Ion pair formation of phosphorylated amino acids and lysine and arginine side chains: A theoretical study

Proteins: Structure, Function and Genetics

Volumn 24, Issue 4, 1996, Pages 495-501

  Mavri, Janez ^a,c   Vogel, Hans J ^b  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF CALGARY   (Canada)

^c NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

ab initio calculations; density functional theory; hydrogen bonding; phosphoserine; phosphothreonine; phosphotyrosine; semiempirical calculations; solvent reaction field

Indexed keywords

ARGININE; LYSINE; PHOSPHOSERINE; PHOSPHOTHREONINE; PHOSPHOTYROSINE;

AMINO ACID METABOLISM; ARTICLE; CELL DENSITY; ENZYME ACTIVATION; ENZYME DEGRADATION; ENZYME PHOSPHORYLATION; HYDROGEN BOND; ION PAIR EXTRACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

AMINO ACIDS; ANIONS; ARGININE; HYDROGEN BONDING; LYSINE; MODELS, THEORETICAL; PHOSPHORYLATION; THERMODYNAMICS;

EID: 0029937871     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199604)24:4<495::AID-PROT8>3.0.CO;2-D     Document Type: Article

References (49)

1. Graves, D., Wang, J., Martin, B. "Post- and Co-Translational Modification of Proteins." Oxford: Oxford University Press, 1994.
2. Krebs, E.G. Protein phosphorylation and cellular regulation I (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 32: 1122-1129, 1993.
3. Fischer, E.H. Protein phosphorylation and cellular regulation II (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 32:1130-1137, 1993.
4. Cohen, P. Signal integration at the level of protein kinases, protein phosphatases and their substrates. Tr. Biochem. Sci. 17:408-413, 1992.
5. Kemp, B.E., Pearson, R.B. Protein kinase recognition sequence motifs. Tr. Biochem. Sc. 15:342-346, 1990.
6. Kemp, B.E., Parker, M.W., Hu., S., Tigania, T., House, C. Substrate and pseudosubstrate interactions with protein kinases: Determinants of specificity. Tr. Biochem. Sc. 19: 440-444, 1994.
7. Taylor, S.S., Radzio-Adzelm, E. Three protein kinase structures define a common motif. Structure 2:345-355, 1994.
8. Morgan, D.O., DeBondt, H.L. Protein kinase regulation: Insights from crystal structure analysis. Curr. Opin. Cell Biol. 6:239-246, 1994.
9. Barford, D., Flint, A.J., Tonks, N.K. Crystal structure of human protein tyrosine phosphatase IB. Science 263: 1397-1404, 1994.
10. Su, X.-D., Taddel, N., Stefani, M., Ramponi, G., Nordlund, P. The crystal structure of a low-molecular weight phosphotyrosine phosphatase. Nature 370:575-578, 19XX.
11. Johnson, L.N., Barford, D. The effects of phosphorylation on the structure and function of proteins. Annu. Rev. Biophys. Biomol. Struct. 22:199-232, 1993.
12. Vogel, H.J. Phosphorus-31 NMR studies of phosphoproteins. Meth. Enzymol. 177:263-282, 1989.
13. Norbury, C., Nurse, P. Animal cell cycles and their control. Annu. Rev. Biochem. 61:441-470, 1993.
14. Hanks, S.K., Quinn, A.M. Protein kinase catalytic domain sequence database: Identification of conserved features of primary structure and classification of family members. Meth. Enzymol. 200:38-62, 1991.
15. Pawson, T., Gish, G.D. SH2 and SH3 domains: From structure to function. Cell 71:359-362, 1992.
16. Waksman, G., Kominos, D., Kuriyan, J. Crystal structure of the phosphotyrosine recognition domain SH2 of V-src complexed with tyrosine-phosphorylated peptides. Science 358:646-653, 1992.
17. Overduin, M., Rios, C.B., Mayer, B.J., Baltimore, D., Cowburn, D. Three-dimensional solution structure of the src homology 2 domain of c-abl. Cell 70:697-704, 1992.
18. Waksman, G., Shoelson, S.E., Pant, N., Cowburn, D., Kuriyan, J. Binding of a high affinity phosphotyrosyl peptide to the src SH2 domain: Crystal structures of the complexed and peptide free forms. Cell 72:779-790, 1993.
19. Mavri, J., Vogel, H.J. Ion pair formation involving methylated lysine side chains: A theoretical study. Proteins 18: 381-389, 1994.
20. Deerfield, D.W., Nicholas, H.B., Hiskey, R.G., Pedersen, L.G. Salt or ion bridges in biological systems: A study employing quantum and molecular mechanics. Proteins 6:168-192, 1989.
21. 2S, imidazole, formaldehyde and chloride as ligands: An ab initia study. Proteins 21:244-255, 1995.
22. Caldwell, J.W., Kollman, P.A. Cation-π interactions: Non-additive effects are critical in their accurate representation. J. Am. Chem. Soc. 117:4177-4178, 1995.
23. Gresh, N., Pullman, B. A theoretical study of the interaction of ammonium and guanidium ions with the phosphodiester linkage. Theor. Chim. Acta (Berl). 52:67-73, 1979.
24. Salunke, D.M., Vijayan, M. Specific interactions involving guanidyl group observed in crystal structures. Int. J. Pept. Protein Res. 18:348-351, 1981.
25. Alagona, G., Ghio, C., Kollman, P. Bifurcated vs. linear hydrogen bonds: Dimethyl phosphate and formate anion interactions with water. J. Am. Chem. Soc. 105:5226-5230, 1983.
26. 2+ in the presence of water. J. Am. Chem. Soc. 106:8079-8086, 1984.
27. Sapse, A.M., Russell, C.S. Ab initio calculations of guanidinium-carboxylate interaction. Int. J. Quant. Chem. 26: 91-99, 1984.
28. Frisch, M.J., et al. Gaussian 92/DFT, Revision G.1. Pittsburgh: Gaussian, Inc., 1993.
29. Saint Martin, H., Otega-Blake, I., Lez, A., Adamowitz, L. Ab initio calculations of the pyrophosphate hydrolysis reaction. Biochim. Biophys. Acta. 1080:205-214, 1991.
30. Colvin, M.E., Evleth, E., Akacem, Y. Quantum chemical studies of pyrophosphate hydrolysis. J. Am. Chem. Soc. 117:4357-4362, 1995.
31. Becke, A.D. Density-functional thermochemistry. The role of exact exchange. J. Chem. Phys. 98:5648-5652, 1993.
32. Lee, C., Yang, W., Parr, E.G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B. 37:785-789, 1988.
33. Cramer, C.J., Lynch, G.G., Hawkins, G.D., Truhlar, D.G. AMSOL 4.0, QCPE 606, QCPE Bull. 13:78, 1993.
34. Tomasi, J., Persico, M. Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent. Chem. Rev. 94:2027-2094, 1994.
35. Cramer, C.J., Truhlar, D.G. General parametrized SCF model for free energies of solvation in aqueous solution. J. Am. Chem. Soc. 113:8305-8311, 1991.
36. Cramer, C.J., Truhlar, D.G. An SCF solvation model for the hydrophobic effect and absolute free energies of aqueous solvation. Science 256:213-217, 1992.
37. Cramer, C.J., Truhlar, D.G. AM1-SM2 and PM3-SM3 parametrized SCF solvation models for free energies in aqueous solution. J. Comp. Aid Molec. Des. 6:629-666, 1992.
38. Hehre, W.J., Radom, L., Schleyer, P. von R., Pople, J.A. Ab initio molecular orbital theory. New York: Wiley, 1986.
39. Ziegler, T. Approximate density functional theory as a practical tool in molecular energetics and dynamics. Chem. Rev. 91:651-667, 1991.
40. Stanton, R.V., Merz, K.M., Jr. Density functional study of symmetric proton transfers. J. Chem. Phys. 101:6658-6665, 1994.
41. Ruiz, E., Salahub, D.E., Vela, A. Defining the domain of density functionals: Charge transfer complexes. J. Am. Chem. Soc. 117:1141-1141, 1995.
42. Kieninger, M., Suhai, S. Density functional studies on hydrogen-bonded complexes. Int. J. Quantum. Chem. 52: 465-478, 1994.
43. Vogel, H.J., Bridger, W.A. Phosphorus-31 NMR pH-titration experiments of the phosphoproteins tropomyosin and glycogen phosphorylase. Can. J. Biochem. 61:363-369, 1983.
44. Rose, G.D., Wolfenden, R. Hydrogen bonding, hydrophobicity, packing and protein folding. Annu. Rev. Biophys. Biomol. Str. 22:381-415, 1993.
45. 4 lysozyme. Biochemistry 29:2403-2408, 1990.
46. Stewart, J.A. MOPAC: A semiempirical molecular orbital program. J. Comp. Aided Molec. Design. 4:1-104, 1990.
47. Alkorta, I., Villar, H.O., Ferez, J.J. Comparison of methods to estimate the free energy of solvation. J. Comp. Chem. 14:620-626, 1993.
48. Thorsness, P.E., Koshland, D.E., Jr. Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate. J. Biol. Chem. 262: 10422-10425, 1987.
49. Marcus, F., Rittenhouse, J., Moberly, L., Edelstein, I., Hiller, E., Rogers, D.T. Yeast fructose-1,6-bisphosphatase; properties of phospho- and dephospho-forms and two mutants in which serine 11 has been changed by site-directed mutagenesis. J. Biol. Chem. 263:6058-6062, 1988.