Sequence/Structure Variability in the Major Histocompatibility Complex Protein Class I alpha chain. Errol Archibold, Mark Maloney and Rafael Tosado. BioQuest / SCALE-IT Curriculum Workshop, 2009 Introduction to MHC MHC I Alpha Chain from Different Species SIXFRAME Analysis of Human MHC alpha I DNA Sequence >BWB5471 Translated - Frame 1 KAVYGLGSPSLGDSPTPQFLFSLSQPM*GPSSWILTTRTQFSLPSGVGFPEKPISVVAVAVLKSARTHRD SDSPQTPRMAVMAPRTLVLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDS DAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWR FLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKET LQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVV VPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVITGAVVAAVMWRRKSSDRKGG SYSQAASSDSAQGSDVSLTACKV* >BWB5471 Translated - Frame 2 RRCMDWGVPALGIPQLRSFFSPSPNLCRVLLPGYSRRGPSSHSHRVSGFQRSQSVSSRSRF*SPHAPTGT QILPRRRGWPSWRPEPSSCYSRGLWP*PRPGRALTP*GISSHPCPGPAAGSPASSQWATWTTRSSCGSTA TPRARGWSRGRRG*SRRVRSIGTGRHGK*RPTHRLTEWTWGPCAATTTRARPVLTPSRGCMAATWGRTGA SSAGTTSTPTTARITSP*KRTCALGPRRTWQLRPPSTSGRRPMWRSS*EPTWRARAWSGSADTWRTGRRR CSARTPPKRI*LTTLSLTMKPP*GAGP*ASTLRRSH*PGSGMGRTRPRTRSSWRPGLQGMEPSRSGRLWW CLLDRSRDTPAMCSMRVCPSPSP*DGSRLPSPPSPSWASLLAWFSLEL*SLELWSLL*CGGGRAQIEKEG ATLRLQAVTVPRALMCLSQLVKC >BWB5471 Translated - Frame 3 GGVWIGESQPWGFPNSAVSFLPLPTYVGSFFLDTHDADPVLTPIGCRVSREANQCRRGRGSKVRTHPPGL RFSPDAEDGRHGAPNPRPATLGGSGPDPDLGGLSLHEVFLHIRVPARPRGAPLHRSGLRGRHAVRAVRQR RREPEDGAAGAVDRAGGSGVLGRGDTESEGPLTDSPSGPGDPARLLQPERGRFSHRPEDVWLRRGVGLAL PPRVPPVRLRRQGLHRPERGPALLDRGGHGSSDHQAQVGGGPCGGAVESLPGGHVRGVAPQIPGEREGDA AAHGRPQNAYDSPRCL*P*SHPEVLGPELLPCGDHTDLAAGWGGPDPGHGARGDQACRGWNLPEVGGCGG AFWTGAEIHLPCAA*GFAQAPHPEMGAVFPAHHPHRGHHCWPGSLWSCDHWSCGRCCDVEEEELR*KRRE LLSGCKQ*QCPGL*CVSHSL*SV >BWB5471 Translated - Frame 4 SHFTSCERHIRALGTVTACSLRVAPSFSI*ALPPPHHSSDHSSSDHSSKENQASNDAHDGDGGLGRRLPS QGEGLGQTLMLHMAGVSLLLSRRHHHSRPLLEGSIPCRPGLHELRVLGLVLPIPLPGQCDLRRVEAQGPA PQGGFMVRDSVVSHMRFGGVRALQRLLPVLQVSAEPLHARALQVGSQLLRHMGRLPLVLGGLSCHVRRGP RAQVLFQGDVILAVVGVLVVPAEEAPVRPHVAAIHPLDGVRTGLALVVVAAQGPQVHSVSL*VGLHFPCL PVPILRTLLLYPRRPRLHPLARGVAVEPHELRVVHVAHCDEAGLPAAGPGHGCEEIPHGVRARPGLGQGQ SPRE*QDEGSGRHDGHPRRLGRI*VPVGACGL*NRDRDDTDWLLWKPDTRWE*ELGPRREYPGRRTLHRL GEGEKKLRSWGIPKAGTPQSIHRL >BWB5471 Translated - Frame 5 HTLQAVRDTSEPWALSLLAA*E*LPPFLSELFLLHITAATTAPVITAPKRTRPAMMPTMGMVGWEDGSHL RVRGLGKPSCCTWQVYLCSCPEGTTTAAHFWKVPSPAGLVSTSSVSWVWSSPSRCQVSVISAG*KLRAQH LRVASWSETAW*VICVLGASVRCSVSFPFSRYLRSHSTHVPSR*ALNCSATWAASHLCLVV*AAMSAAVQ ERRSSFRAM*SLPS*AYWWYPRRKRQSDPTSQPYILWTV*EPASLWL**PRRVPRSTR*VCEWAFTFRVS PSQYSGPSCSIHGARGSILWLAASLSNRTNCVSST*PTAMKRGSPRPGRDTDVKKYLME*EPAQVWVRAR APESSRTRVRGAMTAILGVWGESESRWVRADFRTATATTLIGFSGNPTPDGSENWVRVVSIQEEGPYIGW EREKRNCGVGESPRLGLPNPYTA >BWB5471 Translated - Frame 6 TLYKL*ETHQSPGHCHCLQPESSSLLFYLSSSSSTSQQRPQLQ*SQLQREPGQQ*CPRWGWWAGKTAPIS G*GAWANPHAAHGRCISAPVQKAPPQPPTSGRFHPLQAWSPRAPCPGSGPPHPAARSV*SPQGRSSGPST SGWLHGQRQRGESYAFWGRPCAAASPSRSPGICGATPRTCPPGRLSTAPPHGPPPTCAWWSELPCPPRSK SAGPLSGRCNPCRRRRTGGTRGGSASPTPRRSHTSSGRCENRPRSGCSSRAGSPGPLGESVSGPSLSVSP RPNTPDPPALSTAPAAPSSGSRRRCRTARTACRPRSPLR*SGAPRGRAGTRM*RNTSWSESPPRSGSGPE PPRVAGRGFGAP*RPSSASGENLSPGGCVRTLEPRPRRH*LASLETRHPMGVRTGSAS*VSRKKDPT*VG RGRKETAELGNPQGWDSPIHTPP MHC I Alpha Chain Human Variants MHC I Alpha Chain Structure MHC I Alpha Chain Species Tree Conclusions Presentation of antigenic peptides to T cells. Rejection of transplanted tissues. Highly polymorphic genes. Unlike enzymes, variation tends to be in the “active” site Class I and II molecules Class I in all nucleated cells. Class II in Antigen (Ag) Presenting Cells (APC). T-cell receptor (TCR) –Ag complex CD8 interact with Ag on MHCI CD4 interact with Ag on MHCII Crystal Structure revealed differences and similarities Antigen-binding groove Opposing alpha helixes at the opening Beta chains for the floor of the groove MHC I Alpha (heavy) chain + Beta micro-globulin Ag groove within the alpha chain MHC II Equivalent alpha and beta chains Both chains combine to form the Ag groove MHC Structure Class I alleles are more variable than WE had imagined! Despite the variation inherent in MHC genes, interspecies variation of MHC class I alleles was overall in line with other dendrograms based on hemoglobin or cytochrome c Investigation of the human HLA-A2 alpha chain using SIXFRAME and BLASTp analyses revealed alleles corresponding to both frame 1 and frame 3 ConSurf analysis indicated that the majority of variation at the peptide binding groove was in only one of the two alpha helices Future Directions In the future, we would determine where the interspecies variation is highest one the MHC class I molecules. We would also like to further define the relationship between HLA-A alleles and alleles of the other MHC class I loci (HLA-B and HLA-C).