Molecular dynamics studies on the domain swapped Salmonella typhimurium survival protein SurE: insights on the possible reasons for catalytic cooperativity

Stationary phase survival protein SurE from Salmonella typhimurium is a dimeric protein formed by the swapping of a tetramerization loop involved in the formation of a loose tetramer and a C-terminal helix. It functions as a phosphatase. The two-fold symmetry of the dimeric protein was lost in the mutants H234A and D230A/H234A in which a crucial hydrogen bond in the hinge involved in C-terminal helix swapping was eliminated. The catalytic activity of both mutants was drastically reduced. In contrast to the native protein, H234A exhibited positive cooperativity in its catalytic activity. In order to relate these observations to the dynamics of the native and distorted mutants, molecular dynamics (MD) simulations were carried out using GROMACS v4.0.7. In all the simulations, the swapped segments and a segment near the active site were found to be highly flexible. These segments exhibited distinct dynamic features in the two protomers (A and B) of the dimeric protein. The dimeric organization was more significantly affected in the mutants when compared to the native structure, suggesting that the mutations enhance the intrinsic flexibility of the protein. The larger flexibility of the mutants affects the relative movement between the loops near the two active sites. The positive cooperativity observed in H234A mutant is most likely due to this increased flexibility and loop movement.