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Prediction of Secondary Ionization of the Phosphate Group in Phosphotyrosine Peptides

Czasopismo : BIOPHYSICAL JOURNAL   Tom: 84, Zeszyt: 2, Strony: 750-756
2003 angielski
Abstrakty ( angielski )
A computational approach, based on a continuum molecular electrostatics model, for the calculation of the pK a values of secondary ionization of the phosphate group in phenyl phosphate derivatives is described. The method uses the ESP atomic charges of the mono-anionic and di-anionic forms of the ionizable phosphate group, computed with the use of the density functional method, and applies a new concept of the model group, being the reference state for the pK a calculations. Both conformational flexibility and tautomeric degrees of freedom are taken into account in the calculations. The method was parameterized using experimentally available pK a values of four derivatives of phenyl phosphates, and phosphotyrosine. Subsequently this parameterization was used to predict pK a of the phosphate group in a short peptide Gly-Gly-Tyr(P)-Ala, and in a longer peptide consisting of 12 residues, the latter in water, and in a complex with a protein—phospholipase. The agreement between the computed and the experimental pK a values is better than ±0.3 pH units for the optimized solute dielectric constant of 11–13. This approach is promising and its extension to other phospho-amino acids is in progress.
  1. Antosiewicz, J.& Błachut-Okrasińska, E.& Grycuk, T.& Lesyng, B., "A correlation between protonation equilibria in biomolecular systems and their shapes: studies using a Poisson-Boltzmann model", Kenmochi, N. (Eds.), GAKUTO International Series, Mathematical Science and Applications, vol. 14, 2000, p.11-17
  2. Antosiewicz, J.& Briggs, J.M.& Elcock, A.E.& Gilson, M.K.& McCammon, J.A., "Computing the ionization states of proteins with a detailed charge model", J. Comp. Chem., vol. 17, 1996, p.1633-1644
  3. Antosiewicz, J.& McCammon, J.A.& Gilson, M.K., "Prediction of pH-dependent properties of proteins", J. Mol. Biol., vol. 238, 1994, p.415-436
  4. Bashford, D.& Karplus, M., "pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model", Biochemistry, vol. 29, 1990, p.10219-10225
  5. Beltman, J.& Sonnenburg, W.K.& Beavo, J.A., "The role of protein phosphorylation in the regulation of cyclic nucleotide phosphodiesterases", Mol. and Cellular Biochem., vol. 128, 1993, p.239-253
  6. Bernstein, F.C.& Koettzle, T.F.& Williams, G.J.B.& Meyer, E.F.& Brice, M.D.& Rodgers, J.R.& Kennard, O.& Shimanouchi, T.& Tasumi, M.J., "The protein data bank: a computer-based archival file for molecular structures", J. Mol. Biol., vol. 123, 1977, p.557-594
  7. Błachut-Okrasińska, E.& Lesyng, B.& Briggs, J.M.& McCammon, J.A.& Antosiewicz, J.M., "Poisson-Boltzmann model studies of molecular electrostatic properties of the cAMP-dependent protein kinase", Eur. Biophys. J., vol. 28, 1999, p.457-467
  8. Bourne, N.& Williams, A., "Effective charge on oxygen in phosphoryl (-PO) group transfer from an oxygen donor", J. Org. Chem., vol. 49, 1984, p.1200-1204
  9. Brunger, A.T.& Karplus, M., "Polar hydrogen positions in proteins: empirical energy placement and neutron diffraction comparison", Proteins: Struct. Func. Gen., vol. 4, 1988, p.148-156
  10. Chanley, J.D.& Feageson, E., "The mechanism of the hydrolysis of organic phosphates. III. Aromatic phosphates", J. Am. Chem. Soc., vol. 77, 1955, p.4002-4004
  11. Davis, M.E.& Madura, J.D.& Luty, B.A.& McCammon, J.A., "Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program", Comp. Phys. Commun., vol. 62, 1991, p.187-197
  12. Dekel, N., "Protein phosphorylation/dephosphorylation in the meiotic cell cycle of mammalian oocytes", Rev. Reprod., vol. 1, 1996, p.82-88
  13. Feng, M.& Philippopoulos, M.& MacKerell Jr., A.D.& Lim, C., "Structural characterization of the phosphotyrosine binding region of a high-affinity domain-phosphopeptide complex by molecular dynamics simulation and chemical shift calculations", J. Am. Chem. Soc., vol. 118, 1996, p.11265-11277
  14. Frisch, M.J.& Trucks, G.W.& Schegel, H.B.& Gill, P.M.W.& Johnson, B.G.& Robb, M.A.& Cheeseman, J.R.& Keith, T.A.& Petersson, G.A.& Montgomery, J.A.& Raghavachari, K.& Al-Laham, M.A.& Zakrzewski, V.G.& Ortiz, J.V.& Foresman, J.B.& Cioslowski, J.& Stefanov, B.B.& Nanayakkara, A.& Challacombe, M.& Peng, C.Y.& Ayala, P.Y.& Chen, W.& Wong, M.W.& Andres, J.L.& Replogle, E.S.& Gomperts, R.& Martin, R.L.& Fox, D.J.& Binkley, J.S.& Defrees, D.J.& Baker, J.& Stewart, J.P.& Head-Gordon, M.& Gonzalez, C.& Pople, J.A., "Gaussian 94, Rev. E2", 1995
  15. Gilson, M.K.& Honig, B.H., "The dielectric constant of a folded protein", Biopolymers, vol. 25, 1986, p.2097-2119
  16. Greengard, P., "Phosphorylated proteins as physiological effectors", Science, vol. 199, 1978, p.146-152
  17. Grycuk, T., "Revision of the model system concept for the prediction of pKa's in proteins", J. Phys. Chem. B., vol. 106, 2002, p.1434-1445
  18. Gupta, S.C.& Islam, N.B.& Whalen, D.L.& Yagi, H.& Jerina, D.M., "Bifunctional catalysis in the nucleotide-catalysed hydrolysis of (±)-7 β,8α-dixydroxy-9α,10α-epoxy-7,8,9,10- tetrahydrobenzo[a]pyrene", J. Org. Chem., vol. 52, 1987, p.3812-3815
  19. Hoffmann, R.& Reichert, I.& Wachs, W.O.& Zeppezauer, M.& Kalbitzer, H.R., "1H and 31P NMR spectroscopy of phosphorylated model peptides", Int. J. Pept. Protein Res., vol. 44, 1994, p.193-198
  20. Johnson, L.N.& Barford, D., "Electrostatic effects in the control of glycogen phosphorylase by phosphorylation", Protein Sci., vol. 3, 1994, p.1726-1730
  21. Kalbitzer, H.R.& Rösch, P., "The effect of phosphorylation of the histidyl residue in the tetrapeptide Gly-Gly-His-Ala. Changes of chemical shift and pK values in 1H- and 31P-NMR spectra", Organic Magnet. Reson., vol. 17, 1981, p.88-91
  22. Kimura, E.& Aoki, S.& Koike, T.& Shiro, M., "A Tris(ZnII-1,4,7,10-tetraazacyclododecane) complex as a new receptor for phosphate dianions in aqueous solution", J. Am. Chem. Soc., vol. 119, 1997, p.3068-3076
  23. King, E.J.& Delory, G.E., "The rates of enzymatic hydrolysis of phosphoric esters", Biochem. J., vol. 33, 1939, p.1185-1188
  24. Kurosawa, M., "Phosphorylation and dephosphorylation of protein in regulating cellular function", J. Pharmacol. Toxicol. Rev., vol. 31, 1994, p.135-139
  25. Maguire, M.H.& Shaw, G., "Synthetic plant hormones. I. Some esters of phosphoric acid", J. Chem. Soc., 1953, p.1479-1482
  26. Martinez-Liarte, J.H.& Iriarte, A.& Martinez-Carrion, M., "Inorganic phosphate binding and electrostatic effects in the active center of aspartate aminotransferase apoenzyme", Biochemistry, vol. 31, 1992, p.2712-2719
  27. Mavri, J.& Vogel, H.J., "Ion pair formation of phosphorylated amino acids and lysine and arginine side chains: a theoretical study", Proteins: Struct. Funct. Genet., vol. 24, 1996, p.495-501
  28. Mehler, E.L.& Guarnieri, F., "A self-consistent, microenvironment modulated screened coulomb potential approximation to calculate pH-dependent electrostatic effects in proteins", Biophys. J., vol. 77, 1999, p.3-22
  29. Mestas, S.P.& Lumb, K.J., "Electrostatic contribution of phosphorylation to the stability of the CREB-CBP activator-coactivator complex", Nat. Struct. Biol., vol. 6, 1999, p.613-614
  30. Nakamura, H.& Sakamoto, T.& Wada, A., "A theoretical study of the dielectric constant of protein", Protein Eng., vol. 2, 1988, p.177-183
  31. Pascal, S.M.& Singer, A.U.& Gish, G.& Yamazaki, T.& Shoelson, S.E.& Pawson, T.& Kay, L.E.& Forman-Kay, J.D., "Nuclear magnetic resonance structure of an sh2 domain of phospholipase c-gamma 1 complexed with a high affinity binding peptide", Cell, vol. 77, 1994, p.461-472
  32. Patarca, R., "Protein phosphorylation and dephosphorylation in physiologic and oncologic processes", Crit. Rev. Oncog., vol. 7, 1996, p.343-432
  33. Peacock, C.J.& Nickless, G., "The dissociation constants of some phosphorus(V) acids", Z. Naturforsch., vol. 24a, 1969, p.245-247
  34. Phillips, J.N., "Strength of chloro-substituted phenoxyacetic and related phosphorus-containing acids", J. Chem. Soc., 1958, p.4271-4276
  35. Robitaille, P.L.& Robitaille, P.A.& Brown Jr., G.G.& Brown, G.G., "An analysis of the pH-dependent chemical-shift behavior of phosphorus-containing metabolites", J. Mag. Res., vol. 92, 1991, p.73-84
  36. Sanchez-Ruiz, J.M.& Martinez-Carrion, M., "Ionization state of the coenzyme 5′-phosphate ester in cytosolic aspartate aminotransferase. A Fourier transform infrared spectroscopic study", Biochemistry, vol. 25, 1986, p.2915-2920
  37. Schutz, C.N.& Warshel, A., "What are the dielectric “constants” of proteins and how to validate electrostatic models", Proteins: Struct. Funct. Genet., vol. 44, 2001, p.400-417
  38. Sham, Y.Y.& Chu, Z.T.& Warshel, A., "Consistent calculations of pK(a)’s of ionizable residues in proteins: Semi-microscopic and microscopic approaches", J. Phys. Chem., vol. 101, 1997, p.4458-4472
  39. Singer, A.U.& Forman-Kay, J.D., "pH titration studies of an SH2 domain-phosphopeptide complex: Unusual histidine and phosphate pKa values", Protein Sci., vol. 6, 1997, p.1910-1919
  40. Vogel, H.J., "Phosphorus-31 NMR of phosphoproteins", Methods Enzymol., vol. 177, 1989, p.263-282
  41. Walaas, S.I.& Greengard, P., "Protein phosphorylation and neuronal function", Pharmacol. Rev., vol. 43, 1991, p.299-349
  42. Weast, R.C., "CRC Handbook of Physics and Chemistry", 1966, 47th ed.
  43. Westheimer, F.H., "Why nature chose phosphates", Science, vol. 235, 1987, p.1173-1178
  44. Widmalm, G.& Pastor, R.W., "Comparison of Langevin and molecular dynamics simulations—equilibrium and dynamics of ethylene glycol in water", J. Chem. Soc. Faraday Trans., vol. 88, 1992, p.1747-1754
  45. Yang, A.S.& Gunner, M.R.& Sampogna, R.& Sharp, K.& Honig, B., "On the calculation of pKas in proteins", Proteins: Struct. Func. Gen., vol. 15, 1993, p.252-265
  46. Yang, H.L.S.Z.& Zhi, G.& Stull, A.J.T.& Trybus, K.M., "Charge replacement near the phosphorylatable serine of the myosin regulatory light chain mimics aspects of phosphorylation", Proc. Natl. Acad. Sci. USA, vol. 91, 1994, p.1490-1494
  47. You, T.J.& Bashford, D., "Conformation and hydrogen ion titration of proteins: a continuum electrostatic model with conformational flexibility", Biophys. J., vol. 69, 1995, p.1721-1733
  48. Zhou, H.& Vijayakumar, M., "Modeling of protein conformational fluctuations in pKa predictions", J. Mol. Biol., vol. 267, 1997, p.1002-1011
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