-threonine protein kinases, whereby catalytic activation requires dual phosphorylation of critical residues in the conserved T-loop (T229) and hydrophobic motif (HM; T389) peptide regions of its catalytic kinase domain (residues 1-398). In addition to its kinase domain, S6K1 contains a C-terminal autoinhibitory domain (AID; residues 399-502), which prevents T-loop and HM phosphorylation; and autoinhibition is relieved on multi-site Ser-Thr phosphorylation of the AID (S411, S418, T421, and S424). Interestingly, 66 of the 104 C-terminal AID amino acid residues were computer predicted to exist in structurally disordered peptide regions, begetting interest as to how such dynamics could be coupled to autoregulation. To begin addressing this issue, we developed and optimized protocols for efficient AID expression and purification. Consistent with computer predictions, aberrant mobilities in both SDS-PAGE and size-exclusion chromatography, as well as low chemical shift dispersion in (1)H-(15)N HSQC NMR spectra, indicated purified recombinant AID to be largely unfolded. Yet, trans-addition of purified AID effectively inhibited PDK1-catalyzed T-loop phosphorylation of a catalytic kinase domain construct of S6K1. Using an identical purification protocol, similar protein yields of a tetraphospho-mimic mutant AID(D(2)ED) construct were obtained; and this construct displayed only weak inhibition of PDK1-catalyzed T229 phosphorylation. Purification of the structurally 'disordered' and functional C-terminal AID and AID(D(2)ED) constructs will facilitate studies aimed to understand the role of conformational plasticity and protein phosphorylation in modulating autoregulatory domain-domain interactions.     

Threonine 34 phosphorylation by phosphoinositide-dependent protein kinase 1 facilitates dissociation of Akt from the plasma membrane

Akt is a key mediator of cell proliferation, survival and metabolism. After translocation to the membrane and phosphorylation at T308 and S473, the activated Akt dissociates from the plasma membrane to cytoplasm, which is an important step to phosphorylate its downstream targets. In addition to its central role in regulating the kinase activity, phosphorylation of T308 in the kinase loop has been reported to be necessary for this dissociation process. However, it is not clear whether the membrane detachment requires further mechanisms. In the present report, we demonstrate that membrane dissociation of Akt requires phosphoinositide-dependent protein kinase 1 (PDK1) which directly phosphorylates not only T308 but also T34 in the pleckstrin homology (PH) domain. Like T308, T34 was phosphorylated in a phosphatidylinositol 3,4,5-trisphosphate- and phosphatidylserine-dependent manner. Phosphorylation of T34 also occurred in cells following growth factor stimulation, concurrently with T308 phosphorylation. Moreover, when T34 was mutated to aspartic acid (T34D) to mimic its phosphorylation, Akt-membrane association assessed by surface plasmon resonance spectroscopy was significantly reduced. In cells, this mutation impaired the IGF-induced Akt membrane translocation and subsequent phosphorylation at T308 and S473. Taken together, our results demonstrate that T34 phosphorylation by PDK1 promotes the membrane dissociation of activated Akt for its downstream action through attenuating membrane binding affinity. This membrane dissociation mechanism offers a new insight for Akt activation process and provides a potential new target for controlling the Akt-dependent cellular processes.     

Site specificity of four pyruvate dehydrogenase kinase isoenzymes toward the three phosphorylation sites of human pyruvate dehydrogenase

Activity of the mammalian pyruvate dehydrogenase complex is regulated by phosphorylation-dephosphorylation of three specific serine residues (site 1, Ser-264; site 2, Ser-271; site 3, Ser-203) of the alpha subunit of the pyruvate dehydrogenase (E1) component. Phosphorylation is carried out by four pyruvate dehydrogenase kinase (PDK) isoenzymes. Specificity of the four mammalian PDKs toward the three phosphorylation sites of E1 was investigated using the recombinant E1 mutant proteins with only one functional phosphorylation site present. All four PDKs phosphorylated site 1 and site 2, however, with different rates in phosphate buffer (for site 1, PDK2 > PDK4 approximately PDK1 > PDK3; for site 2, PDK3 > PDK4 > PDK2 > PDK1). Site 3 was phosphorylated by PDK1 only. The maximum activation by dihydrolipoamide acetyltransferase was demonstrated by PDK3. In the free form, all PDKs phosphorylated site 1, and PDK4 had the highest activity toward site 2. The activity of the four PDKs was stimulated to a different extent by the reduction and acetylation state of the lipoyl moieties of dihydrolipoamide acetyltransferase with the maximum stimulation of PDK2. Substitution of the site 1 serine with glutamate, which mimics phosphorylation-dependent inactivation of E1, did not affect phosphorylation of site 2 by four PDKs and of site 3 by PDK1. Site specificity for phosphorylation of four PDKs with unique tissue distribution could contribute to the tissue-specific regulation of the pyruvate dehydrogenase complex in normal and pathophysiological states.     

Characterization of PDK2 activity against protein kinase B gamma

Protein kinase B (PKB), also known as Akt, is a serine/threonine protein kinase controlled by insulin, various growth factors, and phosphatidylinositol 3-kinase. Full activation of the PKB enzyme requires phosphorylation of a threonine in the activation loop and a serine in the C-terminal tail. PDK1 has clearly been shown to phosphorylate the threonine, but the mechanism leading to phosphorylation of the serine, the PDK2 site, is unclear. A yeast two-hybrid screen using full-length human PKBgamma identified protein kinase C (PKC) zeta, an atypical PKC, as an interactor with PKBgamma, an association requiring the pleckstrin homology domain of PKBgamma. Endogenous PKBgamma was shown to associate with endogenous PKCzeta both in cos-1 cells and in 3T3-L1 adipocytes, demonstrating a physiological interaction. Immunoprecipitates of PKCzeta, whether endogenous PKCzeta from insulin-stimulated 3T3-L1 adipocytes or overexpressed PKCzeta from cos-1 cells, phosphorylated S472 (the C-terminal serine phosphorylation site) of PKBgamma, in vitro. In vivo, overexpression of PKCzeta stimulated the phosphorylation of approximately 50% of the PKBgamma molecules, suggesting a physiologically meaningful effect. However, pure PKCzeta protein was incapable of phosphorylating S472 of PKBgamma. Antisense knockout studies and use of a PDK1 inhibitor showed that neither PKB autophosphorylation nor phosphorylation by PDK1 accounted for the S472 phosphorylation in PKCzeta immunoprecipitates. Staurosporine inhibited the PKCzeta activity but not the PDK2 activity in PKCzeta immunoprecipitates. Together these results indicate that an independent PDK2 activity exists that physically associates with PKCzeta and that PKCzeta, by binding PKBgamma, functions to deliver the PDK2 to a required location. PKCzeta thus functions as an adaptor, associating with a staurosporine-insensitive PDK2 enzyme that catalyzes the phosphorylation of S472 of PKBgamma. Because both PKCzeta and PKB have been proposed to be required for mediating a number of crucial insulin responses, formation of an active signaling complex containing PKCzeta, PKB, and PDK2 is an attractive mechanism for ensuring that all the critical sites on targets such as glycogen synthase kinase-3 are phosphorylated.     

PDK1 protein phosphorylation at Thr354 by murine protein serine-threonine kinase 38 contributes to negative regulation of PDK1 protein activity

Murine protein serine-threonine kinase 38 (MPK38) is a member of the AMP-activated protein kinase-related serine/threonine kinase family, which acts as cellular energy sensors. In this study, MPK38-induced PDK1 phosphorylation was examined to elucidate the biochemical mechanisms underlying phosphorylation-dependent regulation of 3-phosphoinositide-dependent protein kinase-1 (PDK1) activity. The results showed that MPK38 interacted with and inhibited PDK1 activity via Thr(354) phosphorylation. MPK38-PDK1 complex formation was mediated by the amino-terminal catalytic kinase domain of MPK38 and the pleckstrin homology domain of PDK1. This activity was dependent on insulin, a PI3K/PDK1 stimulator, as well as various apoptotic stimuli, including TNF-α, H(2)O(2), thapsigargin, and ionomycin. MPK38 inhibited PDK1 activity in a kinase-dependent manner and alleviated PDK1-mediated suppression of TGF-β (or ASK1) signaling, probably via the phosphorylation of PDK1 at Thr(354). In addition, MPK38-mediated inhibition of PDK1 activity was accompanied by the modulation of PDK1 binding to its positive and negative regulators, serine/threonine kinase receptor-associated protein and 14-3-3, respectively. Together, these findings suggest an important role for MPK38-mediated phosphorylation of PDK1 in the negative regulation of PDK1 activity.     

A chimeric mechanism for polyvalent trans‐phosphorylation of PKA by PDK1

Phosphorylation on the activation loop of AGC kinases is typically mediated by PDK1. The precise mechanism for this in‐trans phosphorylation is unknown; however, docking of a hydrophobic (HF) motif in the C‐tail of the substrate kinase onto the N‐lobe of PDK1 is likely an essential step. Using a peptide array of PKA to identify other PDK1‐interacting sites, we discovered a second AGC‐conserved motif in the C‐tail that interacts with PDK1. Since this motif [FD(X)_1‐2Y/F] lies in the active site tether region and in PKA contributes to ATP binding, we call it the Adenosine binding (Ade) motif. The Ade motif is conserved as a PDK1‐interacting site in Akt and PRK2, and we predict it will be a PDK1‐interacting site for most AGC kinases. In PKA, the HF motif is only recognized when the turn motif Ser338 is phosphorylated, possibly serving as a phosphorylation “switch” that regulates how the Ade and HF motifs interact with PDK1. These results demonstrate that the extended AGC C‐tail serves as a polyvalent element that trans‐regulates PDK1 for catalysis. Modeling of the PKA C‐tail onto PDK1 structure creates two chimeric sites; the ATP binding pocket, which is completed by the Ade motif, and the C‐helix, which is positioned by the HF motif. Together, they demonstrate substrate‐assisted catalysis involving two kinases that have co‐evolved as symbiotic partners. The highly regulated turn motifs are the most variable part of the AGC C‐tail. Elucidating the highly regulated cis and trans functions of the AGC tail is a significant future challenge.