Insights into the specific binding site of adenosine to the Stx2, the protein toxin from Escherichia coli O157:H7 using molecular dynamics simulations and free energy calculations

To achieve the structural basis to produce a more accurate model of the catalytic active site of Stx2, we carried out molecular docking and molecular dynamics simulations of adenosine–Stx2 complex, and used the molecular mechanics/Poisson–Boltzmann surface area method to determine the associated free energy profiles. The results reveal that the electrostatic interactions play an important role in the stabilisation of the binding site of Stx2–adenosine, and the key residues of Ser113, Arg119, Arg125 and Arg170 in Stx2–adenosine complex are identified based on the residue decomposition analysis. With this approach, we are able to demonstrate that the substrate adenosine is located in the cavity formed by A-subunit, which is similar to the available experimental binding pattern of Stx2–adenine except for adenine being more close to the residues of Arg170, Tyr77 and Val78. The conformational difference that lies in adenosine is stabilised by the residues around the binding site of adenosine–Stx2, which leads to that the adenine base and furan ring of adenosine are dragged by the residues in the opposite direction during the catalytic process. The above results indicate that the residues around the binding site of adenosine in Stx2 should be used as catalytic active site to depurinate a specific adenine base from 28S rRNA.