Molecular Dynamics Simulation Of The Stability Of Transcription Factor-nucleic Acid Complex

Transcription factor is a sequence specific DNA-binding protein.With the rapid development of protein crystal analysis technology,there has accumulated a large amount of complex crystal structure data of transcription factor and nucleic acid.How these data still cannot explain the dynamic mechanism of DNA methylation.It has become a feasible research protocol to explore the dynamic regulation mechanism of protein-nucleic acid interaction between Mg²⁺ion and gene substitutions by using the molecular simulation technology.After literature research and crystal structure data search,CREB transcription factor was selected as the research system of metal ion magnesium and WRKY as the research system of single base substitution.The research idea of this thesis is to study the regulatory mechanism of transcription factors and nucleic acids by comparing the effects of deletion of Mg²⁺ion and base substitution on the stability of transcription factors and nucleic acid complex in different systems.To this end,the molecular dynamics simulation of the selected system was carried out for a long time,and then we analyze and compare from the perspectives of RMSD,RMSF,Rg,SASA,hydrogen bond,DNA structural parameters,protein relative conformation and binding free energy.The following research progresses were made:Firstly,taking CREB protein binding to consistent DNA sequence CRE as an example,the effects of Mg²⁺interaction between transcription factor and DNA was studied.It is illustrated that the number of hydrogen bonds formed at the interface between protein and DNA is significantly increased when the Mg²⁺ion is added.Hence,an obvious change in the structure of the DNA is observed.Then the DNA base groove and base pair parameters are analyzed.We find that due to the introduction of the Mg²⁺ion,the DNA base major groove becomes narrower.A potential mechanism for this observation is proposed.It is confirmed that the Mg²⁺ion can enhance the stability of the DNA–protein complex.Secondly,taking WRKY protein binding to consistent DNA sequence W-box as an example,the effects of single base substitution on the interaction between transcription factor and DNA was studied.It is illustrated that the number and occupancies of hydrogen bonds formed at the interface between protein and DNA is significantly decreased when the T24 was replaced with U.And the compactness of the protein was decreased.It is confirmed that the substitution can reduce the stability of the DNA–protein complex.Finally,the change of binding free energy calculated by MM/PBSA proved this result.This study provides a meaningful molecular model for the understanding of the interaction mechanism of transcription factor protein and nucleic acid.It may provide insights into the combinatorial regulation of transcription in eukaryotes.