112 



Journal of the Kentucky Academy of Science 66(2) 



Table 3. Residues involved in helices 1-7 in the opioid 

 receptors. 





Mu 



Kappa 



Delta 



Helix 



receptor 



receptor 



receptor 



1 



P127-V158 



I54-F82 



A47-V75 



2 



Y170-Y192 



T94-Y119 



T84-Y109 



3 



L203-I231 



G127-I158 



L120-148 



4 



T244-A270 



A174-A193* 



L167-V188** 



5 



L295-V314** 



F225-V244** 



S204-V233*** 



6 



L339-I366 



R270-V296 



R258-V283 



7 



T379-F411 



A308-F341 



L3()2-K326 



* P172 terminates this helix. 

 ** P162 terminates this helix. 



*** Helix is termmated early on the intracellular surface. 



Docking 



Morphine was docked into the three recep- 

 tor models mu, kappa, and delta. The resulting 

 databases were evaluated visually based on 

 placement in the helical bundle, the number 

 of hydrogen bonds to side chains of the re- 

 ceptor, and the number of aromatic residues 

 within 3 A. The best complex was then mini- 

 mized to an RMSG of 0.1 Kcal/mol-A using 

 the MMFF94 force field. The results for each 

 receptor are listed in Table 4. 



Mu with Moq3hine 



Of the 25 complexes for mu with moiphine, 

 12 had hydrogen bonds between the ligand 

 and the receptor. Four of these complexes 

 were rejected due to position in the receptor. 

 Of the eight remaining, one had hydrogen 

 bonding to two side chains of the receptor: 

 His361 and Asp211. PheSOl and Trp382 were 

 within 3 A of the ligand (Figure 2; Table 4). 

 All other docking runs had only one hydrogen 

 bond to the receptor. 



Kappa with Morphine 



Of the 25 docking complexes, only 12 had 

 hydrogen bonding to the receptor. Of the 12 

 complexes, eight were eliminated due to po- 

 sition in the receptor. Of the four remaining 



complexes, three had hydrogen bonds to the 

 side chains of the receptor. All of these com- 

 plexes were minimized to an RMSG of 0.1 

 Kcal/mol-A. One of these three increased hy- 

 drogen bonding to two side chains: Asp 138 

 and His 291. Aromatic residues within 3 A of 

 the ligand were Tyrl39, Phe231, Trp287, and 

 Tyr312 (Figure 3; Table 4). 



Delta with Morphine 



Of the 25 docking runs, six had hydrogen 

 bonding between the receptor and the Hgand. 

 Of these, only three were within the helical 

 bundle. All three were minimized to an 

 RMSG of 0.1 Kcal/mol-A. One increased hy- 

 drogen bonding to two side chains: Asp 128 

 and His278. Only Tyrl29 was within 3 A of 

 the Hgand (Figure 4; Table 4). 



Dynamics 



Each complex was subjected to 100 ps of 

 unrestrained molecular dynamics under NVT 

 conditions. The resulting databases contained 

 100 entries collected over the equilibrium 

 phase. The simulation calculated potential en- 

 ergy (U in Kcal/mol), temperature (T in kel- 

 vins), pressure (P in Kpa), total energy (E, ki- 

 netic and potential in Kcal/mol), and enthalpy 

 (H, E + PV in Kcal/mol). The average, stan- 

 dard deviation and percent standard deviation 

 was calculated for the three databases. The 

 percent standard deviation for each parameter 

 varied from 0.9% to 1.8%. The databases were 

 also visually inspected. The complexes would 

 momentarily lose tertiary structure but would 

 regain that structure in subsequent database 

 entries. The delta/morphine complex main- 

 tained the same hydrogen bonds throughout 

 the course of the simulation. The kappa/mor- 

 phine complex would vary a hydrogen bond 

 between His291 and Cys315. The hydrogen 

 bond/ion pair with Asp 138 was in every entry 

 in the database. The mu/morphine simulation 



Table 4. Summary of" docking results for morphine and all opioid receptor models. values are in nM from Lattanzi 

 et al. 2005. sc indicates side chain interaction, bb indicates backbone interaction. 



Hcceptor 



K,* 



Hydrogen Bonding Residues 



Aromatic Residues 



Mu 



6.55 



Asp211 sc, His361 sc, Ser381 bb 



Phe301, Trp382 



Kappa 



113 



Asp 138 sc, His291 sc, Cys315 sc (in some 



Trp287, Phe231, Tyrl39, 







dynamics complexes) 



Tyr312 



Delta 



217 



Asp 128 sc, His278 sc 



Tyrl29 



