The Journal of Physical Chemistry B ARTICLE Figure 4. Hydrogen bond interactions for individual water molecules for the 1FTJ-AMPA model system (A) WG, (B) W1, (C) W2, (D) W3, (E) W4, and (F) W5. are similar in both modes of binding. The L-WsP interaction energy for 1FTM-AMPA ( 327.93 kcal mol 1) is slightly less favorable than for 1FTJ-AMPA ( 329.53 kcal mol 1). Thus glutamate clearly has a strong preference for a binding mode, but AMPA it would seem is energetically capable of adopting a “glutamate-binding” pose. We then proceeded to examine the origin of this in more detail by examining the interaction energies of water molecules within the binding pocket. 3.3. Water System Interaction Energies. Figures 3 4 de- scribe the water interactions in the four models. We first discuss what we refer to above as the “pharmacophoric water”, which is the water that appears to act as a surrogate part of the ligand in either the glutamate (WG, see Figure 2, panels A and D) or AMPA (WA, see Figure 2, panels B and C) complexes. Before an in depth analysis, one might expect that the interaction energy of WG or WA would be more favorable in the poses adopted in the crystal. However, the interaction energy of the pharmaco- phoric water with the remainder of the system (WA-WsLP and WG-WsLP cells in Table 2) presents a different perspective of what is observed in the crystal structures. We find that regardless of the ligand bound WA appears to be iso-energetic with a 0.67 kcal mol 1 difference between the glutamate bound ( 5.59 kcal mol 1) mode and the AMPA bound ( 6.26 kcal mol 1) mode. In the 1FTJ-based models, WG appears to also be iso-energetic albeit with a slight preference of 1.88 kcal mol 1 for the AMPA bound ( 9.75 kcal mol 1) mode than the glutamate bound ( 7.87 kcal mol 1) mode. One might expect these to be exactly isoenergetic, but the optimizations are done in the presence of ligands and thus there will be some small effects on the final positions of the protein atoms dictated by the ligand. In the 1FTJ- based models, WG forms hydrogen bonds (Figures 3A and 4A) with the backbone NH group of Glu705, the water W2 and an oxygen atom from the ligand (one of the carboxylate oxygens for Glu, and the ring oxygen for AMPA). In the 1FTM-based models, WA forms hydrogen bonds (Figures 5A and 6A) with the OH group of Ser 654, the backbone NH of Thr 655, W5 and two oxygen atoms from the ligand in each case. The detailed breakdown of how this water interacts with the various components of the binding pocket (the WG or WA rows in Table 2) shows that the overall interaction energy 7090 dx.doi.org/10.1021/jp200776t |J. Phys. Chem. B 2011, 115, 7085–7096