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“…The HF/6-31G* calculation was also performed to determine the restrained electrostatic potential (RESP)-fitted charges for POPC molecules. The similar RESP-fitting calculations based on the first-principles electronic structure method were used in our previous computational studies of other protein-ligand systems and led to satisfactory binding structures (41)(42)(43)(44)(45). The relative orientation of DAT in the lipid bilayer was determined by referring the similar orientation of the LeuT Aa structure (34), i.e., transmembrane helix 12 in parallel with the normal of the membrane, the binding sites of two Na 1 placed at the midpoint of the membrane, and the two terminals (both N-terminal and C-terminal) intracellularly located.…”
Section: Homology Modeling and Structural Optimization Of Dat In A Phmentioning
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“…The HF/6-31G* calculation was also performed to determine the restrained electrostatic potential (RESP)-fitted charges for POPC molecules. The similar RESP-fitting calculations based on the first-principles electronic structure method were used in our previous computational studies of other protein-ligand systems and led to satisfactory binding structures (41)(42)(43)(44)(45). The relative orientation of DAT in the lipid bilayer was determined by referring the similar orientation of the LeuT Aa structure (34), i.e., transmembrane helix 12 in parallel with the normal of the membrane, the binding sites of two Na 1 placed at the midpoint of the membrane, and the two terminals (both N-terminal and C-terminal) intracellularly located.…”
Section: Homology Modeling and Structural Optimization Of Dat In A Phmentioning
“…Thus, residues G116, G117, and A199 were the standard residues as supplied by AMBER 7 in the MD simulations. The general procedure for carrying out the MD simulations in water is essentially the same as that used in our previously reported computational studies (26,27,(36)(37)(38)(39). Each aforementioned starting TS1 structure was neutralized by adding chloride counterions and was solvated in a rectangular box of TIP3P water molecules (40) with a minimum solute-wall distance of 10 Å.…”
Section: Methodsmentioning
“…PGE2 was previously docked into a 15-PGDH homology model by Hamza et al [ 13 ]. The model was based on levodione reductase (33% sequence identity with 15-PGDH) and Tropinone Reductase (23% sequence identity with 15-PGDH).…”
Section: Resultsmentioning