MD_Mismatch-Repair-by-Mismatch-Repair-Protein-MutSB
Description
This dataset consists of the MD models for the three systems, namely, mismatched DNA control, MutSbeta control and the combined system along with the parameter and configuration files that can be utilized to reproduce the simulation trajectories for the given system. These system models were utilized in understanding the interactions of the mismatch repair protein, MutSBeta, with a 50/51 base-pair mismatched DNA pointing out the crucial events that take place at the interface of a mismatched DNA and the mismatch repair protein during the first 500ns of a molecular dynamics simulation run. The parameter files accompanying the PSF and PDB files details the exact structure of the models in the presence of water molecules and sodium chloride ions. The configuration files are made available for anyone who would like to verify the simulations for the individual control and combined systems. Modeling and Simulation software used in this study, VMD (Visual Molecular Dynamics) and NAMD (Nanoscale Molecular Dynamics), is freely available from the Theoretical and Computational Biophysics group at the NIH Center for Macromolecular Modeling and Bioinformatics at the University of Illinois at Urbana-Champaign (http://www.ks.uiuc.edu/Research/vmd/). Atomic coordinate (protein data bank, PDB) file for the MutSbeta protein, 3THY, was obtained from the database located at the Research Collaboratory for Structural Bioinformatics (RCSB), www.rcsb.org (https://www.rcsb.org/structure/3THY). To create the protein structure files (PSF) and to carry out all-atom simulations, the necessary topology and force field parameter files were obtained from the Chemistry at Harvard Macromolecular Mechanics (CHARMM) database located at the MacKerell Lab at the University of Maryland, School of Pharmacy, (http://mackerell.umaryland.edu/charmm_ff.shtml). A 50-51 base pair strand of DNA was modeled using an online DNA modeler tool called: The Sequence Manipulation Suite (https://www.bioinformatics.org/sms2/) and VMD was used to create the mismatched base pair by editing the PDB file, specifically the mismatch site, the Resid84 on the mismatched DNA.