Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers

The oligomeric metalloenzymes protein phosphatases dephosphorylate OH group s of Ser/Thr or Tyr residues of proteins whose actions depend on the phosph orus signal. The catalytic units of Ser/Thr protein phosphatases 1, 2A and 2B (PP1c, PP2Ac and PP2Bc, respectively), which exhibit about 45% sequence similarity, have their active centers practically identical. This feature s trongly suggests that the unknown structure of PP2Ac could be successfully homology-modeled from the known structures of PP1c and/or PP2Bc. Initially, a theoretical model of PP1c was built, including a phosphate and a metal d ication in its catalytic site. The latter was modeled, together with a stru ctural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), compos ed of two metal cations (double Zn or Mn, respectively) and the OH- group. To the free PP1c two inhibitor sequences n(29)RRRPpTPAaMLFR(40) of DARPP-32 and R(30)RRRPpTPATLVLT(42) of Inhibitor-1, and two putative substrate sequ ences LRRApSVA and QRRQRKpRRTI were subsequently docked. In the next step, a free PP2Ac model was built via homology re-modeling of the PP1c template and the same four sequences were docked to it. Thus, together, 20 starting model complexes were built, allowing for combination of the Zno and Mno pse udo-molecules, free enzymes and the peptide ligands docked in the catalytic sites of PP1c and PP2Ac. All models were subsequently subjected to 250-300 ps molecular dynamics using the AMBER 5.0 program. The equilibrated trajec tories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited incr eased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 264, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" res idues 6-10 and 14-18 exhibited an increased mobility in the inhibitor compl exes while no areas of increased mobility were found in the substrate compl exes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units .