多肽设计原理和方法

多肽设计原则和方法 多肽抗原的特点 含有的epitope数目少 抗原性比融合蛋白弱 产生的抗原特异性通常比融合蛋白强 是一种半抗原 需要连接载体蛋白 多肽设计的原则 Hydrophilicity tobesuretheantigenisonthesurfaceoftheprotein Antigenicity aminoacidprovidesgoodbonds N orC terminalpeptide fortheyareexposedinmostproteins ContainsMHCIIpreferredmotifs SuchasD Y P andFwhoappearsinMHCmoleculesmostfrequently Nohomologywithotherproteinsbyblast Preferthecytoplasmicdomainforatransmembraneprotein fortheyaremoreimmunogenicAvoidglycosylationandphosphorylationsitesifpossibleAvoidcystininthemiddlepartofthepeptide 20种氨基酸的抗原性比较 什么时候选用多肽做抗原 我们没有基因的抗原 有基因 但是蛋白质和其他蛋白质有较强的同源性 或者蛋白质属于同源性较强的蛋白家族 有基因 需要区分该基因编码的蛋白质加工后的不同亚型 抗原是修饰蛋白质 包括磷酸化 乙酰基化蛋白质等 案例1我们没有的蛋白质 NM 004445 EPHB6MATEGAAQLGNRVAGMVCSLWVLLLVSSVLALEEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFEACHVAGAPPGTGQDNWLQTHFVERRGAQRAHIRLHFSVRACSSLGVSGGTCRETFTLYYRQAEEPDSPDSVSSWHLKRWTKVDTIAADESFPSSSSSSSSSSSAAWAVGPHGAGQRAGLQLNVKERSFGPLTQRGFYVAFQDTGACLALVAVRLFSYTCPAVLRSFASFPETQASGAGGASLVAAVGTCVAHAEPEEDGVGGQAGGSPPRLHCNGEGKWMVAVGGCRCQPGYQPARGDKACQACPRGLYKSSAGNAPCSPCPARSHAPNPAAPVCPCLEGFYRASSDPPEAPCTGPPSAPQELWFEVQGSALMLHWRLPRELGGRGDLLFNVVCKECEGRQEPASGGGGTCHRCRDEVHFDPRQRGLTESRVLVGGLRAHVPYILEVQAVNGVSELSPDPPQAAAINVSTSHEVPSAVPVVHQVSRASNSITVSWPQPDQTNGNILDYQLRYYDQAEDESHSFTLTSETNTATVTQLSPGHIYGFQVRARTAAGHGPYGGKVYFQTLPQGELSSQLPERLSLVIGSILGALAFLLLAAITVLAVVFQRKRRGTGYTEQLQQYSSPGLGVKYYIDPSTYEDPCQAIRELAREVDPAYIKIEEVIGTGSFGEVRQGRLQPRGRREQTVAIQALWAGGAESLQMTFLGRAAVLGQFQHPNILRLEGVVTKSRPLMVLTEFMELGPLDSFLRQREGQFSSLQLVAMQRGVAAAMQYLSSFAFVHRSLSAHSVLVNSHLVCKVARLGHSPQGPSCLLRWAAPEVIAHGKHTTSSDVWSFGILMWEVMSYGERPYWDMSEQEVLNAIEQEFRLPPPPGCPPGLHLLMLDTWQKDRARRPHFDQLVAAFDKMIRKPDTLQAGGDPGERPSQALLTPVALDFPCLDSPQAWLSAIGLECYQDNFSKFGLCTFSDVAQLSLEDLPALGITLAGHQKKLLHHIQLLQQHLRQQGSVEV共1021aa N 15aa为信号肽 案例1我们没有的蛋白质 2 WDEVSVLDDQRRLTRTFEAC 案例1我们没有的蛋白质 3 GENEID 2051EPHB6 EPHreceptorB6 Homosapiens Query1WDEVSVLDDQRRLTRTFEAC20WDEVSVLDDQRRLTRTFEACSbjct41WDEVSVLDDQRRLTRTFEAC60GENEID 814CAMK4 calcium calmodulin dependentproteinkinaseIVQuery1WDEVS VLDDQRRLTRTFEA19WDEVSVLD RLTTF ASbjct69WDEVSLNAKDLVRKLIVLDPKKRLT TFQA97 案例2家族性蛋白的多肽设计 transgelin Thetransgelinfamilyisagroupofproteinsthatbelongto22kdactin relatedcorpninsuperfamily Ofallthreeisoforms transgelin1isthebestcharacterized Transgelin1 alsoknownasSM22alpha isaspecificmarkerfordifferentiatedsmoothmusclecells Transgelin2 alsoknownasSM22beta isexpressedbybothsmoothmuscleandnon smoothmusclecellsinatemporallyandspatiallyregulatedpattern Trangenlin3 alsoknownasNP25 isonlyfoundinhighlydifferentiatedneuronalcells 案例2家族性蛋白的多肽设计 transgelin 2 案例2家族性蛋白的多肽设计 transgelin 3 Transgelin1 KYDEELEERLVEWIIVQCTransgelin2 QPGRENFQNWLKDGTVLC 案例3家族性蛋白的多肽设计RAB3A 3B 3C Sequence2 NM 002866 RAB3A memberRASoncogenefamilySequence3 NM 002867 RAB3B memberRASoncogenefamilySequence4 NM 138453 RAB3C memberRASoncogenefamily 案例4家族性蛋白的多肽设计actin 对应的处理方法 案例5同一蛋白质不同亚型的多肽设计NFKB1 NFKB1 NUCLEARFACTORKAPPA B SUBUNIT1 NFKB1Alternativetitles symbolsTRANSCRIPTIONFACTORNFKB1NUCLEARFACTOROFKAPPALIGHTCHAINGENEENHANCERINBCELLS1NFKBp105 INCLUDEDNFKBp50 INCLUDED 案例5同一蛋白质不同亚型的多肽设计NFKB1 Thisgeneencodesa105kDproteinwhichcanundergocotranslationalprocessingbythe26Sproteasometoproducea50kDprotein The105kDproteinisaRelprotein specifictranscriptioninhibitorandthe50kDproteinisaDNAbindingsubunitoftheNF kappa B NFKB proteincomplex 1 433aminoacidsoffulllength968p105proteinformp50 案例5同一蛋白质不同亚型的多肽设计NFKB1 MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEPVVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQRHLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWATLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKI 案例5同一蛋白质不同亚型的多肽设计NFKB1 案例6同一蛋白质不同亚型的多肽设计CXCR3 TheCXCR3proteinbelongstoGprotein coupledreceptorfamily Severalalternativelysplicedtranscriptvariantsencodingdistinctisoformshavebeenreported TheCXCR3Bproteincontains416aminoacidsandhasalongerNterminusthatdiffersfromtheoriginal368 aminoacidCXCR3protein CXCR3A inthefirst52residues Thisantibody 60065 1 Ig isspecificforCXCR3B notbinding