| P53, known as a cancer inhabited factor, plays a key role in tumor occurrence,development and treatment. P53 has“gene guard”function, participating in many biologicalprocesses, such as cell cycle arrest and/or apoptosis and DNA repair. P53 may lose itsfunction when binding with other proteins or appearing gene mutation. In malignant tumor,mutations in P53 are associated with over 50% of human mutations found in tumors,furthermore mainly located in P53-DNA binding domain. In human tumor, P53 mutations arelocated in highly conserved regions, especially 175, 245, 248, 249, 273 and 282 residues aremutated frequently. There are 3“host spots”in region IV (residue 234 -255). The study oneffect of residue mutations on P53 structure was important for the prevention and treatmentthe diseases caused by tumor.Molecular dynamics simulation, as an effective supplement method to experiment, hasimportant effects on studying structure and function about biological molecules. In this study,the structural characters of the P53 segment were studied by molecular dynamics simulationswith different mutations R249S, R248W and G245S. Four independent simulations forwild-type segment wtP53, one-point mutation segment P53-R249S, two-point mutationsegment R249S/R248W and three-point mutation segment R249S/R248W/G245S whichwere located in the P53-DNA binding domain (from residue 230 to 258) were performed withGROMACS soft package and GROMOS 43A1 force field. Each simulation was lasted for500 ns. The effects of different residue mutations on structure were studied by analyzing theseparameters such as the secondary structure, the tertiary structure, the structure heterogeneityand the structural stability. The results were as follow.(1) Compared with wtP53 segment, when R249S was mutated, the conformations werestill mainlyβstructures, but the probability decreased and the tendency to produce theα-helix conformation increased. The formation of the strand structures reduced at both ends of thesegment, but near the mutant the probability of forming the strand structures increased. Thefreedom energy of the conformation was lower to cause the structure stably. The structure andthe heterogeneity near the mutation R249S had no changes; meanwhile the structures near theresidues 245 and 248 had no changes. The mutation R249S had effect on the formation ofsecondary structure for some residues, but had little effect on the mode of the ternarystructure.(2) On the other hand, the R249S/R248W mutation strengthened the effect of R249S onthe segment. The conformation could still mainly keepβstructures, but the probability of theα-helix conformation increased. The formation of the secondary structures which showed 2turns and 3 strands motif, varied considerably; simultaneously a great change of ternarystructure was induced. Based on the mutation R249S, the structure near the mutation becamevery compact and more stable because of R248W. The structure heterogeneity of P53 segmentwhich had the small fluctuation became very low.(3) The changes of the peptide segment caused by R249S/R248W could decrease withthe mutation G245S. The distribution of potentially mean forces obtained from ramachandranwas similar to wtP53 segment. The formation of secondary structures was similar toP53-R249S segment, but the ternary structure formation was similar to wtP53 segment. Itrevealed that the mutation G245S had an opposite effect on the peptide segmentcorresponding to the mutation R249S/R248W. The structure heterogeneity of P53 segmentchanged very much, especially near the mutation G245S the residues had large fluctuationand the structure was relatively loose.This paper was divided into 5 chapters. The first chapter was an introduction in which weintroduced P53 protein, the structure and function of calcium protein and the mutation locatedin P53-DNA binding domain. In the second part, molecular dynamics simulation wasintroduced including molecular dynamics simulation principles, the application anddevelopment of molecular dynamics simulation and the GROMACS simulation softwarefrequently used. In the third part, we introduced the research system and methods containingthe system selection, the simulation scheme and several analysis methods of the simulation trajectory. We analyzed the simulation systems in various degrees in the fourth part. At first ,we proved the simulation was ensured convergence. We calculated the secondary structure,the ternary structure, the structure heterogeneity and the structural stability for the differentmutation systems. The summary and prospect were presented in the last chapter. |
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