Structural Recognition And Modification Of Key Amino Acids In Peptides And Proteins By Molecular Dynamics Simulation

Determining the key structures of biological macromolecules and their targeted transformation have become the research difficulties today.The following two problems are studied with MD simulation in this paper:1)Identify the key structure of hepcidin;2)Transform the amino lyase directionally.The work is as follows:1)Determining the key structures of hepcidin.Hepcidin has been proven to be a major regulator of iron homeostasis in vertebrates,thus it is important to determine the structure of hepcidin.Molecular dynamics simulation was performed to investigate the effects of different disulfide connectivity patterns on the structure of hepcidin in this paper.The potential energies of 105 isomers were calculated,which can provide a reference for future work.The geometric rationality of 10 isomers with the lowest energy was checked by PROCHECK,three most probable hepcidin isomers were selected.In addition to validate the known disulfide connectivity pattern of hepcidin?Cys1-Cys8,Cys3-Cys6,Cys2-Cys4 and Cys5-Cys7,P95?,two other possible disulfide connectivity patterns are being proposed:Cys1-Cys7,Cys2-Cys4,Cys3-Cys6,Cys5-Cys8?P80?and Cys1-Cys6,Cys2-Cys5,Cys3-Cys4,Cys7-Cys8?P67?.The present research provides a basis on understanding the structure activity relationship of the protein complex interaction in other study,and will have important values in application of hepcidin and its homologues in medical diagnosis.2)Directional transformation of amino lyase.In the process of synthesizing the final product of adipic acid using lysine-2-hydroxyadipic acid,2-hydroxyadipic acid cannot be dehydrated to produce 2,3-dehydroadipic acid,so the final product,adipic acid,cannot be synthesized.MD simulation was performed in this paper to directionally transform aspartate lyase,to make it catalyzes the deamination of aminoadipate to obtain 2,3-dehydroadipate.MD simulation was performed to study the interaction between wild AspB and aminoadipate,and four key sites were found:187-THR,MET₃21,LYS₃24,and 326-ASN.These four sites were subjected to one-site saturation mutation,and some better mutants were found.Then,the better mutants were arranged and combined to obtain 27 three-site mutations and MD simulation was performed.At the same time,through the better mutants reported in the literature,16 new mutants obtained,and MD simulation was performed.Through bonding free energy,hydrogen bond,etc,several better mutants were selected for experimental confirmation,which provided a theoretical basis for the experimental exploration.