Elucidation of the Role of a Conserved Methionine in Glutamate Transporters and Its Implication for Force Fields.

Glutamate transport through the excitatory amino acid transporters is coupled to the cotransport of three Na ions, the binding sites (Na1-Na3) of which are conserved from archaea to mammalians. Molecular dynamics (MD) simulations reproduce the Na1 and Na3 binding sites observed in the crystal structures but fail in the case of Na2. A distinguishing feature of the Na2 site is that an S atom from a conserved methionine residue is in the coordination shell of Na. We perform MD simulations on the recent Glt structure and show that the problem with the Na2 site arises from using an inadequate partial charge for S. When methionine is appropriately parametrized, both the position and the binding free energy of Na at the Na2 site can be reproduced in good agreement with the experimental data. Other properties of methionine, such as its dipole moment and the solvation energy of its side chain analog, also benefit from this reparametrization. Thus, the Na2 site in glutamate transporters provides a good opportunity for a proper parametrization of methionine in MD force fields.