多肽设计原理和方法

1、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, to be sure the antigen is on the surface of the protein. Antigenicity, amino acid provides good bonds. N- or C-terminal peptide, for they are exposed in most proteins. Contains MHC II preferred mot

2、ifs. Such as D, Y, P, and F who appears in MHC molecules most frequently. No homology with other proteins by blast. Prefer the cytoplasmic domain for a transmembrane protein, for they are more immunogenic Avoid glycosylation and phosphorylation sites if possible Avoid cystin in the middle part of th

3、e peptide,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， EPHB6 MATEGAAQLGNRVAGMVCSLWVLLLVSSVLALEEVLLDTTGETSEIGWLTYPPGGWDEVSVLDDQRRLTRTFEACHVAGAPPGTGQDNWLQTHFVERRGAQRAHIRLHFSVRACSSLGVSGGTCRETFTLY

4、YRQAEEPDSPDSVSSWHLKRWTKVDTIAADESFPSSSSSSSSSSSAAWAVGPHGAGQRAGLQLNVKERSFGPLTQRGFYVAFQDTGACLALVAVRLFSYTCPAVLRSFASFPETQASGAGGASLVAAVGTCVAHAEPEEDGVGGQAGGSPPRLHCNGEGKWMVAVGGCRCQPGYQPARGDKACQACPRGLYKSSAGNAPCSPCPARSHAPNPAAPVCPCLEGFYRASSDPPEAPCTGPPSAPQELWFEVQGSALMLHWRLPRELGGRGDLLFNVVCKECEGRQEPASGGGGTCHRCRDEV

5、HFDPRQRGLTESRVLVGGLRAHVPYILEVQAVNGVSELSPDPPQAAAINVSTSHEVPSAVPVVHQVSRASNSITVSWPQPDQTNGNILDYQLRYYDQAEDESHSFTLTSETNTATVTQLSPGHIYGFQVRARTAAGHGPYGGKVYFQTLPQGELSSQLPERLSLVIGSILGALAFLLLAAITVLAVVFQRKRRGTGYTEQLQQYSSPGLGVKYYIDPSTYEDPCQAIRELAREVDPAYIKIEEVIGTGSFGEVRQGRLQPRGRREQTVAIQALWAGGAESLQMTFLGRAAVLGQFQHPNI

6、LRLEGVVTKSRPLMVLTEFMELGPLDSFLRQREGQFSSLQLVAMQRGVAAAMQYLSSFAFVHRSLSAHSVLVNSHLVCKVARLGHSPQGPSCLLRWAAPEVIAHGKHTTSSDVWSFGILMWEVMSYGERPYWDMSEQEVLNAIEQEFRLPPPPGCPPGLHLLMLDTWQKDRARRPHFDQLVAAFDKMIRKPDTLQAGGDPGERPSQALLTPVALDFPCLDSPQAWLSAIGLECYQDNFSKFGLCTFSDVAQLSLEDLPALGITLAGHQKKLLHHIQLLQQHLRQQGSVEV 共1021aa，

7、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）,GENE ID: 2051 EPHB6 | EPH receptor B6 Homo sapiens Query 1 WDEVSVLDDQRRLTRTFEAC 20 WDEVSVLDDQRRLTRTFEAC Sbjct 41 WDEVSVLDDQRRLTRTFEAC 60 GENE ID: 814 CAMK4 | calcium/calmodulin-dependent protein kinase IV Query 1 WDEVS- VLDDQRRLTRTFEA 1

8、9 WDEVS VLD +RLT TF+A Sbjct 69 WDEVSLNAKDLVRKLIVLDPKKRLT- TFQA 97,案例2 家族性蛋白的多肽设计（transgelin）,The transgelin family is a group of proteins that belong to 22kd actin-related corpnin superfamily. Of all three isoforms, transgelin 1 is the best characterized. Transgelin 1, also known as SM22alpha, is a

9、specific marker for differentiated smooth muscle cells. Transgelin 2, also known as SM22 beta, is expressed by both smooth muscle and non-smooth muscle cells in a temporally and spatially regulated pattern. Trangenlin 3, also known as NP25, is only found in highly differentiated neuronal cells.,案例2家

10、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,Transgelin 1:KYDEELEERLVEWIIVQC Transgelin 2:QPGRENFQNWLKDGTVLC,案例3 家族性蛋白的多肽设计 RAB3A,3B,3C,Sequence 2: NM_002866, RAB3A, member RAS oncogene family Sequence 3: NM_002867, RAB3B, member RAS oncogene family Sequence 4: NM_138453, RAB3C, member RAS onc

11、ogene family,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, NUCLEAR FACTOR KAPPA-B, SUBUNIT 1; NFKB1 Alternative titles; symbols TRANSCRIPTION FACTOR NFKB1NUCLEAR FACTOR OF KAPPA LIGHT CHAIN GENE ENHANCER IN B CELLS 1NFKB p105, INCLUDEDNFKB p50, INCLUDED,案例5 同一蛋白质不同亚型的多肽设计 NFKB1,This g

12、ene encodes a 105 kD protein which can undergo cotranslational processing by the 26S proteasome to produce a 50 kD protein. The 105 kD protein is a Rel protein-specific transcription inhibitor and the 50 kD protein is a DNA binding subunit of the NF-kappa-B (NFKB) protein complex. 1433 amino acids o

13、f full length 968 p105 protein form p50.,案例5 同一蛋白质不同亚型的多肽设计 NFKB1,MAEDDPYLGRPEQMFHLDPSLTHTIFNPEVFQPQMALPTADGPYLQILEQPKQRGFRFRYVCEGPSHGGLPGASSEKNKKSYPQVKICNYVGPAKVIVQLVTNGKNIHLHAHSLVGKHCEDGICTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHPDLAYLQAEGGGDRQLGDREKELIRQAALQQTKEMDLSVVRLMFTAFLPDSTGSFTRRLEP

14、VVSDAIYDSKAPNASNLKIVRMDRTAGCVTGGEEIYLLCDKVQKDDIQIRFYEEEENGGVWEGFGDFSPTDVHRQFAIVFKTPKYKDINITKPASVFVQLRRKSDLETSEPKPFLYYPEIKDKEEVQRKRQKLMPNFSDSFGGGSGAGAGGGGMFGSGGGGGGTGSTGPGYSFPHYGFPTYGGITFHPGTTKSNAGMKHGTMDTESKKDPEGCDKSDDKNTVNLFGKVIETTEQDQEPSEATVGNGEVTLTYATGTKEESAGVQDNLFLEKAMQLAKRHANALFDYAVTGDVKMLLAVQR

15、HLTAVQDENGDSVLHLAIIHLHSQLVRDLLEVTSGLISDDIINMRNDLYQTPLHLAVITKQEDVVEDLLRAGADLSLLDRLGNSVLHLAAKEGHDKVLSILLKHKKAALLLDHPNGDGLNAIHLAMMSNSLPCLLLLVAAGADVNAQEQKSGRTALHLAVEHDNISLAGCLLLEGDAHVDSTTYDGTTPLHIAAGRGSTRLAALLKAAGADPLVENFEPLYDLDDSWENAGEDEGVVPGTTPLDMATSWQVFDILNGKPYEPEFTSDDLLAQGDMKQLAEDVKLQLYKLLEIPDPDKNWA

16、TLAQKLGLGILNNAFRLSPAPSKTLMDNYEVSGGTVRELVEALRQMGYTEAIEVIQAASSPVKTTSQAHSLPLSPASTRQQIDELRDSDSVCDSGVETSFRKLSFTESLTSGASLLTLNKMPHDYGQEGPLEGKI,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,The CXCR3 protein belongs to G protein-coupled receptor family. Several alternatively spliced transcript variants encoding distinct isoforms have been reported.The CXCR3B protein contains 416 amino acids and has a longer N terminus that differs from the original 368-amino acid CXCR3 protein, CXCR3A, in the first 52 residues. This antibody, 60065-1-Ig, is specific for CXCR3B, not bindi