Analysis of interactions interfaces of N-terminal domain of P. aeruginosa MutL using All Atom and Coarse Grained Molecular dynamics simulation

IRGINIA MIGUEL, CARLOS E. ARGARAÑA, MARCOS A. VILLARREAL

Congreso; 2do Congreso Argentino de Bioinformática y Biología Computacional. Mayo 2011; 2011

<!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } --> SUMARY Background Bacterial mismatch repair system (MRS) corrects mutations arising from DNA replication that escape from DNA polymerase proofreading activity. MutL has a role as a matchmaker protein, coordinating the action of most of the proteins involved in repair. MutL is a dimeric protein that contains a C-terminal (CTD) dimerization domain connected by an unstructured linker to an N-terminal (NTD) ATPase domain. MutL is a member of GHL ATPase family. In E. coli, ATP binding results in NTD dimerization, while in some other bacterial species, dimerization occurs even in absence of nucleotide. Furthermore, the ATPase cycle has been proposed to modulate MutL´s interactions during the repair process. We used molecular dynamics simulations (MD), using all-atom and coarse-grained models, to characterize protein-protein interaction surfaces of NTD of Pseudomonas aeruginosa’s MutL. Results Since the crystal structure of P. aeruginosa NTD is not known, we constructed a homology model with MODELLER, using as templates the crystal structures of E. coli NTD bound to different nucleotides. After this, 200 ns MD simulations using the NTD models with or without ATP were carried out using GROMACS in order to analyze structural differences between the holo- and the apo-protein. Using cluster analysis we were able to identify the main structures in both simulations, as well as conformational differences between the apo and holo protein. With the representative structures from MD in water, we made simulations in mixed solvent (water-20% iPrOH) in order to identify areas with a high tendency to desolvate. This analysis showed two putative interaction interfaces. One could correspond to the known homologue region of E. coli dimerization and DNA binding patch, while the second interface currently has no assigned function. Simulations with coarse-grained models of free proteins showed that the second interface is capable of protein-protein interaction. This allowed us to identify the NTD dimerization interface, DNA binding patch and potential binding sites of MutL with its protein partners.