Molecular Simulation Of Methylation Regulation Mechanism In Interaction Of BZIP Transcription Factors And DNA

Transcription is the first step in gene expression.The regulation of eukaryotic transcription levels is a multi-stage and complicated process,due to the interactions of protein-protein and protein-DNA,and the formation of complex macromolecular complexes.Transcription factors,as a sequence-specific DNA-binding protein,can control the transcription rate of genetic information from DNA to mRNA by binding to promoters and enhancers in cis-elements.Experimental studies have shown that DNA methylation can dynamically regulate this binding process,thereby regulating gene active or silencing and ensuring their correct expression.Recent studies have also found that DNA methylation levels are closely related to human development and tumor diseases.Therefore,it is of great significance to study the mechanism of DNA methylation recognition and regulation in the process of TF-DNA interaction,and it has become a research hotspot in epigenetics and epigenomics.With the rapid development of technologies especially deep sequencing,there has accumulated a large amount of DNA methylation data in different biological processes and races,but these data still cannot explain the dynamic mechanism of DNA methylation.The relationship between DNA methylation and physiological outcomes remains a challenging issue.the molecular simulation method is needed to solve this problem.Using molecular simulation techniques to explore the mechanism of dynamic regulation of protein-nucleic acid interactions has also become a viable research protocol.Therefore,this study selected the molecular dynamics simulation method to study the regulation mechanism of methylation on protein-DNA interaction.After literature research and crystal structure data search,we selected the bZIP family transcription factor as the research system.The research idea of this thesis is to study the regulation mechanism of 5mC methylation by comparing the effects of different single methylation sites and symmetric dimethylation sites on the interaction between transcription factors and nucleic acids.To this end,we first performed long-term and multiple parallel dynamics simulations on methylated and unmethylated structures(the total simulation time reached the order of microseconds),and then the binding free energy,entropy and enthalpy equilibrium,hydrogen bond,RMSF,DNA structure parameters,protein relative conformation and steric hindrance effects were analyzed and systematically compared.The following research progresses were made:Firstly,taking C/EBP protein binding to consistent DNA sequence containing a single methylated cytosine as an example,the mechanism of the influence of single-site methylation on the interaction between transcription factor and DNA was studied.Secondly,taking Jun/Jun homodimers-DNA complex as examples,the effects of single-site and double-site methylation on the interaction between transcription factors and DNA were studied.Thirdly,in the above two aspects of research,we found that the accuracy of the evaluation of binding free energy by molecular dynamics method is not enough,and it is necessary to use the ab initio quantum dynamics method to carry out related research.Therefore,we use the ab initio dynamics method to conduct an exploratory method test using the oxygen activation process as an example.