Protein Eng.-2003-Li-629-35
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塞旦医堂盘壹!螋箜簦踅鲞第一璺塑泛素连接酶E3和肿瘤关系的研究进展决定蛋白质最后命运的是一类蛋白水解酶.在真核细胞中主要有两种蛋白质水解体系负责蛋白质的降解:溶酶体(1ysome和泛素一蛋白酶体(ubiquitin. proteasome。
前者为人们所熟知,后者是近20年来科学家重点研究的目标。
蛋白质泛素一蛋白酶体降解途径包括两个组成部分:首先是泛素与一系列关联酶协同作用,把要降解的目标蛋白质泛素化,使蛋白质变性并打上标记,以便为蛋白酶体所识别:第二部分是26S 的蛋白酶体复合物.它降解泛素化的蛋白质.同时释放出游离的泛素.并可再次被利用。
泛素是一个只有76个氨基酸残基组成的小的可溶性蛋白质.在大多数真核细胞中它都以高浓度存在,细胞中一半的泛素多与蛋白质耦联存在。
蛋白质的一级结构非常保守.酵母和人之间只有3个氨基酸的差别卜“。
泛素激活酶(ubiquitin.activating enzyme.E1在泛素化反应中起关键作用,它是催化泛素活化的第一步反应。
这个反应本身就是一个多步反应,而且是一个ATP依赖过程。
泛素结合酶(ubiquitin.conjugating enzyme, E2接受El转来的泛素形成相应的E2一Ub硫醚。
该酶是一个大的家族.该家族成员在分子大小、结构和功能上都有差别。
某些E2在体外能直接把泛素转移到底物.但在大多数情况下是泛素连接酶(ubiquitin ligase.E3参与底物的识别,它在凋节泛素与底物连接的特异性上起着中心作用L4-s]。
26S蛋白酶体是一个由70多个亚基所组成的巨大的复合分子,分子量接近2000000。
它由两部分组成:20S核心蛋白酶体及19S调节复合物或1IS调节复合物。
已发现20S蛋白酶体有j种明显的酶活性:类似胰凝乳蛋白酶活性、类似胰蛋白酶活性和谷氨酰后水解活性[6-7]。
泛素一蛋白酶体系统降解蛋白的特异性由泛素连接酶E3决定,因此,泛素连接酶E3引起研究人员的极大关注。
速效人胰岛素研究摘要:近年来,胰岛素蛋白质工程研究进展很快.主要介绍具有临床意义的速效长效和高效胰岛素研.包括分子设什基础。
生物活睦和应用前景等.此外.还4 }f 论了胰岛素的受体结合部位及胰岛素与其受体相互作用的研究近况。
目的:构建和制备出一种新型速效人胰岛素类似物(Pins),进行其性质研究。
方法:采用加端PCR的方法,扩增出在天然人胰岛素原N端添加精氨酸、脯氨酸、赖氨酸、脯氨酸4个氨基酸残基的重构胰岛素原基因片段,将其插入通用表达载体pET28a 后,再将经过改构后的硫氧还蛋白(卜20aa)的基因片段与重构胰岛素原基因的5端通过赖氨酸连接,成功构建了速效人胰岛素原类似物融合蛋白(FKPPIns)的表达载体(pET28a·FKPPIns)。
此融合蛋白在大肠杆菌BL一21(DE3)中以包涵体的形式表达,经包涵体洗涤和DEAE阴离子交换树脂纯化后进行复性、酶切。
酶切产物经RP—HPLC纯化后,质谱法测定其分子量;等电聚焦法测定此蛋白的等电点;凝胶过滤法测定其自身的缔合性质。
对新西兰大白兔肌肉注射纯化后Pins,进行初步的药效学评价。
结果:获得了结构为R—P—K—P—Insulin的Pins纯品,其等电点为7.3,自身缔合性较标准胰岛素显著下降。
结论:Pins与标准人胰岛素相比,起效快、达峰时间及持续时间短。
关键词:人胰岛素的研究背景胰岛素蛋白质工程胰岛素调节血糖问题速效胰岛素研究1研究背景胰岛素作为治疗糖尿病的特效药物,它所取得的巨大成功是医药史上划时代的奇迹之一而且也是蛋白质化学史上研究得最为广泛和深入的蛋自质之一。
随着DNA重组技术的发展,现在人们已能大规模生产重组人胰岛素.为了研究胰岛素结构与功能的关系和改善睫岛素的治疗学性质,需要制备各种各样的胰岛素类似物,而胰岛素蛋白质工程则是当前用来获得这些类似物的新技术和主要途径.迄今,人们已获得约300多种胰岛素类似物,其中包括70多种不同种属动物的胰岛素,80多种化学合成的类似物和150多种基因工程突变的类似物。
Vol.6 No.6Dec. 2020生物化工Biological Chemical Engineering第 6 卷 第 6 期2020 年 12 月蛋白质相互作用研究王芬,裴会敏,文狄,李静(黔南民族师范学院 生物与农学院,贵州都匀 558000)摘 要:蛋白质是细胞中最重要的功能元件之一,蛋白质相互作用网络是蛋白质组学研究的热点之一。
蛋白质相互作用网络的研究,不仅有助于理解蛋白质在网络中的功能,还可以解释细胞中大部分的生物功能,并为疾病诊断提供理论依据,使通过系统的理解信号转导网络治疗各种疾病成为可能。
大规模的蛋白质相互作用网络对于理解生物过程是必要的,在蛋白质相互作用网络中寻找关键蛋白,发现新药物靶标、诊断标记物和治疗靶点,可以为医治相关病症、定向开发药物提供依据,协助探究病害的发病机理。
关键词:蛋白质;相互作用网络;功能;疾病中图分类号:Q51 文献标识码:AThe Research on Protein-protein InteractionWANG Fen, PEI Huimin, WEN Di, LI Jing(The Department of Life Science and Agriculture, Qiannan Normal University for Nationalities, Guizhou Duyun 558000)Abstract: Protein is one of the most important functional components in cell. Protein interaction network is one ofthe hotspots in proteomics. Studying protein-protein interaction network not only help to understand the function of proteins, but also explain most biological functions in cell. It can also provide theoretical basis for disease diagnosis and make it possible to treat a variety of diseases through a systematic understanding of signal transduction network. Large-scale protein interaction networks areneeded to understand biological processes. Searching hubs and find drug targets, diagnostic marker and therapeutic target can provide references for the targeted drug design and development, also assist to explore the the pathogenesis of diseases.Keywords: protein; interaction network; function; disease人类基因组计划完成之后,蛋白质组学[1]的研究方兴未艾,其是探索生物体内所有蛋白质表达模式的科学,对蛋白质相互作用网络(PPIN)[2]的探索是其中重要领域之一。
壳聚糖一羧甲基纤维素徽球用作蛋白质载体张俐娜‟金勇刘海清杜予民(武汉大学化学与环境科学学院武汉430072)擅要:本文用一种新的乳液-相分离法制各壳聚糖和羧甲基纤维素共混的复合微球.研究了不同合成条件对成球及微球表面形貌的影响。
通过红外光谱、读数显微镜和扫描电镜表征了其结构。
用微球包埋牛血清清蛋白的体外溶出实验结果证明,该微球具有较好的蛋白质结合能力,并且在模拟胃液条件下几乎无释放,而在模拟肠液条件下有很好的缓释性能.是一种有前途的适合于口服蛋自质的药物输送载体。
O前言通过一种或多种高分子在溶液中形成微球或微胶囊并用作包合、传递、靶向载体是近二十年迅速发展起来的一项新技术。
反应主体或药物通过包合、吸附等方式达到控制释放或定向释放,因此可用于食品、医药、农药、香水化妆品及环保等各个领域【lj。
壳聚糖(C S)贮量丰富且是自然界少见的碱性天然氨基多耱,由蟹、虾壳中的甲壳素经脱乙酰基反应而得【2】。
作为一种聚阳离子多糖,CS因其良好的粘合性DJ、生物降解性、生物相容性和无毒性【4…5J被广泛应用于药物控制释放系统中16“。
高分子复合物一般由两种不同的高分子通过氢键、库仑力、电子给受体相互作用、范德华力、疏水键等次价键聚集而成【l o】。
C S含有大量的羟基、胺基,可以与羧甲基纤维素(C MC)等其他天然高分子形成高分子复合物。
天然高分子复合物具有不溶于水、优良的质量传递性能、对水和氧等低分子有可透过性等特点,而且无毒,具有良好的生物相容性,适合用于蛋白质的释放载体㈨121。
目前蛋白质在治疗给药方面主要通过注射。
但是重复剂量会导致药物在血液中的浓度不稳定,同时频繁的注射也会给患者带来不便。
口服给药是解决这一问题的最简便办法.但是胃液的酸性往往使蛋白质很快变性和降解.而用高分子微球或微胶囊包合蛋白质则可延缓释放。
当C S和阴离子接触时会发生胶凝作用,使C S珠粒易于在较温和的条件下形成ll^”J.这种珠粒具有依赖于pH值的溶胀行为,因而能在胃肠液环境中适当的传递药物.但是由于粒径较大限制了其应用。
Nucleic Acids Research,2007,Vol.35,Web Server issue W473–W476doi:10.1093/nar/gkm423PIC:Protein Interactions CalculatorK.G.Tina,R.Bhadra and N.Srinivasan*Molecular Biophysics Unit,Indian Institute of Science,Bangalore560012,IndiaReceived January31,2007;Revised April17,2007;Accepted May9,2007ABSTRACTInteractions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes.There are several weak and strong interactions that render stability to a protein struc-ture or an assembly.Protein Interactions Calculator (PIC)is a server which,given the coordinate set of 3D structure of a protein or an assembly,computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions,hydrogen bonds,aromatic–aromatic interactions,aromatic–sulphur interactions and cation–n interactions within a protein or between proteins in a complex.Interactions are calculated on the basis of standard,published criteria.The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site.It also determines the accessible surface area and residue-depth,which is the distance of a residue from the surface of the er can also recognize specific kind of interactions,such as apolar–apolar residue interactions or ionic interac-tions,that are formed between buried or exposed residues or near the surface or deep inside. INTRODUCTIONAnalyses of atomic interactions in tertiary structures of proteins contribute richly to our understanding of sequence–structure relationships,structural basis of pro-tein stability and protein evolution.Studies on interac-tions between sidechains are commonly used in designing methods and identifying strategies for remote homology detection,protein fold recognition,protein structural comparisons and comparative protein modelling(1–6). For example,remote homology detection between pro-teins can rely on conservation of structural motifs involving interacting sidechains(1).Such studies also serve as guidelines in designing site-directed mutagenesis experiments(7)and in the understanding of the basis for residue conservation in homologous proteins(8). Interactions between subunits of multimeric proteins and interactions between interacting protein modules are also areas of intense study(9–13).Analyses on nature of sidechain–sidechain interactions across interacting inter-faces between protein modules have enlightened us on evolutionary conservation of protein–protein interactions and in distinguishing transient and permanent complexes (14–16).Different kinds of interactions have been noted in the stabilization of tertiary structures,quaternary structures and assemblies of proteins.Roles and importance of interactions between apolar residues and hydrogen bonds are very well known(2).Importance of interactions such as aromatic–aromatic,aromatic–sulphur,cation–p and ionic interactions in the structure and function of proteins is also well realized(17–20).Observations and analyses of less common features such as exposed cluster of hydro-phobic residues,partially buried salt bridges and interac-tions of buried charged residues are also of specific interest (21–24)Here we report the development of a web-based service, PIC(Protein Interactions Calculator),to aid recognition and analyses of various kinds of interactions in tertiary structures of proteins and structures of protein–protein complexes.We have also integrated solvent accessibility calculations in PIC to aid recognition of interacting motifs that are exposed or buried.Further,the residue depth calculations are also made possible in PIC so that interactions deep inside the protein structure or near the surface can be recognized.Advantage of using residue depth parameter is that it can distinguish residues with no solvent accessible surface area in terms of how deep they are from the protein surface.MATERIALS AND METHODSOrganization of PICPIC server accepts atomic coordinate set of a protein structure in the standard Protein Data Bank(PDB) format.The user is prompted with selecting one or more of the following interaction types:Interaction between apolar residues,disulphide bridges,hydrogen bond*To whom correspondence should be addressed.Tel:+918022932837;Fax:+918023600535;Email:ns@mbu.iisc.ernet.inß2007The Author(s)This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License(/licenses/ by-nc/2.0/uk/)which permits unrestricted non-commercial use,distribution,and reproduction in any medium,provided the original work is properly cited.between main chain atoms,hydrogen bond between main chain and sidechain atoms,hydrogen bond between two sidechain atoms,interaction between oppositely charged amino acids(ionic interactions),aromatic–aromatic inter-actions,aromatic–sulphur interactions and cation–p interactions.The input coordinate set is accepted,under each section of the page,for recognition of interactions within a polypeptide chain.If an ensemble of NMR-derived structures is input then thefirst model in thefile is taken as a representative and is used by the PIC server. The output corresponds to the list of residues involved in interaction type of interest.An option is provided,using RasMol(25)interface and Jmol interface,for enabling visualization of structure in the graphics with interactions highlighted.It is possible to get the results by e-mail.It is also possible to download the outputfiles of the original programs.A separate panel is available for identification of various types of interactions between polypeptide chains when a multi-chain PDBfile is subjected to the analysis. All the said interactions could be explored for their occurrence across the inter-polypeptide chain interface. Thus this panel facilitates recognition of interactions between different subunits in a multimeric protein structures or between proteins in a protein–protein complex structure.Figure1show ionic interactions between oppositely charged sidechains across the inter-face,formed between cyclin-dependent protein kinase and bound cyclin(26),recognized using PIC server.Solvent accessibility calculations could be used to identify different kinds of interactions between buried or between solvent exposed residues.Solvent accessibility calculations are performed using NACCESS program (Hubbard,S.J.and Thornton,J.M.,1993,NACCESS Computer Program,Department of Biochemistry and Molecular Biology,University College London.).The exposed and buried residues are identified by47%and 47%residue accessibility,respectively.Under this facility list of all the interaction types are displayed prompting the user to select list of interaction types of interest.For example,a user may prefer to identify interactions between apolar residues that are exposed.Figure2 shows interactions between solvent exposed apolar resi-dues,in crambin(27),recognized using PIC server. Depth of an atom in a protein is defined as the distance from the nearest atom in the surface of the protein structure.Mean depths of atoms of a residue defines the residue depth(28,29).Analogous to the panel on solvent accessibility,panel on residue depth enables the users to identify specific types of interactions near the protein surface or deep inside the core of the structure.Based on the analysis of residue depth parameter by Chakravarty and Varadarajan(28)we consider those residues with depths45A as close to the protein surface and others as deep ing this part of the PIC server it is possible to identify interactions between,say,aromatic residues near the protein structural surface.As calculation of residue depths takes a few minutes for most protein structures,results involving depth calculation are sent by e-mail to the user if a valid e-mail address is provided. Recognition of interactionsVarious types of interactions are recognized from the atomic coordinates using the standard criteria that are published.We used mainly the criteria suggested by NCI server(30)to identify non-canonical interactionsin Figure 1.Interactions between oppositely charged amino acid side-chains in the interaction interface of cyclic dependent protein kinase2(CDKs)and cyclin identified using PIC server.The folds of CDK2andcyclin and the charged residues in the interface formed by the twoproteins are represented in different colours.The ion pairs arehighlighted by black dotted lines.Thisfigure is produced usingSETOR(35).Figure2.Structure of crambin with solvent exposed and interactingapolar sidechains,recognized using PIC.Interactions between apolarsidechains is shown by green dots.Disulphide bonds are shown inyellow.Thisfigure is produced using SETOR(35).W474Nucleic Acids Research,2007,Vol.35,Web Server issueproteins.The aromatic–aromatic,aromatic–sulphur and cation–p interactions are recognized between appropriate sidechains using the criteria proposed by Burley and Petsko(17),Reid et al.(18)and Satyapriya and Vishveshwara(19),respectively.Disulphide bonds are recognized using the distance criteria employed originally in the MODIP program(31).Hydrogen bonds are recognized using HBOND routine developed by Overington et al.(32)and described in Mizuguchi et al.(33).The hydrogen bonds are categorized as main chain–main chain,main chain–sidechain and sidechain–side-chain.Only standard hydrogen bonds are recognized in PIC as NCI server(30)is available for identification of interactions such as C–H...O.Interactions between hydrophobic sidechains are identified using a distance cut-offof5A between apolar groups in the apolar sidechains.Though various interactions are recognized using the standard criteria,user has an option of changing the distance cut-offin recognizing any of the types of interactions.CONCLUSIONSAnalysing the interactions that stabilize tertiary and quaternary structures and protein–protein complexes is a common situation in structural biology.For example,a structure just solved using X-ray analysis or nuclear magnetic resonance may be subjected to such an analysis. In protein engineering and design experiments,a good understanding of the structural roles of various residues is essential before taking decisions on residues to mutate by site-directed mutagenesis and the replacing e of combinations of features available in PIC such as various kinds of interactions and solvent exposure or buried nature or depths of residues is also expected to aid recognition of common and uncommon structural fea-tures in a given protein structure.Analysis of such interactions in homologous protein structures(34)enables recognition of evolutionary constraints critical for the retention of fold of the protein family.The PIC server is available at:http://crick.mbu.iisc. ernet.in/ PICACKNOWLEDGEMENTSThis research is supported by the Department of Biotechnology(DBT),Government of India.K.G.T. and R.B.are supported by grants to N.S.by DBT. Funding to pay the Open Access publication charges for this article was provided by Oxford University Press. Conflict of interest statement.None declared. 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利用同源建模预测蛋白质的三级结构首先声明一下,以下纯属个人观点,方法步骤仅供参考,不可作为规范标准,结果出来之后请自行分析结果。
我用的是SWISS-MODEL同源建模的方法进行的蛋白质高级结构预测,其实这个方法是有限制条件的,不过作为一个选修课作业,我们不用深入探究,所以有时不够严谨,大家知道就行!对于一个未知结构的蛋白质,白质建立结构模型。
那么,我们首先要做的就是找到和我们空格和“—”的氨基酸序列,例如:【字母大小写没有影响】vlqdsigyirilsmmdpvvdefdrayqqvkdfpdlmvdvrengggnsgngkkiceylihkpqphcvspdweiiprkd)同源的、相似度最高的、已知三级结构的蛋白质作为模版。
打开SWISS-MODEL网站:/,选择“Template Identification,提交蛋白质序列进行模板识别,如图所示,注意:邮箱必填,名称随便填写,序列粘贴过去就行,下面会有很多选项,建议不知道的不要乱动,直接提交(Sbumit)吧。
这个东东跟BLAST差不多,你等它自动刷新吧,它会返回结果的,在结果页面,你会看到跟BLAST差不多的结果,选择相似度最高的那个蛋白作为下一步的三维模版(一般是第一个蛋白就是),如图:大家看红线标出的部分(是我标的),那个就是我们要找的模版,大家也可以在结果页面的下面仔细看看,找到最匹配的蛋白。
这里还有一点要作说明,就是上图标出的代码是PDB编号,前四个表示PDB- Code,最后一位表示Chain-ID,具体什么意思,大家有兴趣就去了解一些吧。
接下来,去NCBI串串门吧,在NCBI中搜索上面查到的蛋白的PDB号,一般输入前四位就行啦,注意:搜索蛋白库(Protein)。
找到以后,以FASTA格式显示。
接下来,我们再回到SWISS-MODEL,接下来就是重点和难点啦,在线提交序列进行同源建模分析,这个在线提交不是大家想象的那么容易,这个耗费了我大部分的时间,说到这里我就想画个圈圈诅咒它,大家注意啦~~~~~~~~~~~SWISS-MODEL 是一个自动化的蛋白质比较建模服务器,该服务器提供用户三种模式可选择:Automatic mode(简捷模式): 用于建模的氨基酸序列或是Swiss-Prot/TrEMBL (/sprot )编目号(accession)可以直接通过web界面提交。
蛋白质结构预测原理概述蛋白质结构预测技术已经有很多发展,但是基本原理未变,可以参考;基本操作也可以参考下文。
摘自:阎隆飞,孙之荣主编,蛋白质分子结构,清华大学出版社,1999.现在计算机互联网高速发展,已经成为遍布全球的一个网络,成为科学研究的有力工具,也是进行蛋白质结构和功能研究的重要工具。
国际上一些著名的分子生物学实验室都在互联网上建立了蛋白质结构预测服务器。
可以在互联网上进入这些服务器,利用这些服务器提供的软件进行蛋白质结构预测研究。
下面以欧洲分子生物学实验室蛋白质结构预测服务器为例作一说明。
13.6.1欧洲分子生物学实验室蛋白质结构预测服务器(1)该实验室提供的服务内容欧洲分子生物学实验室(EuropeanMolecular BiologyLabraroty,EMBL)提供的服务包括:①多序列联配的生成(MaxHom);②二级结构预测(PHDsec);③溶剂可及性的预测(PHDacc);④跨膜螺旋预测(PHDhtm);⑤跨膜蛋白拓扑结构预测( PHDtopology);⑥用基于预测的Threading方法进行折叠子识别(PHDthreader);⑦二级结构预测结果评估(EvalSec)。
用Email或WWW方式访问该服务器,可完成以上7种功能。
其Email或WWW地址如下:WWW.embl—heidelberg.de/predictprotein/predictprotein.html把要预测序列发往PredictProtein@EMBL-Heidelberg.DE;如有问题可以给Predict-Help@EMBL-Heidelberg.DE发电子邮件。
(2)结构预测步骤已知蛋白质一级序列的结构,预测步骤如下:①在序列库(SWISSPROT)中搜索同源序列;②用MaxHom程序进行多序列联配;③把多序列联配的结果作为基于profile的神经网络预测方法的输入,进行结构预测。
在交互验证实验中,其预测率如下:对水溶性球蛋白其三态预测率(螺旋、折叠和其他)大于72%[34,35];跨膜螺旋的两态(跨膜和非跨膜)预测率大于95%;优化后的跨膜螺旋和拓扑结构预测,螺旋预测率为89%左右,拓扑结构预测率大于86%[39]。
Changgui Li 1,Miang Lon Patricia Ng 1,Yong Zhu 1,Bow Ho 2and Jeak Ling Ding 1,3Departments of 1Biological Sciences and 2Microbiology,14Science Drive 4,National University of Singapore,117543Singapore3Towhom correspondence should be addressed.E-mail:dbsdjl@.sgEndotoxin,also known as lipopolysaccharide (LPS),is the major mediator of septic shock due to Gram-negative bac-terial infection.Chemically synthesized S3peptide,derived from Sushi3domain of Factor C,which is the endotoxin-sensitive serine protease of the limulus coagula-tion cascade,was previously shown to bind and neutralize LPS activity.For large-scale production of this peptide and to mimick other pathogen-recognizing molecules,tan-dem multimers of the S3gene were constructed and expressed in Escherichia coli .The recombinant tetramer of S3(rS3-4mer)was puri®ed by anion exchange and digested into monomers (rS3-1mer).Both the rS3-4mer and rS3-1mer were functionally analyzed for their ability to bind LPS by an ELISA-based method and surface plas-mon resonance.The LAL inhibition and TNF a -release test showed that rS3-1mer can neutralize the LPS activity as effectively as the synthetic S3peptide,while rS3-4mer displays an enhanced inhibitory effect on LPS-induced activities.Both recombinant peptides exhibited low cyto-toxicity and no haemolytic activity on human cells.This evidence suggests that the recombinant sushi peptides have potential use for the detection,removal of endotoxin and/or anti-endotoxin strategies.Keywords :endotoxin binding and neutralization/Factor C/limulus/S3tandem repeats/Sushi3peptideIntroductionSepsis remains a leading cause of death in critical care units,and is also frequently associated with serious consequences such as multiple organ failure.Gram-negative bacterial endotoxin,also known as lipopolysaccharide (LPS),has been suggested to play a pivotal role in such septic complications (Houdijk et al .,1997).The acute phase plasma protein,LPS binding protein (LBP),binds circulating LPS to extract it from micelles,and transfers it to either soluble or membrane-bound CD14receptor in monocytes and macrophages.The interaction of this complex with Toll-like receptors is thought to initiate intracellular signaling reactions,via transcription factor NF-k B (Ulevitch and Tobias,1999).Activation of protein kinases mediates the production of in¯ammatory cytokines,which contribute to septic shock.It has also been shown that in the absence of plasma LBP,the LPS is able to directly interact with CD14,yielding similar effects (Wyckoff et al .,1998).Thus,treatment of endotoxaemia and sepsis would be greatly aided by blocking the activity of endotoxins and/or removing themfrom the body ¯uids of patients,as cationic peptides and synthetic analogues do (de Haas et al .,1998;Scott et al .,2000).LPS from Gram-negative bacteria induces the amoebocytes of limulus to aggregate and degranulate.This response underlies the important defense mechanism of limulus against invasion of Gram-negative bacteria (Ding et al .,1995).As a molecular biosensor,Factor C can be autocatalytically acti-vated by femtograms of LPS to trigger the coagulation cascade (Ho,1983),suggesting that it contains high af®nity LPS-binding domains.Recently,two regions of Factor C that exhibit exceptionally high LPS binding af®nity were de®ned as the Sushi1and Sushi3domains (Tan et al .,2000a).Two 34-mer synthetic peptides,S1and S3,that span the 171±204and 268±301amino acid residues of Factor C (DDBJ/EMBL/GenBank accession No.S77063)are derived from Sushi1and Sushi3domains,respectively.Both peptides inhibit the LPS-induced limulus amoebocyte lysate (LAL)reaction and LPS-induced hTNF-a secretion (Tan et al .,2000b).Thus,the S1and S3peptides are promising endotoxin antagonists.The application value of these two peptides would be boosted if they could be obtained by cost-effective and large-scale methods such as recombinant expression in prokaryotic systems.However,expression of small peptides tends to encounter technical dif®culties (Le and Trotta,1991;Latham,1999).It is reported that some of these problems were resolved by multimerization of the small peptide followed by in vitro digestion to restore their activity (Mauro and Pazirandeh,2000).Besides Factor C,the tachylectin family members identi®ed in circulating hemocytes and hemolymph plasma also contribute to the recognition of invading pathogens.Five types of lectins,named tachylectin-1to -5,have different speci®cities for carbohy-drates exposed on pathogens.Interestingly,all these lectins contain a different number of tandem repeats in their structure (Iwanaga,2002).Thus,studying the tandem repeats of S3may provide explanations as to why these proteins adopt repetitive structures,and how they contribute strategically towards pathogen recognition.In this work,tandem repeats of S3gene were cloned into a modi®ed vector,which was subse-quently transferred to an expression vector,pET22b.Induced expression of the most robust tetramer clone was scaled-up.Recombinant S3tetramer (rS3-4mer)was puri®ed and digested into monomers (rS3-1mer)by acid treatment,and both the recombinant peptides were tested for their endotoxin-binding and -neutralizing activities.Materials and methodsMaterialsLPS from Escherichia coli 055:B5was purchased from Sigma (St.Louis,MO).LAL kinetic-QCL kit was supplied by BioWhittaker (Walkersvile,MD).Human TNF-a kit (OptEIA ELISA)was from Pharmingen (San Diego,CA).CellTiter 96Aqueous One Solution Reagent for cytotoxicity assay was purchased from Promega (Madison,WI).Enzymes for DNATandem repeats of Sushi3peptide with enhanced LPS-binding and -neutralizing activitiesProtein Engineering vol.16no.8pp.629±635,2003DOI:10.1093/protein/gzg078Protein Engineering vol.16no.8ãOxford University Press 2003;all rights reserved629at Kunming Medical University on October 31, 2013/Downloaded frommanipulation and polymerase reactions were purchased from NEB (Beverly,MA).DNA puri®cation and extraction kits were from Qiagen (Chatsworth,CA).Pyrogen-free water for making buffers was from Baxter (Morton Grove,IL).Construction of multimers of S3geneUsing a cloned Factor C Sushi3domain,pAC5.1Sushi3EGFP (Tan et al .,2000b),the LPS-binding motif,S3,was ampli®ed by PCR.A cloning strategy,which allows for directional multimerization and cloning is shown in Figure 1.Brie¯y,the ampli®cation vector pBBSI (Lee et al .,1998)was modi®ed to include an Nde I site containing the start codon adjacent to Bbs I site.This modi®ed vector was named pBC.Forward primer 5¢-TCGAAGAC GGCCCC AG GATCCC CATGCTGAACACA-AGG-3¢was designed with Bbs I restriction site (GAAGAC)followed by GGCCCC in addition to the S3¯anking sequence.On the reverse primer,5¢-TAGAAGAC CCGGGG GTCCA-TCAAAGAAAGTAGTTA-3¢,a similar motif,was alsointro-Fig.1.Schematic representation of the multimerization of S3gene using the gene ampli®cation vector,pBC.The Bbs I site was introduced into the S3primers,and the ampli®ed gene was cloned into pBC vector.After the Bbs I digestion,the S3gene with overhang terminals was self-ligated at 16°C for 2h,and inserted into pBC which was previously linearized with Bbs I.The CCCC head motif on the sense strand and the GGGG tail motif on the anti-sense strand allowed the fragments to self-ligate directionally,giving rise to multimers of pBCS3-nMer constructs.These multimeric inserts were subsequently released and recloned into expression vector pET22b.C.Li et al.630duced.Digestion of the PCR product by Bbs I yielded fragments with a complementary overhang of CCCC on the sense strand and GGGG on the anti-sense strand,which can be used for directional multimerization and cloning.In addition,the GATCCC sequence,which codes for aspartate(D)and proline (P),was introduced into the forward primer.The peptide bond between D and P can be cleaved under acidic conditions(Szoka et al.,1986),thus releasing single S3units from the recombinant multimers.In this case,the PCR products of S3 were cloned into pBC vector,and the S3gene was released by Bbs I digestion and allowed to self-ligate®rst,before cloning into the pBC vector,which was previously linearized with Bbs I.The multimers of S3gene were selected and identi®ed by enzyme digestion and sequencing.Expression of the multimers of S3gene in E.coliTo construct expression vectors bearing tandem S3genes under the control of T7promoter,the fragments¯anked by Nde I and Hin dIII(containing the multimeric S3genes)were cloned into the vector pET22b,previously linearized with Nde I and Hin dIII.The constructs were transformed into the E.coli host, BL21(DE3),for expression.The colonies were cultured overnight in LB medium with100m g/ml ampicillin at37°C, then diluted1:100into fresh LB medium with100m g/ml ampicillin and grown to an OD600nm of0.6before induction with0.5mM IPTG(Promega).The cells were harvested every hour up to12h,and the expressed products were monitored by SDS±PAGE.Solubilization of inclusion bodies and puri®cation of rS3-4merOne litre cultures were pelleted at5000g for10min at4°C and resuspended in60ml of lysis buffer containing20mM Tris±Cl, pH8.0and0.5mM DTT.The bacterial cells in the suspension were passed through a French Press(Basic Z0.75KW Benchtop Cell Disruptor,UK)operated at15kpsi for four rounds in order to generate>90%cell disruption.The inclusion bodies were recovered by centrifugation at12000g for20min at4°C and washed with20mM Tris±Cl buffer containing1M urea and0.5%Triton X-100.The inclusion bodies were denatured and solubilized in20mM Tris±Cl with8M urea at room temperature for2h.Insoluble materials were removed by centrifugation at16000g for20min,and the supernatant was ®ltered and puri®ed by anion exchange using AÈKTA explorer (Pharmacia).Brie¯y,30ml of solubilized proteins were applied to a Q-Sepharose column(26Q300mm)equilibrated with buffer A(4M urea,20mM Tris±Cl pH6.7).After washing with four column volumes of buffer A,the proteins were eluted with a linear gradient of0±30%buffer B(4M urea, 20mM Tris±Cl pH6.7,1M NaCl)and the fractions were collected for SDS±PAGE analysis.The collected fractions were pooled and dialyzed in10kDa molecular weight cut-off (MWCO)pore size dialysis tubing(Snakeskin;Pierce,IL), against refolding buffer A containing50mM glycine,pH9.5, 10%sucrose,1mM EDTA and2M urea at4°C for16h, followed by buffer B containing20mM diethanolamine pH 9.5,10%(w/v)sucrose and1mM EDTA at4°C for another8h. Monomerization of rS3-4mer into rS3-1mer by acid digestionTwo adjacent amino acids,aspartate and proline were added between the S3units,so as to act as cleavable DP linkers.The renatured rS3-4mer was precipitated with nine volumes of ethanol,frozen at±80°C for1h or at±20°C overnight.The mixture was centrifuged at16000g for10min and the pellet was washed with90%ethanol,dried,dissolved in digestion buffer(70%formic acid,6M guanidine±Cl)and digested at 42°C for72h.The®nal products were subjected to ethanol precipitation and dissolved in20mM Tris±Cl pH7.3.The cleaved rS3peptides were then dialyzed overnight against the same buffer using dialysis tubing of1.5kDa MWCO pore size (Sigma),thus removing the small linkers and residual salt.The endotoxin contaminant in rS3-4mer and rS3-1mer was removed by Triton X-114phase separation(Liu et al.,1997) followed by polymyxin B af®nity chromatography(Detoxi-GelÔ;Pierce).Tricine SDS±PAGE and western blot analysisThe recombinant proteins were resolved on tricine SDS±PAGE,using5%stacking gel and15%separating gel,and detected by Coomassie blue staining(Schagger and von Jagow, 1987).Western blot analysis was performed according to the manufacturer's instruction,using an ECL western analysis system(Pierce).The blot was probed with polyclonal rabbit anti-S3antibody followed by goat anti-rabbit secondary antibody conjugated to horseradish peroxidase(HRP;Dako, CA).The blots were visualized using Supersignal West Pico Chemiluminescent Substrate and exposed to X-ray®lm. ELISA-based LPS-binding assayThe polysorp96-well plate(MaxiSorpÔ;Nunc)was®rst coated with100m l per well of4m g/ml(~1m M)of LPS diluted in pyrogen-free phosphate-buffered saline(PBS).The plate was sealed and incubated overnight at room temperature.The wells were aspirated and washed four times with300m l wash solution(PBS containing0.05%Tween-20).The wells were blocked with wash solution containing2%BSA for1h at room temperature.After washing twice,varying concentrations of peptides were allowed to interact with bound LPS at room temperature for3h.Bound peptides were detected by incubation with rabbit anti-S3antibody and1:2000of goat anti-rabbit antibody conjugated with HRP.Each antibody was incubated for2h at37°C.In the®nal step,100m l of substrate, ABTS(Boehringer Mannheim),was added.The absorbance was measured at405nm with reference wavelength at490nm. Endotoxin neutralization assay based on anti-LAL testThe LAL Kinetic±QCL kit utilizes the initial part of the LPS-triggered cascade in LAL to achieve an enzymatic reaction, which catalyzes the release of p-nitroaniline from a synthetic substrate,producing a yellow color,which is quanti®able by absorbance at405nm.The ENC50(endotoxin neutralization concentration)refers to the peptide concentration required to neutralize50%of a predetermined quantity of endotoxin.A low ENC50indicates high potency of the peptide for endotoxin neutralization.In this assay,peptides of different concentrations were incubated for1h at37°C with or without an equal volume of LPS in disposable,endotoxin-free borosilicate tubes.Fifty microliters of each mixture was then dispensed into wells of a sterile microtiter plate(NunclonÔD surface;Nunc).Fifty microliters of freshly reconstituted LAL reagent was dispensed into each well.The absorbance at405nm of each well was monitored after45min,and the concentration of peptides corresponding to50%inhibition of LAL activity was desig-nated ENC50.LPS neutralized by tandem repeat of Sushi3631Suppression of LPS-induced hTNF-a secretion in human THP-1cellsTHP-1cells were cultured at37°C in a humidi®ed environment in the presence of5%CO2.RPMI1640medium was supplemented with10%fetal bovine serum(FBS),penicillin (100U/ml)and streptomycin(100m g/ml).The cells were maintained at a density of 2.5Q105±6cells/ml.THP-1 monocytes were transformed into macrophages by addition of phorbol myristic acid(PMA;Sigma)at a stock of0.3mg/ml in dimethyl sulfoxide to give a®nal concentration of30ng/ml and0.01%dimethyl sulfoxide.PMA-treated cell suspensions were immediately plated into96-well microtiter plate at a density of4Q105cells/ml and allowed to differentiate for48h at37°C.The culture medium was removed and the cells were washed twice with serum-free RPMI1640.Thereafter,the macrophages were stimulated with50EU/ml LPS(a speci®c activity of LPS that has been standardized by LAL test against FDA-approved LPS standards),peptides alone or LPS(pre-incubated with various concentrations of peptides)and incu-bated at37°C.After6h,the culture medium was collected and hTNF-a concentration in the supernatants was assayed using ELISA.Real time interaction analysis between peptides and LPS Surface plasmon resonance(SPR)analysis of the real time interaction between peptides and LPS was performed with BIAcore2000(Pharmacia)using HPA chip(Tan et al.,2000b). The af®nity constant was calculated using BIAevaluation software3.0.The mean values were obtained from three independent experiments.Cytotoxicity of peptides in eukaryotic cellsTHP-1monocytes in50m l of2Q104cells/ml in RPMI1640 were mixed in a microtiter plate with50m l of two-fold serial dilutions of peptides ranging in concentration,and incubated for60min at37°C.To determine the cytotoxicity induced by the peptides,20m l of CellTiter96Aqueous One Solution Reagent was added into each well for90min at37°C.MTS [3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium]is bioreduced by metabol-ically active cells into a colored formazan product that is soluble in tissue culture medium.For detection,the absorbance was measured at490nm.To determine the ratio of cell lysis induced by the peptides,two controls were included by incubating cells in PBS containing0.2%Tween-20instead of medium only.This absorbance value corresponds to the background,as those cells could not metabolize MTS.ResultsRecombinant expression of S3tandem repeats,puri®cation and cleavage to monomersA143bp S3gene fragment was obtained by PCR using pAC5.1Sushi3EGFP as the template.The S3gene was cloned into pBC vector by digestion with Bbs I.After multimerization, the clones containing one,two,four and eight copies of S3were selected(Figure2a)and named pBCS3-1,-2,-4and-8mer,respectively.The Nde I and Hin dIII-¯anking fragments of these clones were inserted into pET22b for expression of the multimeric S3gene,and the expression levels were examined by SDS±PAGE.Of all the expression cassettes,the tetramer yielded the highest expression level,giving the expected recombinant S3tetramer(rS3-4mer)of18.4kDa,which represented25%of the total cell proteins(Figure2b).The monomer construct was not expression-competent,while the octamer construct expressed poorly.The rS3-4mer was expressed as inclusion bodies in E.coli. The solubilization in8M urea and puri®cation through Q-Sepharose anion exchange chromatography produced more than95%purity of rS3-4mer(Figure2b),yielding42mg rS3-4mer per litre of culture.The puri®ed protein was dialyzedand Fig.2.Identi®cation of multimers of S3gene and expression in E.coli.(a) Electrophoretic analysis of the multimeric S3genes.The number of S3 inserts cloned in the pBC was determined by digestion with Nde I andHin dIII,which¯ank the multimers.The digests were resolved on2% agarose ne M,100bp DNA ladder;lanes1±4,Nde I and Hin dIII digested pBCS3-1,-2,-4and-8mer,which contain1,2,4and8copies ofS3gene,respectively.(b)Expression of multimers of S3gene in E.coliBL21(DE3).The recombinant peptides were resolved on SDS±PAGE constituting5%stacking gel and18%resolving ne M,peptide markers;lane1,BL21containing pET22b;lanes2±5,BL21containing S3-1, -2,-4and-8mer,respectively;lane6,puri®ed rS3-4mer.The arrows indicate the recombinant proteins.C.Li et al. 632urea was removed gradually to allow the samples to refold.Dialysis also removed unspeci®c small molecular weight bacteria proteins,hence further improving the purity of the rS3-4mer.SDS±PAGE under non-reducing conditions showed a majority of one band with the expected size (data not shown).A minor form of a larger aggregate was removed by size exclusion using a Superose â12column (Pharmacia).The refolded protein was precipitated with 90%ethanol and redissolved in acid digestion buffer to obtain the monomers (rS3-1mer).The process of acid digestion is time dependent.A 1day treatment yielded polymeric mixtures of four kinds of rS3peptides:rs3-4mer,rS3-3mer,rS3-2mer and rS3-1mer (Figure 3a).Within 2days,>90%of the multimers were cleaved to the monomers.Recombinant Sushi3peptides show stronger binding potency to LPSSamples from the total cell protein,puri®ed rS3-4mer,partially digested rS3polymers,rS3-1mer and synthetic S3peptide were resolved on tricine SDS±PAGE and subjected to western blot analysis against anti-S3antibody.The rS3-1mer and itspartially digested polymeric repeats (2,3and 4mers)were immunoreactive to the polyclonal rabbit anti-S3antibody (Figure 3b).Thus,the antibody can be employed for the ELISA-based LPS-binding assay.ELISA-based LPS-binding assay revealed different binding capabilities with rS3-1mer,rS3-4mer and synthetic S3.At 4m g/ml,both recombinant peptides reached saturation of binding to LPS (Figure 4),while the synthetic peptide continued linearly and required 20m g/ml to reach saturation of binding with LPS (data not shown).The EBC 50of the peptide,which achieves 50%of maximum binding to LPS on the ELISA plate,re¯ects the binding activity of peptide to LPS,with the lower EBC 50indicating higher potency.The rS3-4mer,rS3-1mer and synthetic S3peptides displayed EBC 50at 0.41,1.02and 9.74m g/ml,respectively.The kinetics of binding of peptides to LPS in 20mM Tris±Cl pH 7.3,was also measured by SPR analysis with BIAcore 2000using HPA chip,which was immobilized with LPS.The K d values of synthetic S3,rS3-1mer and rS3-4mer are (7.80T 2.18)Q 10±7M,(4.74T 2.34)Q 10±8M,(1.71T 1.86)Q 10±8M,respectively.Thus,both the results from ELISA and SPR suggest that rS3-4mer is most ef®cient at binding LPS.The recombinant S3peptides inhibit endotoxin-induced LAL reaction and hTNF-a release from THP-1cellsThe ENC 50value of the peptides against 5EU/ml of LPS was determined to be 5.4m g/ml for rS3-4mer,9.2m g/ml for rS3-1mer and 11.2m g/ml for synthetic S3(Figure 5a).A lower ENC 50indicates higher potency of endotoxin neutralization.The binding isotherm of the two monomeric peptides,whether it is recombinant or synthetic,is similar,but rS3-4mer shows a 2-fold stronger LPS neutralization ef®cacy.Similar results were also obtained by measuring the ability of rS3-4and rS3-1mer to inhibit LPS-induced hTNF-a production by THP-1cells,which were incubated with 50EU/ml of LPS containing various concentrations of peptides.As shown in Figure 5b,rS3-1mer required 83.2m g/ml,whereas rS3-4mer required 40.4m g/ml to achieve 50%inhibition.The peptides show minimal cytotoxicity to eukaryotic cells Both recombinant peptides had minimal effect on cell permeabilization (data not shown).At the highestconcentra-Fig.3.Time course of formic acid cleavage of rS3-4mer into monomers and western blot analysis of recombinant peptides.(a )Digestion of rS3-4mer into monomers.The rS3-4mer was dissolved in cleavage buffer andincubated at 42°C with constant and gentle shaking.At 12,24,36and 48h,aliquots of 100m l of samples were sampled and added to 900m l of ethanol,chilled at ±20°C for 30min,centrifuged at 15000g for 10min,anddissolved in loading buffer for electrophoretic resolution on tricine SDS±PAGE with 5%stacking gel and 15%resolving nes 1±4,samples digested for 12,24,36and 48h,respectively;lane 5,intact rS3-4mer.(b )Western blot analysis of recombinant ne 1,total expressed cell proteins.The expressed 18.4kDa rS3-4mer strongly reacts with anti-S3antibody;lane 2,partially digested peptide mixtures containing rs3-4mer,rS3-3mer,rS3-2mer and rS3-1mer;lane 3,rS3-1mer derived from the rS3-4mer;lane 4,synthetic S3peptide.All peptides derived from rS3-4mer reacted with theantibody.Fig.4.ELISA-based LPS binding assay.LPS was coated overnight on 96-well plates.Varying concentrations of peptides were allowed to interact with the immobilized LPS.The amount of bound peptides was determined by rabbit anti-S3IgG and quantitated by ABTS substrate.The average OD 405nm values of the triplicate samples were calculated and plotted with the corresponding concentration.LPS neutralized by tandem repeat of Sushi3633tion of 50m M,rS3-4mer caused only 2±3%of cell lysis,indicating that the recombinant multimers of S3would have negligible contraindications,although the LPS-binding activity is ampli®ed signi®cantly.DiscussionS3has been shown to be one of the LPS-binding sites of Factor C,and is able to suppress the LPS-induced cytokine production in macrophages (Tan et al .,2000b).The immobilized S3peptide analogue can remove LPS from culture medium with high ef®ciency (Ding et al .,2001).Thus,this promising reagent can be applied to prevent sepsis due to circulating LPS,which is released by viable or injured Gram-negative bacteria.Chemical synthesis is an uneconomical approach to obtain a large quantity of this peptide,whereas expression in E.coli may be more cost-effective (Latham,1999).However,the yield from E.coli may be low and unstable (Le and Trotta,1991).Thus,expression of the multimers of peptides would circum-vent the above mentioned problems (Kajino et al .,2000).A more important attribute for recombinant multimers of S3is the expected enhancement in ligand-binding af®nity and LPS-neutralization activity achieved through synergistic effects of multiple LPS-binding units in one molecule (Mauro and Pazirandeh,2000).Many methods can be applied to construct the tandem repeats of a peptide (Dolby et al .,1999;Lee et al .,2000;Mauro and Pazirandeh,2000).We chose the ampli®cation vector that readily allows us to obtain various multimers of S3gene.Furthermore,we designed the DP linker between the repetitive units,to afford convenient cleavage under mildly acidic buffer to release the monomers.The multimeric constructs exhibit different expression levels.No expression was observed with the pETS3-1mer.As the copy number increases,the expression level improved dramatically,especially with the S3tetramer,where the expression level reached 25%of the total cell proteins.However,further doubling to 8mer reduced the expression level,suggesting that the copy number is not always proportional to the expression level for this peptide.The ELISA-based LPS-binding test and SPR results show differ-ential binding ef®ciencies of rS3-4mer,rS3-1mer and the synthetic S3for LPS,with highest binding achieved by rS3-4mer.Both the LAL inhibition test and suppression of TNF-a release in THP-1cells showed that rS3-1mer works equally well as the synthetic S3peptide to neutralize LPS,while rS3-4mer displayed a 2-fold higher anti-LPS activity.However,the rS3-1mer and synthetic S3showed inconsistent results in ELISA and SPR tests.Two major forces mediate the interaction between LPS and LPS-binding peptides.The positive charge on the peptides forms an electrostatic attraction with the nega-tively charged phosphate head groups of the LPS.The other is the hydrophobic interaction between them (Farley et al .,1988;Goh et al .,2002).In fact,mutation of amino acid residues of S3aimed at introducing positive charges,only achieved a slight increase in LPS-neutralizing activity (Tan et al .,2000b).Besides charge modi®cation,little effort has been taken to enhance the LPS-binding ability of such peptides.Herein,by creating tandem repeats of the LPS-binding units,instead of increasing the number of positive charges,we demonstrate a two-fold improvement in the activity of the tetramer compared to the original monomeric unit,thus providing an alternative strategy to improve the LPS-binding activity of similar peptides.The result of secondary structure analysis by the DNAMAN program (Version 4.15,Lynnon Biosoft)shows that both S1and S3have a distinctive structure of four regular b -sheets alternately spaced by turns and coils.We presume that this structure may be important to the interaction with LPS,and in addition,the multiple b -sheets in rS3-4mer,may form the b -barrel structure to provide better shielding of hydrophobic acyl chains of LPS (Ferguson et al .,1998).Further structure analysis by CD or NMR will helptoparison of rS3-4mer and rS3-1mer with synthetic S3in inhibition of the LPS-induced LAL assay and hTNF-a secretion in human THP-1cells.(a )Inhibition of the LPS-induced LAL assay.Binding of the peptides to LPS would competitively inhibit the chromogenic reaction in the kinetic-QCL LAL test.The ENC 50values of rS3-4,rS3-1mer and synthetic S3peptide were determined to be 5.4,9.2and 11.2m g/ml,respectively.(b )Suppression of LPS-induced hTNF-a secretion in human THP-1cells.The rS3-4mer and rS3-1mer were tested for their ability to suppress LPS-induced hTNF-a secretion from THP-1cells.Both peptides inhibit hTNF-a production in a dose-dependent manner,albeit with different ef®ciency.rS3-4mer required only 40.4m g/ml to achieve ENC 50,compared to 83.2m g/ml needed for rS3-1mer.The decrease in TNF-a secretion was expressed as a percentage of control (LPS only).C.Li et al.634。