The Journal of Physical Chemistry B ARTICLE Figure 5. Hydrogen bond interactions for individual water molecules for the 1FTM-AMPA model system (A) WA, (B) W1, (C) W2, (D) W3, (E) W4, and (F) W5. (WG/WA-WsLP) does not arise from the contribution of the ligand solely but instead appears to be related to the whole environment of the system in which each ligand is bound. Table 2 also demonstrates that the fragments are clearly nonadditive in nature. WG appears to have favorable interaction energies with all fragments. However, the interaction of WA with protein alone appears to be nonfavorable. W1 was found to have the least favorable interaction energies in all and indeed in none of the models does W1 make a hydrogen bond with the ligand. W2 is most energertically favorable in the 1FTM-AMPA system. W2 makes contacts with Tyr 702 and Thr 688 in all models. The pattern of interaction energies relates directly to the number and geometry of the hydrogen bonds formed. W3 makes hydrogen bonds with Leu 650 and Leu 730 in all four models (Figures 3 4D), and a third hydrogen bond to the ligand. The interaction energy (Table 2) is most favorable in the 1FTJ-Glu mode and is a result of an optimal arrangement of both ligand and protein. W4 was found to maintain comparable interaction energies across the models and could be associated with the fact that it forms a tetrahedral association with mostly charged side-chain of the residues; Glu 705, Lys 730, Ser 654, and Thr 655 in all four models. This water does not form any direct interaction with the ligands and occupies a well-deﬁned site apparently serving a structural role, presumably helping to deﬁne the shape of the binding pocket. W5 is another water molecule that occupies a well-deﬁned site and is also a well conserved water molecule, found in the majority of published high-resolution ligand-bound iGluR structures. In the 1FTJ derived models (Figures 3F and 4F) W5 makes four direct hydrogen bonds to the ligand, Leu 650, Thr 655, and Lys 656 and has an identical interaction energy of 14.87 kcal mol 1 regardless if glutamate or AMPA is bound. In the 1FTM derived models W5 can also be considered iso-energetic with a 0.27 kcal mol 1 between the glutamate bound ( 11.76 kcal mol 1) mode and the AMPA bound ( 12.03 kcal mol 1) mode. It does not make any direct hydrogen bond with the ligand but instead makes a hydrogen bond with WA. W5 makes three further hydrogen bonds with Leu 650 and Lys 656 in 1FTM- AMPA (Figure 5F) and with the backbone carbonyl of 7091 dx.doi.org/10.1021/jp200776t |J. Phys. Chem. B 2011, 115, 7085–7096