生物信息学预测与实验验证相结合策略筛选鉴定新的人分泌蛋白基因

使用生物信息学预测结合实验验证的策略筛选鉴定人新的分泌蛋白基因。用SignalP、SOSUI、PSORT和BLAST等程序对UniProt蛋白数据库进行生物信息学分析 ,筛选出用于实验验证的 1 4个功能未知基因。采用RT PCR方法 ,克隆得到 1 4个基因的全长编码序列 ,并构建到真核表达载体pcDNA3.1 ( - ) Myc His质粒。采用蛋白质印迹与免疫荧光分析 ,检测到其中 7个基因的表达。除其中一个在细胞核表达外 ,其余 6个只在细胞质中表达 ;其中的 4个基因的表达产物在细胞培养液中可被检测到 ,鉴定为 4个新的分泌蛋白基因。     

生物信息学在新基因全长cDNA序列分析及功能预测中的应用

差异表达基因的检测与分析已成为研究具有差异的生物学表型的常规策略.对通过实验所获得的差异基因片段进行生物信息学分析,主要包括基于国际互联网的序列相似性分析、片段重叠群分析和全长cDNA序列分析,以及如何构建局域网并采用本地服务器进行规模化的数据分析,从而为研究人员提供可参考的生物信息学数据分析方案.     

生物信息学技术克隆人类神经髓鞘蛋白零家族基因

为克隆新的髓鞘蛋白相关基因,将ＭＰＺ基因编码区ｃＤＮＡ与ＥＳＴ数据库进行同源性比较,得到与ＭＰＺ显著相似的２个ＥＳＴ,构建成８０１ｂｐ的重叠群。此重叠群与定位在１ｑ２４的１２８ｋｂ ｇＤｎＡ的相似性为１００％。计算机分析有ｂｐ和重叠群可能存在一个４３５ｂｐ的阅读框架。在重叠群上设计两个引物与文库载体臂上的引物配对,扩增各种ｃＤＮＡ文库ＤＮＡ作巢式ＰＣ拓所得ｃＤＮＡ上再设计引物进行巢式ＰＣＲ,最终克     

Protein Function Prediction: From Traditional Classifier to Deep Learning

Deep learning demonstrates greater competence over traditional machine learning techniques for many tasks. In last several years, deep learning has been applied to protein function prediction and a series of good achievements has been obtained. These findings extensively advanced our understanding of protein function. However, the accuracy of protein function prediction based upon deep learning still has yet to be improved. In article number 1900019, Issue 12, Zhang et al. construct DeepFunc, a deep learning framework using derived feature information of protein sequence and protein interactions network. They find that implementing DeepFunc for protein function prediction is more accurate than using DeepGO, a similar method reported previously. Meanwhile, they find that the method of combining multiple derived feature information in DeepFunc is much better than the method of using only single derived feature information. Due to its fully exploiting feature representation learning ability, deep learning with more derived feature information will enable it to be a promising method for solving more complicated protein function prediction problems and other bioinformatics challenges. Recent researches have provided some major insights into the value for using deep learning to protein function prediction problem.     

A Novel Method for Prediction of Protein Domain Using Distance-Based Maximal Entropy

Detecting the boundaries of protein domains is an important and challenging task in both experimental and computational structural biology. In this paper, a promising method for detecting the domain structure of a protein from sequence information alone is presented. The method is based on analyzing multiple sequence alignments derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence. Then they are combined into a single predictor using support vector machine. What is more important, the domain detection is first taken as an imbal- anced data learning problem. A novel undersampling method is proposed on distance-based maximal entropy in the feature space of Support Vector Machine （SVM）. The overall precision is about 80%. Simulation results demonstrate that the method can help not only in predicting the complete 3D structure of a protein but also in the machine learning system on general im- balanced datasets.     

DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions

Annotation of protein functions plays an important role in understanding life at the molecular level. High‐throughput sequencing produces massive numbers of raw proteins sequences and only about 1% of them have been manually annotated with functions. Experimental annotations of functions are expensive, time‐consuming and do not keep up with the rapid growth of the sequence numbers. This motivates the development of computational approaches that predict protein functions. A novel deep learning framework, DeepFunc, is proposed which accurately predicts protein functions from protein sequence‐ and network‐derived information. More precisely, DeepFunc uses a long and sparse binary vector to encode information concerning domains, families, and motifs collected from the InterPro tool that is associated with the input protein sequence. This vector is processed with two neural layers to obtain a low‐dimensional vector which is combined with topological information extracted from protein–protein interactions (PPIs) and functional linkages. The combined information is processed by a deep neural network that predicts protein functions. DeepFunc is empirically and comparatively tested on a benchmark testing dataset and the Critical Assessment of protein Function Annotation algorithms (CAFA) 3 dataset. The experimental results demonstrate that DeepFunc outperforms current methods on the testing dataset and that it secures the highest F_max = 0.54 and AUC = 0.94 on the CAFA3 dataset.     

四份中国HCV阳性血清中包膜蛋白E1/E2准种基因的序列分析及新型插入突变的发现

为分析四份中国丙型肝炎病毒（HCV）阳性血清中包膜蛋白E1/E2基因的准种特征。本研究对从4份中国HCV阳性血清（1b亚型：274、366、383;2a亚型：283）中提取的HCV核酸,采用逆转录-聚合酶反应扩增编码全长E1/E2蛋白（191～764aa）的基因片段,随机挑取多个克隆测序。根据E1/E2基因核苷酸的序列与其他相关序列（来自于GenBank）构建亲缘性关系进化树,进行核苷酸与氨基酸同源性分析并对重要的基因位点进行分析。共获得阳性克隆序列43个（274株10个,283株12个,366株13个,383株8个）,发现高变区HVR1、HVR2的基因异质性高,而其他抗体中和表位及跨膜区I、II及N末端糖基化位点相对保守。并首次发现在HCV 2a亚型（283血清）中多个准种序列存在1279nt（E1区,313aa）处单碱基插入优势基因突变,导致HCV包膜蛋白编码突变与中断（E2区,398aa）。本研究对中国HCV代表株包膜蛋白E1/E2编码基因的准种多样性及一种新型插入突变进行了描述,可为进一步研究HCV免疫逃避与慢性化机制提供重要信息。关键词：丙型肝炎病毒;包膜蛋白;序列分析;准种;插入突变     

利用一种新的网上工具Scansite进行蛋白质磷酸化预测

Scansite分析软件是近两年建立的一种新的利用因特网,基于蛋白质分子中较短的模序进行蛋白质磷酸化和蛋白质蛋白质相互作用预测的工具。这里综述了Scansite的使用方法、功能介绍及与其他磷酸化分析软件的比较,并展望了Scansite在进行磷酸化预测中面临的问题和应用前景。     

盐穗木功能未知蛋白 (HcUKPP)的亚细胞定位

藜科的极端盐生植物盐穗木（Halostachys caspica）的高盐胁迫抑制差减文库中有39%的功能未知蛋白（proteins with obscure features, POFs）,利用亚细胞定位分析可以初步判断其可能的功能.将盐穗木的1个POF-cDNA序列HcUKPP的编码区构建至pCAMBIA1301-GFP植物表达载体上,冻融法将重组质粒pCAMBIA1301-HcUKPP-GFP转化农杆菌EH105A,利用花序浸染法将基因导入拟南芥,经潮霉素筛选获得T1代阳性幼苗.通过激光扫描共聚焦显微镜观察转基因拟南芥植株的根部细胞. 结果显示,表达GFP蛋白的对照转基因植株中,绿色荧光在细胞核、细胞膜以及细胞质中均能检测到,而表达HcUKPP-GFP融合蛋白的转基因植株中,绿色荧光只在细胞质膜上表达,说明HcUKPP蛋白为细胞质膜相关蛋白.本研究为深入探讨盐穗木未知蛋白的功能奠定了基础.     

全基因组预测目标基因的新方法及其应用

运用隐马尔可夫模型, 利用Perl编程, 以几种模式生物的蛋白质数据库为基础, 构建了目标基因的全基因组预测的新方法。该方法具有高通量, 准确度高且操作简易等优点, 特别在多结构域蛋白家族预测上更显优势。应用该方法对几种模式生物的全基因组PPR和TPR蛋白家族进行了预测, 其中粳稻日本晴中含有536个PPR蛋白、199个TPR蛋白; 籼稻9311中含有519个PPR蛋白、177个TPR蛋白; 拟南芥中含有735个PPR蛋白、292个TPR蛋白; 红藻中6个PPR蛋白、32个TPR蛋白; 蓝细菌以及古细菌中没有PPR蛋白, 但蓝细菌含有10个TPR蛋白, 古细菌有4个TPR蛋白, 并对所得结果进行了进一步生物信息学分析。     

Proteomic and Metabolic Analyses of S49 Lymphoma Cells Reveal Novel Regulation of Mitochondria by cAMP and Protein Kinase A

Cyclic AMP (cAMP), acting via protein kinase A (PKA), regulates many cellular responses, but the role of mitochondria in such responses is poorly understood. To define such roles, we used quantitative proteomic analysis of mitochondria-enriched fractions and performed functional and morphologic studies of wild-type (WT) and kin⁻ (PKA-null) murine S49 lymphoma cells. Basally, 75 proteins significantly differed in abundance between WT and kin⁻ S49 cells. WT, but not kin⁻, S49 cells incubated with the cAMP analog 8-(4-chlorophenylthio)adenosine cAMP (CPT-cAMP) for 16 h have (a) increased expression of mitochondria-related genes and proteins, including ones in pathways of branched-chain amino acid and fatty acid metabolism and (b) increased maximal capacity of respiration on branched-chain keto acids and fatty acids. CPT-cAMP also regulates the cellular rate of ATP-utilization, as the rates of both ATP-linked respiration and proton efflux are decreased in WT but not kin⁻ cells. CPT-cAMP protected WT S49 cells from glucose or glutamine deprivation, In contrast, CPT-cAMP did not protect kin⁻ cells or WT cells treated with the PKA inhibitor H89 from glutamine deprivation. Under basal conditions, the mitochondrial structure of WT and kin⁻ S49 cells is similar. Treatment with CPT-cAMP produced apoptotic changes (i.e. decreased mitochondrial density and size and loss of cristae) in WT, but not kin⁻ cells. Together, these findings show that cAMP acts via PKA to regulate multiple aspects of mitochondrial function and structure. Mitochondrial perturbation thus likely contributes to cAMP/PKA-mediated cellular responses.     

Bagging with CTD- A Novel Signature for the Hierarchical Prediction of Secreted Protein Trafficking in Eukaryotes

Protein trafficking or protein sorting in eukaryotes is a complicated process and is carried out based on the information contaified in the protein. Many methods reported prediction of the subcellular location of proteins from sequence information. However, most of these prediction methods use a flat structure or parallel architecture to perform prediction. In this work, we introduce ensemble classifiers with features that are extracted directly from full length protein sequences to predict locations in the protein-sorting pathway hierarchically. Sequence driven features, sequence mapped features and sequence autocorrelation features were tested with ensemble learners and their performances were compared. When evaluated by independent data testing, ensemble based-bagging algorithms with sequence feature composition, transition and distribution （CTD） successfully classified two datasets with accuracies greater than 90%. We compared our results with similar published methods, and our method equally performed with the others at two levels in the secreted pathway. This study shows that the feature CTD extracted from protein sequences is effective in capturing biological features among compartments in secreted pathways.     

MutL融合蛋白的高效表达及其伴侣功能研究(英文)

DNA错配修复蛋白MutL和其它的修复蛋白相互作用来共同完成大肠杆菌甲基介导的错配修复过程 .为研究修复蛋白MutL的体外生物功能构建了融合蛋白Trx His6 Linkerpeptide MutL(THLL)的表达载体并使其高效表达及易于纯化 .mutL基因片段是以E .coliK 12基因组为模板经PCR扩增获得 ,并通过基因的体外拼接成功构建了融合蛋白THLL表达载体pET32a linkerpeptide mutL .重组菌株E .coliAD4 94 (DE3) pET32a linkerpeptide mutL经过IPTG的诱导表达了融合蛋白THLL .收集菌体细胞、超声波破碎后离心取上清进行SDS PAGE分析 ,结果表明有一与预期分子量(84kD)相应的诱导表达条带出现 ,其表达量约占全细胞蛋白的 30 %且以可溶形式存在 .利用固定化金属离子 (Ni2 +)配体亲和层析柱纯化融合蛋白THLL ,其纯度达到 90 % .通过非变性凝胶电泳分析 ,对融合蛋白THLL在DNA错配修复过程中的分子伴侣生物功能进行了系统研究 .结果表明 ,THLL能增加融合蛋白Trx His6 Linkerpeptide MutS (THLS)与含有错配碱基DNA双链的结合 ,但受ATP的浓度变化影响很大     

胰岛素受体底物PH结构域相互作用蛋白结构和功能研究进展

PHIP是一种与胰腺β细胞中胰岛素受体底物（IRS）的PH结构域相互作用的蛋白。根据小鼠PHIP（mPHIP）mRNA翻译的不同起始位点,除全长的PHIP1外,mPHIP基因还编码其他3种不同变异体。在胰岛素诱导的信号途径中,主要分布于细胞核的PHIP1和IRS-1的PH结构域相互作用,介导IRS蛋白酪氨酸的磷酸化。IRS-2和PHIP1的共表达能诱导IRS在细胞膜上的定位,促进葡萄糖转运蛋白4（GLUT4）向细胞质膜的转移。PHIP1的表达能提高β-细胞内细胞周期蛋白D2的表达,促进β细胞的生长。PHIP1的表达活化蛋白激酶B（PKB）,活化的PKB能明显抑制β细胞的凋亡。PHIP与胰岛素信号传导途径中其他信号分子的相互作用机制尚不明确。     

用质粒作底物测定核糖体失活蛋白酶活性的新方法

植物核糖体失活蛋白(ribosome-inactivating protein,RIP)是一类能作用于核糖体最大RNA的独特蛋白质.它是研究蛋白质生物合成中核糖体RNA结构与功能的有力工具.利用RIP能在DNA中脱去一些腺嘌呤碱基使超螺旋DNA解旋的特点,分别以常用的质粒PUC18、PUC19和PBR322 DNA为底物,建立了测定RIP酶活性的一种新方法,其灵敏度是50ng(天花粉蛋白)和5ng(还原型的辛纳毒蛋白),酶催化反应的时间是60min.这个新方法具有方便、快捷、灵敏的特点,避免了常用方法中制备核糖体、提取RNA的仪器和技术条件的限制,检测的时间由原来的几天缩短到约120min,大大地降低了检测的费用,为广泛和深入地研究RIP提供了有利的条件.     

A Depletion Strategy for Improved Detection of Human Proteins from Urine

With rapidly growing interest in the urine proteome, methods for reducing sample complexity are becoming increasingly important. Depletion strategies for removal of high-abundance proteins from human urine have not been reported. A commercial kit designed for depletion of abundant proteins from plasma was evaluated for removing top proteins from urine of patients with proteinuria. The number of low-abundance proteins identified in urine after depletion increased nearly 2.5-fold.     

A thermostable triple mutant of pyranose 2-oxidase from Trametes multicolor with improved properties for biotechnological applications

In order to increase the thermal stability and the catalytic properties of pyranose oxidase (P2Ox) from Trametes multicolor toward its poor substrate D-galactose and the alternative electron acceptor 1,4-benzoquinone (1,4-BQ), we designed the triple-mutant T169G/E542K/V546C. Whereas the wild-type enzyme clearly favors D-glucose as its substrate over D-galactose [substrate selectivity (k_cat/K_M)_Glc/(k_cat/K_M)_Gal = 172], the variant oxidizes both sugars equally well [(k_cat/K_M)_Glc/(k_cat/K_M)_Gal = 0.69], which is of interest for food biotechnology. Furthermore, the variant showed lower K_M values and approximately ten-fold higher k_cat values for 1,4-BQ when D-galactose was used as the saturating sugar substrate, which makes this enzyme particularly attractive for use in biofuel cells and enzyme-based biosensors. In addition to the altered substrate specificity and reactivity, this mutant also shows significantly improved thermal stability. The half life time at 60°C was approximately 10 h, compared to 7.6 min for the wild-type enzyme. We performed successfully small-scale bioreactor pilot conversion experiments of D -glucose/D -galactose mixtures at both 30 and 50°C, showing the usefulness of this P2Ox variant in biocatalysis as well as the enhanced thermal stability of the enzyme. Moreover, we determined the crystal structure of the mutant in its unligated form at 1.55 Å resolution. Modeling D-galactose in position for oxidation at C2 into the mutant active site shows that substituting Thr for Gly at position 169 favorably accommodates the axial C4 hydroxyl group that would otherwise clash with Thr169 in the wild-type.     

Phosphorylation of LukS by Protein Kinase A is Crucial for the LukS-Specific Function of the Staphylococcal Leukocidin on Human Polymorphonuclear Leukocytes

Staphylococcal leukocidin (Luk) consists of two protein components, LukF and LukS, which cooperatively lyse human and rabbit polymorphonuclear leukocytes. Here, we demonstrate that the phosphorylation of LukS by protein kinase A is crucial for the LukS-specific leukocytolytic function of Luk on HPMNLs by using N-[2(p-bromocinnamylamino)ethyl]-5-isoquinolinesulfonamide (H-89), which is a potent and selective inhibitor of protein kinase A. At 0.5 μM H-89 completely prevented the Luk-induced cell lysis accompanied by blocking of the incorporation of exogenous ³²P-H₃PO₄ into LukS on HPMNLs. However, with LukS and LukF together, 0.5 μM H-89 did not inhibit the cell swelling which takes place before the cell lysis. HPMNLs also became swollen upon treating with both LukF and LukS mutants which could not be phosphorylated.     

A Novel Rieske Iron-Sulfur Protein from the Hyperthermophilic Crenarchaeon Pyrobaculum aerophilum: Sequencing of the Gene, Expression in E. coli and Characterization of the Protein

The crenarchaeon Pyrobaculum aerophilum is with an optimalgrowth temperature of 100 °C one of the most thermophilic organisms knownto possess an aerobic respiratory chain. The analysis of DNA sequences fromthe Pyrobaculum genome project lead to the identification of an openreading frame potentially coding for a Rieske iron-sulfur protein. Thecomplete gene (named parR) was cloned and sequenced. The deducedamino acid sequence displays unusual amino acid exchanges and a so farunknown sequence insertion. The N-terminus shows similarities to bacterialsignal sequences. Several forms of the gene were expressed in E.coli in order to verify the classification as a Rieske protein and tofacilitate biophysical studies. Soluble, thermo-stable proteins withcorrectly inserted iron-sulfur clusters were expressed from two versions ofthe gene. The 1–23 truncated holo-protein is redox active. Itdisplays the typical spectroscopic properties of a Rieske protein. The redoxpotential was determined to be +215 mV at pH 6.5 and is pH dependentabove pH 7.5 revealing the influence of two protonation equilibria with pKavalues of 8.1 and 9.8. Phylogenetic analysis demonstrates that the parRprotein clusters together with the two other available archaeal Rieskesequences from Sulfolobus on a separate branch of the phylogenetictree apart from the proteins from thermophilic bacteria like Aquifexand Thermus.