Coarse-grained Molecular Dynamics Simulations Of The Protein-DNA Interactions Of Msh23 And Msh26 Systems

The DNA mismatch repair(MMR)system maintains genome stability by excising mismatch sites generated during DNA replication and genetic recombination.Repair of MMR in eukaryotic cells is triggered by two dimeric proteins,Msh23 and Msh26,that slide across DNA molecules looking for mismatch sites.Msh26 initiates base-to-base and indel mismatch repair of smaller fragments,while Msh23 repairs indel mismatch repair of larger fragments.The interaction between these two proteins and DNA is the initial step when cells exercise MMR,which has high research significance.Molecular dynamics(MD)can study the structure,dynamics and interaction of the system,the thermodynamics and kinetics of the system at high time resolution and spatial resolution.The Martini coarse-grained force field can be simulated on larger spatial scales and longer time scales by reducing the number of degrees of freedom(compared to full-atom force field).Martini Force Field has developed models and force fields for protein and DNA molecules,providing conditions for the study of DNA and protein interactions.In this thesis,the application of the Martini coarse-grained approach to protein-DNA interactions was tested using two important MMR proteins,Msh23 and Msh26,as examples.Firstly,the all-atom structure model of Msh23 and Msh26 and DNA complex was constructed,and the structure was optimized by all-atom MD simulation,and then converted into Martini coarse-grained model,and a series of coarse-grained MD simulations were carried out.The influence of different parameter settings in Elastic Network on the two systems was tested,and it was found that the force constant had a more obvious effect on it.When the force constant was set to 400 N/m,it was more suitable for studying protein-DNA interactions.Both Msh23 and Msh26 have four domains that make direct contacts with DNA.The correlation analysis of these two systems found that: firstly,in the simulation process,the MBD domain of Msh23 can be largely separated from DNA molecules,while the Msh2-MBD of the Msh26 system can hardly be separated from DNA;secondly,it is observed that Msh2-clamp domains of Msh23 and Msh26 systems all exhibit groovecrossing behavior,among which K498 and K535,K546 and K528 are the important amino acids for the Msh2-clamp domain in crossing grooves,respectively;finally,it is observed that in the Msh23 system,the Msh2-clamp domain was gradually separated from the Msh3-clamp domain,but in the Msh26 system,the Msh2-clamp domain was tightly combined with the Msh6-clamp.In general,the Msh23 system is relatively unstable in binding to DNA,while the binding of Msh26 to DNA molecules is relatively stable.It’s consistent to experimental results that it has been proven that Msh23 can separate from and jump on DNA molecules,while Msh26 generally cannot jump along or cross DNA.The results of this thesis provide a more comprehensive understanding of the two MMR-related DNA-binding protein systems and also confirm that Martini coarse-grained force fields can be used as a powerful tool for studying protein-DNA interactions.