磷酸化蛋白质组学研究中磷酸化肽段富集与分离方法研究进展

对磷酸化蛋白质组（phosphoproteome）进行系统深入的研究依赖于高重复性和特异性的磷酸化肽段富集与分离方法。目前发展了多种不同原理的磷酸化肽段富集方法,它们往往具有不同的选择性和特异性,因此,根据不同的研究目的选择最适合的富集方法显得尤为重要。本文综述了基于亲和色谱法（affinity chromatography）、免疫沉淀法（immunoprecipitation）、化学衍生法（chemical derivatization）、色谱法（chromatography）和其他新发展方法的磷酸化肽段富集方法,详细介绍了各自的优缺点及相关的优化与改进策略。此外,还简单介绍了磷酸化肽段富集与预分方法的不同组合的研究进展。     

胶原蛋白水解肽磷酸化的研究

在三聚磷酸钠作用下,胶原活性肽能够发生非酶磷酸化,共价连接磷酸基团,用正交实验法优选磷酸化条件,反应温度对磷酸化水平影响最大,pH值影响次之,在优选的磷酸化条件下（pH9.0,80℃,反应3h),磷酸化水平约为每分子胶原能够共价连接上约2分子磷酸基团。     

磷酸化蛋白质及多肽相关研究的技术进展

磷酸化修饰是一种重要的蛋白质化学修饰, 对蛋白质功能的完成或改变起到重要作用。该领域的研究存在很多技术难点, 对该领域研究形成了挑战。近年来相关技术有了很多突破, 磷酸化研究也取得了很多新的成就。文章将从磷酸化蛋白的检出、磷酸化蛋白质和肽段的富集、生物质谱技术的改进以及磷酸化蛋白和多肽的定量与比较几个方面介绍该研究领域的技术进展。     

肠炎沙门菌肽脯氨酰顺反异构酶SlyD的基因敲除、表达及酶学特征

【目的】以肠炎沙门菌肽脯氨酰顺反异构酶SlyD为对象,构建基因缺失株及表达纯化该蛋白,为研究其在肠炎沙门菌致病性与应激等方面的作用奠定基础。【方法】参考Gen Bank登录的肠炎沙门菌基因组序列设计用于slyD基因敲除及原核表达的特异引物,运用自杀质粒介导的同源重组技术对肠炎沙门菌C50041 slyD基因进行敲除,构建C50041ΔslyD缺失株;原核表达SlyD蛋白,通过α-糜蛋白酶耦联法对其PPIase活性进行测定;利用生物信息学相关软件,分析SlyD蛋白的氨基酸序列及功能域。【结果】PCR鉴定与测序结果证明成功构建了肠炎沙门菌C50041ΔslyD缺失株,其生长特性与野生株基本一致;SDS-PAGE及PPIase活性分析表明,获得了具有生物活性的可溶性SlyD蛋白;生物信息学分析显示SlyD蛋白由FKBP样肽脯氨酰顺反异构酶结构域、分子伴侣功能域和金属结合区域3个功能区域组成。【结论】成功获得了肠炎沙门菌C50041ΔslyD缺失株和具有PPIase活性的重组SlyD蛋白。     

柠檬醛顺反异构体对黄曲霉超微结构及膜功能的影响

研究柠檬醛顺反异构体（香叶醛和橙花醛）抗菌性是阐明该醛抗菌机理核心所在.用酶转化法合成香叶醛和橙花醛后,用液态或气态的异构单体分别对黄曲霉孢子及菌丝体进行毒化.采用透射电镜、多维显微及激光拉曼散射技术对毒化的黄曲霉孢子及菌丝体进行显微结构观察和膜相关参数的测定.结果表明,无论是液体还是气体毒化方式,柠檬醛顺反异构体单独存在时均有抗黄曲霉作用;二者混合物的抗菌总活性与单体相比表现出一定程度协同性;二个异构单体的抗菌作用不仅表现为破坏黄曲霉超微结构,而且还反映在损伤其细胞膜体积调节功能及变形能力.     

TPO模拟肽与人IgG1 Fc片段的融合表达及其生物学特性研究

依据本室获得的人TPO模拟肽序列,合成了该模拟肽的DNA序列,分别连接至4种不同长度的人IgG1 Fc基因片段的5′端,并克隆至质粒表达载体pET28a( ),转化大肠杆菌BL21（DE3）,筛选获得了4种重组工程菌,其中3种分别高效表达了3种不同长度的融合蛋白,而第4种工程菌未表达,表达的3种融合蛋白的分子量分别约为28kD,12kD和12kD。表达量约占菌体蛋白总量的30％左右,纯化获得了3种TPO模拟肽融合蛋白,3种融合蛋白均有较好的体外活性,维持TPO依赖细胞Ba/F3-mp1生长的EC50分别为：13,10,10nmol/L,用血小板减少症小鼠动物模型,测定了它们的体内活性,3种融合蛋白均有升高血小板和缩短血小板恢复时间的功能,分别比TPO模拟肽活性提高了18,8,8倍,而对白细胞及红细胞无显著影响,分别用3种融合蛋白免疫BALB／c小鼠,均未刺激小鼠产生抗TPO模拟肽抗体,并显示了较好的应用潜力。     

乙醛对人类神经tau磷酸化的影响

用乙醛对人类神经tau进行醛胺化,通过NCLK(neuronal cdc2-like protein kinase)和［γ-³²P］ATP对其磷酸化.磷酸化的产物经胃蛋白酶降解及HPLC(C-18)分析降解片段,发现醛胺化tau的降解物中有两个新的磷酸化肽段(A4和A6).     

TPO模拟肽与人IgG1 Fc片段的融合表达及其生物学特性研究

依据本室获得的人TPO模拟肽序列,合成了该模拟肽的DNA序列,分别连接至4种不同长度的人IgG1 Fc基因片段的5′端,并克隆至质粒表达载体pET28a(+),转化大肠杆菌BL21(DE3),筛选获得了4种重组工程菌,其中3种分别高效表达了3种不同长度的融合蛋白,而第4种工程菌未表达。表达的3种融合蛋白的分子量分别约为28kD、12kD和12kD,表达量约占菌体蛋白总量的30%左右,纯化获得了3种TPO模拟肽融合蛋白。3种融合蛋白均有较好的体外活性,维持TPO依赖细胞Ba/F3-mp1生长的EC50分别为：13、10、10 nmol/L。用血小板减少症小鼠动物模型,测定了它们的体内活性,3种融合蛋白均有升高血小板和缩短血小板恢复时间的功能,分别比TPO模拟肽活性提高了18、8、8倍;而对白细胞及红细胞无显著影响。分别用3种融合蛋白免疫BALB/c小鼠,均未刺激小鼠产生抗TPO模拟肽抗体,并显示了较好的应用潜力。      

肝素对人类神经tau蛋白分子聚集及磷酸化的影响

在老年性痴呆患者的脑中,肝素与超磷酸化的tau蛋白共存[7].采用NCLK(neuronalcdc2-likekinase)及PP2B(phosphoproteinphosphatase2B)在含肝素的体系中对人类神经tau蛋白进行磷酸化和脱磷酸化,结果表明,肝素具有促进tau蛋白被磷酸化的功能,并促进该蛋白磷酸化分子二聚体的形成和单体的减少,其一级动力学常数分别为2.88×10-3s-1和1.74×10-3s-1.PP2B可使磷酸化的tau蛋白脱磷酸化,并且脱磷酸化作用随肝素浓度的增加而增强,提示肝素可能具有调节tau蛋白磷酸化状态的作用     

低氧对小鼠学习记忆力及脑中tau蛋白磷酸化的影响

目的：研究不同低氧暴露对小鼠学习记忆及脑中tau蛋白磷酸化的影响。方法：雄性昆明小鼠40只,随机分为4组（n=10）：对照组（control）、8h低氧暴露组（8h）、7d低氧暴露组（7d）和28d低氧暴露组（28d）。将低氧暴露模型组置于模拟高原海拔5500m的低压氧舱,每天低氧暴露8h,避暗和旷场实验检测其活动能力及学习记忆能力：免疫印迹技术检测小鼠海马和皮层中tau蛋白磷酸化水平。结果：随着低氧时间的增加,小鼠短期学习记忆力及活动能力下降程度增大,28d低氧暴露后其下降程度最大;海马中tau蛋白多个位点的磷酸化水平呈现升高趋势,28d时tau蛋白磷酸化程度最高（P〈0．05）;皮层中的磷酸化水平在低氧暴露7d时达到最高,低氧暴露28d时略有降低,但与control组相比仍有明显差异（P〈0．05）。结论：慢性间歇性低氧可导致小鼠学习记忆能力下降,其机制可能与tau蛋白过度磷酸化相关。     

PBOND： Web Server for the Prediction of Proline and Non-Proline cis / trans Isomerization

PBOND is a web server that predicts the conformation of the peptide bond between any two amino acids. PBOND classifies the peptide bonds into one out of four classes, namely cis imide (cis-Pro), cis amide (cis-nonPro), trans imide (trans-Pro) and trans amide (trans-nonPro). Moreover, for every prediction a reliability index is computed. The underlying structure of the server consists of three stages: (1) feature extraction, (2) feature selection and (3) peptide bond clas- sification. PBOND can handle both s...     

人亲环素18抑制肌酸激酶的去折叠

新生肽链折叠过程中容易出现错误折叠与聚沉,从而导致折叠病等病理现象. 分子伴侣具有辅助其他蛋白质正确折叠,保护蛋白质分子结构的功能.本文选用人肌肌酸激酶为靶蛋白,研究了肽基脯氨酰顺反异构酶人亲环素18（human cyclophilin 18,hCyp18）对人肌肌酸激酶去折叠的作用,发现hCyp18能够抑制人肌肌酸激酶在热变性与化学变性过程中的失活与构象变化,并抑制人肌肌酸激酶在化学变性过程中的聚沉,因此推断hCyp18具有针对人肌肌酸激酶的分子伴侣功能.本文同时研究了hCyp18与人肌肌酸激酶的结合作用,对hCyp18的作用机制进行了初步探讨.     

Effect of the Phosphate Group with Different Negative Charges on the Conformation of Phosphorylated Ser/Thr-Pro Motif

Summary Ser/Thr-Pro motif is a widespread phosphorylated site in proteins, and its reversible phosphorylation is an important regulatory progress in many cell cycles and signal transduction. Recent research reveals that phosphorylation affects the local conformation of the peptide and its binding with the substrate through peptidyl--prolyl cis/trans isomerization. In order to further explore the effect of the phosphate group with different charges, four model peptides containing non- and phosphorylated Ser/Thr-Pro motif were synthesized using the classical solid-phase method. 1H-NMR, TOCSY, and ROESY were employed to characterize the conformation of the model peptides in solution with different pH value and analyze the peptidyl--prolyl isomerization at a molecular level. The results demonstrate that phosphorylation increases the cis conformation in the peptide and the maximum cis/trans ratio is obtained when the phosphate group has two negative charges. Furthermore, the experiments prove that the phosphorylation introduces a hydrogen bond between the phosphate and the NH of Ser/Thr residue, and the charges of the phosphate affect certain conformations of the phosphorylated Ser/Thr-Pro motif.     

Loss of intramolecular electrostatic interactions and limited conformational ensemble may promote self‐association of cis–tau peptide

Self‐association of proteins can be triggered by a change in the distribution of the conformational ensemble. Posttranslational modification, such as phosphorylation, can induce a shift in the ensemble of conformations. In the brain of Alzheimer's disease patients, the formation of intra‐cellular neurofibrillary tangles deposition is a result of self‐aggregation of hyper‐phosphorylated tau protein. Biochemical and NMR studies suggest that the cis peptidyl prolyl conformation of a phosphorylated threonine‐proline motif in the tau protein renders tau more prone to aggregation than the trans isomer. However, little is known about the role of peptidyl prolyl cis/trans isomerization in tau aggregation. Here, we show that intra‐molecular electrostatic interactions are better formed in the trans isomer. We explore the conformational landscape of the tau segment containing the phosphorylated‐Thr²³¹‐Pro²³² motif using accelerated molecular dynamics and show that intra‐molecular electrostatic interactions are coupled to the isomeric state of the peptidyl prolyl bond. Our results suggest that the loss of intra‐molecular interactions and the more restricted conformational ensemble of the cis isomer could favor self‐aggregation. The results are consistent with experiments, providing valuable complementary atomistic insights and a hypothetical model for isomer specific aggregation of the tau protein. Proteins 2015; 83:436–444. © 2014 Wiley Periodicals, Inc.     

Effect of Moniliformis moniliformis density on distribution within the definitive host population (Rattus norvegicus)

The population dynamics of Moniliformis moniliformis was studied in ‘free-ranging’ laboratory rats, Rattus norvegicus, presented with different relative density levels of M. moniliformis in cockroaches, Periplaneta americana. Changes in selected population parameters of the negative binomial distribution were evaluated as indicators of changes in aggregation. A significant increase in the degree of aggregation of parasites occurred as a result of the increase in relative density of infective stages available to the rats. This increase in aggregation was due to the increase in over-dispersion that occurred in female rats only. The degree of aggregation in females was found to be significantly higher than that in males at both treatment levels. The best indicators of the degree of aggregation were found to be the ratio of the variance to the relative density and the ratio of the log-variance to log-relative density. Changes in k were not correlated with changes in over-dispersion or the relative density.     

X-ray crystallography and QM/MM investigation on the oligosaccharide synthesis mechanism of rice BGlu1 glycosynthases

Nucleophile mutants of retaining β-glycosidase can act as glycosynthases to efficiently catalyze the synthesis of oligosaccharides. Previous studies proved that rice BGlu1 mutants E386G, E386S and E386A catalyze the oligosaccharide synthesis with different rates. The E386G mutant gave the fastest transglucosylation rate, which was approximately 3- and 19-fold faster than those of E386S and E386A. To account for the differences of their activities, in this paper, the X-ray crystal structures of BGlu1 mutants E386S and E386A were solved and compared with that of E386G mutant. However, they show quite similar active sites, which implies that their activities cannot be elucidated from the crystal structures alone. Therefore, a combined quantum mechanical/molecular mechanical (QM/MM) calculations were further performed. Our calculations reveal that the catalytic reaction follows a single-step mechanism, i.e., the extraction of proton by the acid/base, E176, and the formation of glycosidic bond are concerted. The energy barriers are calculated to be 19.9, 21.5 and 21.9 kcal/mol for the mutants of E386G, E386S and E386A, respectively, which is consistent with the order of their experimental relative activities. But based on the calculated activation energies, 1.1 kcal/mol energy difference may translate to nearly 100 fold rate difference. Although the rate limiting step in these mutants has not been established, considering the size of the product and the nature of the active site, it is likely that the product release, rather than chemistry, is rate limiting in these oligosaccharides synthesis catalyzed by BGlu1 mutants.     

The effects of cardiolipin on the structural dynamics of the mitochondrial ADP/ATP carrier in its cytosol-open state

Cardiolipin (CL) has been shown to play a crucial role in regulating the function of proteins in the inner mitochondrial membrane. As the most abundant protein of the inner mitochondrial membrane, the ADP/ATP carrier (AAC) has long been the model of choice to study CL-protein interactions, and specifically bound CLs have been identified in a variety of crystal structures of AAC. However, how CL binding affects the structural dynamics of AAC in atomic detail remains largely elusive. Here we compared all-atom molecular dynamics simulations on bovine AAC1 in lipid bilayers with and without CLs. Our results show that on the current microsecond simulation time scale: 1) CL binding does not significantly affect overall stability of the carrier or structural symmetry at the matrix-gate level; 2) pocket volumes of the carrier and interactions involved in the matrix-gate network become more heterogeneous in parallel simulations with membranes containing CLs; 3) CL binding consistently strengthens backbone hydrogen bonds within helix H2 near the matrix side; and 4) CLs play a consistent stabilizing role on the domain 1-2 interface through binding with the R30:R71:R151 stacking structure and fixing the M2 loop in a defined conformation. CL is necessary for the formation of this stacking structure, and this structure in turn forms a very stable CL binding site. Such a delicate equilibrium suggests the strictly conserved R30:R71:R151stacking structure of AACs could function as a switch under regulation of CLs. Taken together, these results shed new light on the CL-mediated modulation of AAC function.