Theoretical models of catalytic domains of protein phosphatases 1 and 2A with Zn2+ and Mn2+ metal dications and putative bioligands in their catalytic centers.
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The oligomeric metalloenzymes protein phosphatases dephosphorylate OH groups of Ser/Thr or Tyr residues of proteins whose actions depend on the phosphorus 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 strongly 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 dication in its catalytic site. The latter was modeled, together with a structural hydroxyl anion, as a triangular pseudo-molecule (Zno or Mno), composed of two metal cations (double Zn2+ or Mn2+, respectively) and the OH- group. To the free PP1c two inhibitor sequences R29RRRPpTPAMLFR40 of DARPP-32 and R30RRRPpTPATLVLT42 of Inhibitor-1, and two putative substrate sequences 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 pseudo-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 trajectories of the final 50 ps were taken for further analyses. The theoretical models of PP1c complexes, irrespective of the dication type, exhibited increased mobilities in the following residue ranges: 195-200, 273-278, 287-209 for the inhibitor sequences and 21-25, 194-200, 222-227, 261, 299-302 for the substrate sequences. Paradoxically, the analogous PP2Ac models appeared much more stable in similar simulations, since only their "prosegment" residues 6-10 and 14-18 exhibited an increased mobility in the inhibitor complexes while no areas of increased mobility were found in the substrate complexes. Another general observation was that the complexes with Mn dications were more stable than those with Zn dications for both PP1c and PP2Ac units.
- Aggen, J.B., Humphrey, J.M., Gauss, C.-M., Huang, H.-B., Nairn, A.C. & Chamberlin, A.R. (1999) The design, synthesis and biological evaluation of analogues of the serine-threonine protein phosphatase 1 and 2A selective inhibitor microcystin LA: rational modifications imparting PP1 selectivity. Bioorg. Med. Chem. 7, 543-564.
- Aggen, J.B., Nairn, A.C. & Chamberlin, R. (2000) Regulation of protein phosphatase 1. Chem. & Biol. 7, R13-R23.
- Barford, D. (1996) Molecular mechanisms of the protein serine/threonine phosphatases. Trends Biochem. Sci. 21, 407-412.
- Bayly, C.I., Cieplak, P., Cornell, W.D. & Kollman, P. (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J. Phys. Chem. 97, 10269-10280.
- Berndt, N. (1999) Protein dephosphorylation and the intracellular control of the cell number. Front. Biosci. 4, 22-42.
- Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.E.J., Brice, M.D., Rodgers, J.R., Kennard,O., Shimanouchi, T. & Tsanumi, M. (1977) The protein data bank: A computer-based archive file for macromolecular structures. J. Mol. Biol. 112, 535-542.
- Brooks, III, C.L., Karplus, M., & Pettitt, B.M. (1988) Proteins: A theoretical perspective of dynamics, structure, and thermodynamics, Adv. Chem. Phys. 71, 1-259.
- Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham III, T.E., Ross, W.S., Simmerling, C., Darden, T., Merz., K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., Ferguson, D.M., Radmer, R., Seibel, G.L., Singh, U.C., Weiner, P.K. & Kollman, P.A. (1997) AMBER, v.5.0, University of California, San Francisco, CA, U.S.A.
- Chu, Y., Lee, E.Y.C. & Schlender, K.K. (1996) Activation of protein phosphatase 1. Formation of a metalloenzyme. J. Biol. Chem. 271, 2574-2577.
- Cohen, P.T.W. (1997) Novel protein serine/threonine phosphatases: Variety is the spice of life. Trends Biochem. Sci. 22, 245-251.
- Das, A.K., Helps, N.R., Cohen, P.T.W. & Barford, D. (1996) Crystal structure of the protein serine/ threonine phosphatase 2C at 2.0 A resolution. EMBO J. 15, 6798-6809.
- Dawson, J.F. & Holmes, C.F.B. (1999) Molecular mechanisms underlying inhibition of protein phoshatases by marine toxins. Front. Biosci. 4, D646-658.
- Egloff, M.P., Johnson, D.F., Moorhead, G., Cohen, P.T.W., Cohen, P. & Barford, D. (1997) Structural basis for the recognition of regulatory subunit by the catalytic subunit of protein phosphatase 1. EMBO J. 16, 1876-1887.
- Egloff, M.P., Cohen, P.T., Reinemer, P. & Barford, D. (1995) Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate. J. Mol. Biol. 254, 942-959.
- Endo, S., Zhou, X., Connor, J., Wang, B. & Shenolikar, S. (1996) Multiple structural elements define the specifity of recombinant human inhibitor-1 as a protein phosphatase-1 inhibitor. Biochemistry 35, 5220-5228.
- Gauss, C.-M., Sheppeck, J.E., Nairn, A.C. & Chamberlin, R. (1997) A molecular modeling analysis of the binding interactions between the okadaic acid class of natural product inhibitors and the Ser-Thr phosphatases, PP1 and PP2. Bioorg. Med. Chem. 5, 1751-1773.
- Goldberg, J., Huang, H., Kwon, Y., Greengard, P., Nairn, A.C. & Kuriyan, J. (1995) Three-dimensional structure of the catalytic subunit of protein serine/ threonine phosphatase-1. Nature 376, 745-753.
- Griffith, J.P., Kim, J.L., Kim, E.E., Sintchak, M.D., Thomson, J.A., Fitzgibbon, M.J., Fleming, M.A., Caron, P.R., Hsiao, K. & Navia, M.A. (1995) X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex. Cell 82, 507-522.
- Herzig, S. & Neuman, J. (2000) Effects of serine/ threonine protein phosphatases on ion channels in excitable membranes. Physiol. Rev. 80, 173-210.
- Hoops, S.C., Anderson, K.W. & Merz, K.M., Jr. (1991) Force-field design for metalloprotein. J. Am. Chem. Soc. 113, 8262-8270.
- Huang, F.L. & Glinsmann, W.H. (1976) Separation and characterization of two phosphorylase phosphatase inhibitors from rabbit skeletal muscle. Eur. J. Biochem. 70, 419-426.
- Huang, H.-B., Horiuchi, A., Watanabe, T., Shih, S.-R., Tsay, H.-J., Li, H.-C., Greengard, P. & Nairn, A.C. (1999) Characterization of the inhibition of protein phosphatase-1 by DARPP-32 and inhibitor-2. J. Biol. Chem. 274, 7870-7878.
- Ingebritsen,T.S. & Cohen, P. (1983) Protein phosphatases: Properties and role in cellular regulation. Eur. J. Biochem. 132, 255-261.
- Jia, Z. (1997) Protein phosphatases: Structures and implications. Biochem. Cell Biol. 75, 17-26.
- Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R. & Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Phys. Chem. 79, 926-935.
- Kissinger, C.R., Parge, H.E., Knighton, D.R., Lewis, C.T., Pelletier, L.A., Tempczyk, A., Kalish, V.J., Tucker, K.D., Showalter, R.E., Moomaw, E.W., Gastinel, L.N., Habuka, N., Chen, X., Maldonado, F., Baker, J.E., Bacquet, R. & Villafranca, J.E. (1995) Crystal structure of human calcineurin and the human FKBP12-FK506- calcyneurin complex. Nature 378, 641-644.
- Klee, B.C., Ren, H. & Wang, X. (1998) Regulation of the calmodulin-stimulated protein phosphatase, calcineurin. J. Biol. Chem. 273, 13367-13370.
- Koradi, R., Billeter, M. & Wuethrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graphics 14, 51-55.
- Kwon, Y.G., Huang, H-b., Desdouits, F., Girault, J.A., Greengard, P. & Nairn, A.C. (1997) Characterization of the interaction between DARPP-32 and protein phosphatase 1 (PP-1): DARPP-32 peptides antagonize the interaction of PP-1 with binding proteins. Proc. Natl. Acad. Sci. U.S.A. 94, 3536-3541.
- Lee, S., Kim, J., Park, J.K. & Kim, K.S. (1996) Ab initio study of the structures, energetics, and spectra of Aquazinc(II). J. Phys. Chem. 100, 14329-14338.
- Lindvall, M.K., Pihko, M. & Koskinen, A.M.P. (1997) The binding mode of calyculin A to protein phosphatase-1. A novel spiroketal vector model. J. Biol. Chem. 272, 23312-23316.
- Merz, K.M. (1991) CO2 binding to human carbonic anhydrase-II. J. Am. Chem. Soc. 113, 406-411.
- Millward, T.A., Zolnierowicz, S. & Hemmings, B.A. (1999) Regulation of protein kinase cascades by protein phosphatase 2A. Trends Biochem. Sci. 24, 186-191.
- Sayle, R. (1996) Rasmol Molecular Graphics, version 2.6, Glaxo Wellcome Research and Development, Stevenage, Hertfordshire, U.K.
- Schmidt, M.W., Baldridge, K.K., Boatz, J.A., Elbert, S.T., Gordon, M.S., Jensen, J.H., Koseki, S., Matsunaga, N., Nguyen, K.A., Su, J.S., Windus, T.L., Dupuis, M. & Montgomery, J.A. (1993) General atomic and molecular electronic structure system J. Comput. Chem. 14, 1347-1363.
- SYBYL 6.2 (1996) Tripos Inc., 1699 South Hanley Rd., St. Lois, Mo. 63144, U.S.A.
- Toh, K.K.H. (1995) PlotMTV Program, Ver. 1.4.1-16 Copyright: (C); e-mail: email@example.com.
- Williams, K.R., Hemmings, H.C. Jr., Lopresti, M.B., Konigsberg, W.H. & Greengard, P. (1986) DARPP-32: Primary structure and homology with protein phosphatase inhibitor-1, J. Biol. Chem. 261, 1890-1903.
- Woźniak, E., Ołdziej, S. & Ciarkowski, J. (2000) Molecular modeling of the catalytic domain of serine/ threonine phosphatase with the Zn+2 and Mn+2 di-nuclear ion centers in the active site. Comput Chem. 24, 381-390.
- Żołnierowicz, S. & Hemmings, B.A. (1996) Protein phosphatases on the piste. Trends Cell Biol. 6, 359-362.
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