Computer-aided Protein Virtual Enzymatic Hydrolysis And Study On The Mechanism Of ACE Inhibitory Peptides And Their Screening

This research constructed a novel method of protein digestion prediction based on multi-disciplinary knowledge including statistics and bioinformatics,to compile the software,namely Protein Digestion Prediction?PDP?,for virtual proteolysis and established a preliminary set of method in predicting anti-hypertensive protein combining with the mechanism of lowering blood pressure.1.By using the model of endo-protease enzymolysis,the specificity of the three gastrointestinal protease?pepsin,trypsin and chymotrypsin?was analyzed and summarized,complying with the cleavage probability of the bond P1-P1'.According to the statistic analysis above,a peptide library was constructed with 13 kinds of amino acids?A,R,D,Q,E,H,L,K,M,F,P,W and Y?at C-terminus,such as 260 dipeptides,5200 tripeptides,and so on.Finally,the novel software of protein digestion prediction,PDP,was compiled through "The ergodic algorithm".2.Twelve angiotensin converting enzyme co-crystals screened from the protein database were superimposed to analyze the binding mechanism,revealing that the position and direction of the 12 ligands lying in the active center of ACE with a high degree of consensus.Further analysis of the active center of ACE discovered that it preferred to bind with the charged amino acids and aromatic amino acids,namely,the peptide containing charged or aromatic amino acid in the sequence would be more conducive to inhibit the activity of ACE.3.Two important parameters?ga_runs and ga_num_evals?during molecular docking with AutoDock software were optimized based on the number of rotable bonds?RBs?in a peptide.After optimizing the parameters of AutoDock,fifty-five peptides collected from literature including dipeptides and tripeptides,of which the IC₅₀ were known,were docked.The relationship between the docking energy value and IC₅₀ was:Binding Free Energy?kcal/mol?-0.7707Log(1/IC₅₀)-7.1688,R²=0.7129.4.Analysis of molecular docking results of 260 dipeptides and 5200 tripeptides,indicating that the peptide containing charged or aromatic amino acid in the sequence would be more conducive to inhibit the activity of ACE,which coincided with the conclusion of crystal analysis.The formula was established to predict the anti-hypertensive protein in a preliminary set of method,following as:In the formula:n is the total number of dipeptides and tripeptides;Pi is the possibility ratio of the peptide;Ei is the Binding Free Energy of the peptide;Xi is correction coefficient of peptide?default=1?;G is the score of ACE inhibitory activity of protein.