Developing a Structural Model of the Msh2-Msh6-Holliday Junction Interaction

Live Poster Session: Zoom Link
Thursday, July 30th 1:15-2:30pm EDT

Abstract: The DNA mismatch repair system (MMR) is a highly conserved system from prokaryotes to eukaryotes that plays a key role in recognizing and repairing post-replicative errors. The eukaryotic Msh2-Msh6 heterodimer is responsible for recognizing and repairing single base pair mismatches and short insertion/deletion loops (IDL). X-ray crystallography has provided important information regarding the crystal structure of human Msh2-Msh6 and shown significant structural homology between prokaryotic and eukaryotic versions of the protein. Mismatch-bound forms of human Msh2-Msh6 have been resolved by crystallography and used in Molecular Dynamics (MD) simulations. Prior studies have shown that Msh2-Msh6 binds with high affinity to Holliday Junction DNA (HJ), a branched nucleic acid structure that forms as an intermediate during recombination and repair. Interestingly, Msh2-Msh6 binds HJ with approximately the same affinity as mismatched DNA but the nature of the binding interaction is not well understood. To address the lack of structural information regarding the Msh2-Msh6-HJ interaction, our research utilizes MD simulations to develop structural models of Msh2-Msh6 bound to a Holliday Junction. To develop a structural model for simulations, we initially needed to model in missing amino acid residues into the human Msh2-Msh6 structure using the program PHYRE2. Topology and coordinate files of this protein were generated using AMBER tLEaP and verified using VMD. Initial assessments of the generated structure indicate that it closely resembles the structures obtained by crystallography. Following the preliminary steps to energy-minimize, heat, and equilibrate the system, the single base pair mismatched DNA will be replaced with Holliday Junction DNA. Further, docking simulations will help us gain a deeper understanding of the time-dependent behavior and conformational changes of Msh2-Msh6 when bound to the Holliday Junction. The ability to create structural models of Msh2-Msh6 provides us with the potential to explore the behavior of Msh2-Msh6 proteins from other organisms; more specifically, future experiments seek to modify the current human Msh2-Msh6 crystal structure to characterize the binding mechanisms of yeast Msh2-Msh6 with its DNA substrates.

Msh2-Msh6-MD-Simulations-Poster-Amy-Du

Live Poster Session: Zoom Link
Thursday, July 30th 1:15-2:30pm EDT