Characterization of the structures of phosphodiesterase 10 binding with adenosine 3',5'-monophosphate and guanosine 3',5'-monophosphate by hybrid quantum mechanical/molecular mechanical calculations

Abstract

Quantum mechanical/molecular mechanical (QM/MM) geometry optimizations of the X-ray crystal structures of PDE10-AMP (PDB code 2OUN ) and PDE10-GMP (PDB code 2OUQ ) complexes have been performed to characterize the state of the AMP and GMP products, respectively. Results show that only one phosphate oxygen atom (O1) is protonated for both AMP and GMP product complexes. In addition, QM/MM calculations have resolved the orientation of the amide group of Gln726 in PDE10-GMP which was in conflict with the assignment of the guanine group of GMP in the X-ray crystal structure. Calculations reveal that the amide oxygen and nitrogen atom of Gln726 are rotated 180 degrees, resulting in two strong hydrogen bonds formed between the amide group of Gln726 and the guanine group of GMP. Binding free energy calculations for both QM/MM-optimized structures confirm the new conformational assignment of Gln726 in PDE10-GMP. The calculated binding free energy of the rotated structure is approximately 22 kcal/mol lower than the X-ray crystal assignment. The lower energy is mainly derived from the formation of two hydrogen bonds between the amide group of Gln726 and the guanine group of GMP. This implies that the orientation of the amide oxygen and nitrogen atoms in PDE10-AMP is different from PDE10-GMP. Finally, our results help to understand why PDE10 can hydrolyze both cAMP and cGMP.

Figure 1

H-bonding interactions of amide group of Asn/Gln in X-ray crystal structures of PDEs. (A) The amide oxygen and nitrogen atoms of Asn641 have sterically unfavorable interactions with the main chain oxygen of Arg664 which has two H-bonds with backbone nitrogen atoms of Gly667 and Leu668 in 2OUQ (PDE10, resolution 1.9Å). (B) The amide oxygen and nitrogen atoms of Gln326 have sterically unfavorable interactions with the main chain oxygen of Leu420 and the ammonium ion of the side chain of Lys359 in PDB code 1ZXL (PDE7, resolution 1.67Å).

Figure 2

QM/MM-optimized PDE10-AMP structure (the charge on AMP is -1) at the B3LYP/6-31G*:Amber level. The QM atoms in the PDE10 active site are represented by balls. The lines and all the other atoms represent MM atoms. (A) From this orientation, one can clearly see the metal sites and the state of AMP. (B) From this orientation, one can clearly see the hydrogen bonded network around Gln726 residue.

Figure 2

QM/MM-optimized PDE10-AMP structure (the charge on AMP is -1) at the B3LYP/6-31G*:Amber level. The QM atoms in the PDE10 active site are represented by balls. The lines and all the other atoms represent MM atoms. (A) From this orientation, one can clearly see the metal sites and the state of AMP. (B) From this orientation, one can clearly see the hydrogen bonded network around Gln726 residue.

Figure 3

QM/MM-optimized PDE10-GMP structure (the charge on GMP is −1) at the B3LYP/6-31G*:Amber level. The QM atoms in the PDE10 active site are represented by balls. All MM atoms are represented as lines. (A) From this orientation, one can see the metal sites and the state of GMP. (B) From this orientation, one can see the hydrogen bonding network around Gln726 residue and one weak hydrogen bond between Gln726 and guanine group of GMP. (C) The comparison between the QM/MM-optimized structure and the X-ray crystal structure while maintaining the original amide position of Gln726. The pink atoms represent the X-ray crystal structure added H-atoms, and the remaining atom-types represent the QM/MM-optimized structure.

Figure 4

Geometry of the PDE10-GMP structure (the charge of GMP is −1) optimized by the QM/MM method at the B3LYP/6-31G*: Amber level. The QM atoms in the PDE10 active site are represented by balls. The lines and all the other atoms represent MM atoms. (A) In this orientation, one can see the metal sites and the state of GMP. (B) In this orientation, one can see the hydrogen bonding network around Gln726 residue after interchange of side chain atoms and the formation of two hydrogen bonds between Gln726 and guanine group of GMP. (C) The comparison between the QM/MM-optimized structure and the X-ray crystal structure in which the amide orientation of Gln726 is changed. The pink atoms represents the X-ray crystal structure added H-atoms, the atoms shown as the atom type represents the QM/MM-optimized structure.

Chart 1

The active site structure of PDE10-GMP complex: Zn(II) is coordinated to His529, His563, Asp564, Asp674, and two phosphate oxygen atoms (O1 and O3); Mg(II) is coordinated to Asp564, two phosphate oxygen atoms (O2 and O3), and three water molecules. refers to a coordination bond. There are unfavorable interactions between the GMP guanine group and Gln726 amide group as these two groups are nearly coplanar.