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Computational Approach To Identification and Immunogenic Characterisation of Chap'S Protein
Computational Approach To Identification and Immunogenic Characterisation of Chap'S Protein
Computational Approach To Identification and Immunogenic Characterisation of Chap'S Protein
PREMNATH.D *
Can target multiple conserved epitopes in rapidly mutating pathogens like HIV and Hepatitis C virus (HCV)
Can induce subdominant epitopes (e.g. against tumor antigens where there is tolerance against dominant epitopes)
EPITOPES
In protein antigens epitopes can be defined in terms of: Amino acid composition Protein location
By properties that epitopes have Hydrophilicity Readily available, but not very accurate
COMPUTATIONAL STRATEGY
Homology modeling. Peptide prediction. PROT PARM svrMHC SVM MAST SIGNAL IP NET chop tool CHARMm Q-site finder. Autodock 3.0.5. ZDOCKpro RDOCKpro.
Protparam Results :
>gi|30525581|gb|AAP32277.1| immunogenic protein ChaPs [Piscirickettsia salmonis] MSAKEVRFGTGSRQKMLDGVNLLANAVKVTLGPRGRNVILEKSFGAPTIT KDGVSVAKEIELSDKFENMGAQMVKEVASKSNDDAGDGTTTATVLAQAII GVKSVAAGMNPMDLKRGIDKATIAAVAALKDLSTPCTDNKAIAQVGTI SANSDEEIGSIIAKAMEKVPTDGVITVEEGSSLENELDVVEGMQFDRGYLSPYFVNKQEKMIAEIESPFILLV DKKISNIRELLPTLESVAKSGKPLFIIAEDVEGEALATLVVNNIRGIVKVCAVKAPGFGDRRKAMLEDIAILTG GTVISEEVGLDLEKATLEHLGTAKRIVVTKDNTTVIDGAGEQNAIEARVTQRAQVEETSSDYDREKLQERVA KLSGGVAVIKVGAATEIEMKEKKDRVDDALHATRAAVEEGVVPGGGVALVRAMAAVKALDFANDEQAQG ANILLRAMSAPLRQIVENAGSEAAVILDKIVNGEGNFGYNAATNEFGDMIEMGILDPTKVTRSALQNAASIA GLMITTEAMVAELPKEDSAGGAGMPDMG
molecular weight of the chaps was 5735.6. The amino acid composition are Ala 12, Arg 3.9, Asn 4.2, Asp 6.1, Cys 0.4, Gln 2.8%, Glu 8.8%, Gly 9.5%, His 0.4%, Ile 7.2%, Leu .3%, Lys 7.0%, Met 4.0%, Phe 2.0%, Ser 5.1%, Thr 5.9, Trp 0.0%, Tyr 0.7%, Val 9.4%.The negatively charged residues are Asp+Glu is 81 and the positively charged residues are 59( Arg + Lys). The domain was predicted from the SMART tool from the position 1-19 the protein was found to be disordered protein and the PFam was observed as
23-525 score.
PEPTIDE IDENTIFICATION
Signal Ip
The phosphorylation tools are used to predict the phosphorylation site in the chaps protein. It was found that Serine, Threonine and Tyrosine amino acids involved in the phosphorylation are 13,18,19,23 and 7 The MHC binding complexes are identified in the chaps protein using the Net phos tool. The Net phos tool predict that the 74 position of amino acid sequences are identified as the MHC binding peptide from 245 sequences
MHC/PEPTIDE COMPLEX
AUTODOCK RESULT
From the autodock result the peptide strongly bind with the region of TYR59,LYS66 3HLA mhc protein
From protein to immunogen 20%processing and 5%HLA binding 50%T-cell response has been functioning in peptide vaccine
PROTEIN-PROTEIN DOCKING
computational determination of the structure of protein complexes from individual protein structures Biological activity depends on the specific molecular recognition of proteins Virtually every cellular process is regulated by proteinprotein interactions Signal transduction cascades e.g. cancer Understanding mechanism of action of therapeutically interesting proteins (protein therapeutics) In the area of rational approaches for drug development and treatment of disease
MHC/peptide
pMHC/TCRs
ZDOCKpro RESULT
The pMHC/TCRs complex has to be bind to the specific binding site amino acid LYS41,SER39 from the qrn-d alpha chain protein and Leu230,Glu232 pMHC complex
OBSERVATION
The epitope peptide TSSAYGGGA (344-352) has the highest MHC binder identified from auto dock result through peptide /MHC complex. The result obtain from the ZDOCKpro have shown that strong binding RMSD value of 7.96 by the amino acid LYS41 ,SER39 from the complex protein.
The project concludes the immunogenic analysis and model of chaps suggested that this protein is a good target for vaccine design for the fish disease pickkerittisea salmon.
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