Bioinformatics Analysis Of Chicken MHC ? Proteins

Classical MHC class I molecules(MHC Is)play important functional roles in antigenic peptide binding,CTL(cytotoxic lymphocyte)activation and proliferation,and in anti-virus immune response.Till now,the structural and functional studies on the MHC Is is less,but Chicken as an important breeding poultry,can bring greater economic benefits.Therefore,based on the structure of chicken MHC,this study aims to use bioinformatics analysis to use DNAMAN,PyMol software and related biological sites for the B2 haplotype chicken MHC I molecule(BF2*0201).The three-dimensional structure of B2 was studied and compared with the known structures of B4 and B21 to elucidate the characteristics of BF2*0201-binding antigenic peptides,providing theoretical basis for future crystal structure,virus polypeptide antigen screening in poultry industry,vaccine design,and disease resistance breeding.The results show that in the BF2*0201,there are three amino acids,positively charged Arg9,negatively charged Asp24,and Asp73.Because of the presence of these three amino acids,the binding groove is negatively charged,to bias the binding of positively charged peptide.However,the uncertainty of the ionic bond between Arg9 and Asp24 and Asp73 has influence on the discovery of the binding polypeptide,and the amino acids that make up the peptide binding groove contain many hydrophilic and hydrophobic tyrosine.The amino acid Tyr also has an indefinite influence on the binding groove,so the binding law of B2 peptide cannot be determined at present.Therefore,comparing the two molecules of B2 and B4,it was found that due to the amino acid difference between the two binding groove,the size and chargeability of the binding groove of the two are different,resulting in different choices on the binding polypeptide.The long side chain Arg111 of B4 replaces the short side chain Tyr111 of B2,so that the middle of the binding groove of B4 becomes obviously narrower and the bound restrictive of amino acid becomes larger;and because of Arg9,Arg80,and Arg111 of B4 and Arg9,Asp24,and Asp73 of B2-specific amino acids,the difference the peptide and the binding groove between the two is very large,B4 binding groove has a strong positive polarity,very biased to bind polypeptides with negatively charged amino acids,indicating that the amino acid species B4 binding peptide has lower selectivity than B2.Then the B2 and the B21 were compared and analyzed.It was also found that the amino acid difference between the two binding grooves resulted in the difference in size and chargeability of the binding groove of the two,resulting in different choices on the binding polypeptide.However,B21's small side chain His111 replaces the short side chain Tyr111 of B2,and very small amino acid of Ser69 and Ser97 make the middle of the 3BEW's binding groove become apparently broad and bound restrictive of amino acid smaller.Moreover,due to the specific amino acids-Arg9,Asp24,and Asp73 of B2 and Arg9,Asp24,and His111 of B21,the effect of the polypeptide and the binding groove differs between the two,and B21 tends to bind polypeptides with negatively charged amino acids,but the large space in the middle can also accommodate other amino acids.Compared with the binding groove characteristic of B2,it can be said that the selectivity of B21 is higher than that of 4CVX in the amino acid type of the binding polypeptide.In summary,the study illuminate the characteristics of its antigen-polypeptide binding by the structure of B2 protein of analysis,and compared with B4 and B21,from the structural point of view,the middle resistance of relationship between B2 haplotype chicken and Marek's disease was demonstrated;and the reason for the difference in elution results of BF protein on the membrane surface was also speculated.