Spatial conformation and topography of the tyrosine aromatic ring in substrate recognition by protein tyrosine kinases

Journal of Medicinal Chemistry

Volumn 49, Issue 6, 2006, Pages 1916-1924

  Ruzza, Paolo ^a   Cesaro, Luca ^b   Tourwé, Dirk ^c   Calderan, Andrea ^a   Biondi, Barbara ^a   Maes, Veronique ^c   Menegazzo, Ileana ^b   Osler, Alessio ^a   Rubini, Chiara ^a   Guiotto, Andrea ^a   Pinna, Lorenzo A ^b   Borin, Gianfranco ^a   Donella Deana, Arianna ^b  

^a CNR   (Italy)

^b UNIVERSITY OF PADOVA   (Italy)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDE; PROTEIN KINASE CSK; PROTEIN KINASE FYN; PROTEIN KINASE LYN; PROTEIN KINASE SYK; PROTEIN TYROSINE KINASE; PROTEIN TYROSINE KINASE INHIBITOR; SYNTHETIC PEPTIDE; TYROSINE; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATION; CONSENSUS SEQUENCE; ENZYME PHOSPHORYLATION; ENZYME SPECIFICITY; ENZYME SUBSTRATE COMPLEX; MOLECULAR RECOGNITION;

KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR CONFORMATION; MOLECULAR MIMICRY; OLIGOPEPTIDES; PHOSPHORYLATION; PROTEIN-TYROSINE KINASES; STEREOISOMERISM; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; TYROSINE;

EID: 33645420693     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm051080q     Document Type: Article

References (50)

1. Marks, F. The Brain of the Cell. In Protein Phosphorylation; Marks, F., Ed.; VCH: Weinheim, 1996; pp 1-31.
2. Ruzza, P.; Calderan, A.; Donella-Deana, A.; Biondi, B.; Cesaro, L.; Osler, A.; Elardo, S.; Guiotto, A.; Pinna, L. A.; Borin, G. Conformational Constraints of Tyrosine in Protein Tyrosine Kinase Substrates: Information About Preferred Bioactive Side-Chain Orientation. Biopolymers 2003, 71, 478-488.
3. Donella-Deana, A.; Ruzza, P.; Cesaro, L.; Brunati, A. M.; Calderan, A.; Borin, G.; Pinna, L. A. Specific Monitoring of Syk Protein Kinase Activity by Peptide Substrates Including Constrained Analogs of Tyrosine. FEBS Lett. 2002, 523, 48-52.
4. Brunati, A. M.; Donella-Deana, A.; Ruzzene, M.; Marin, O.; Pinna, L. A. Site-Specificity of p72 (Syk) Protein-Tyrosine Kinase. Efficient Phosphorylation of Motifs Recognized by Src Homology-2 Domains of the Src Family. FEBS Lett. 1995, 367, 149-152.
5. Ruzzene, M.; Pinna L. A. Assay of Protein Kinases and Phosphatases Using Specific Peptide Substrates. In Protein Phosphorylation: A Practical Approach, 2nd ed.; Hardie, D. G., Ed.; Oxford University Press: Oxford, 1999; pp 221-225.
6. Ruzza, P.; Donella-Deana, A.; Calderan, A.; Filippi, B.; Cesaro, L.; Pinna, L. A.; Borin, G. An Exploration of the Effects of Constraints on the Phosphorylation of Synthetic Protein Tyrosine Kinase Substrates. J. Peptide Sci. 1996, 2, 325-338.
7. Tourwé, D.; Mannekens, E.; Thi Diem, T. N.; Verheyden, P.; Jaspers, H.; Tóth, G.; Péter, A.; Kertész, I.; Török, G.; Chung, N. N.; Schiller, P. W. Side Chain Methyl Substitution in the δ-Opioid Receptor Antagonist TIPP Has an Important Effect on the Activity Profile J. Med. Chem. 1998, 41, 5167-5176.
8. χ2 Dihedral Angles. In Peptidomimetics Protocols; Kazmierski, W. M., Ed.; Humana Press: Totowa, 1999; pp 321-338.
9. Pinder, R. M.; Butcher, B. H.; Buxton, D. A.; Howells, D. J. 2-Aminoindane-2-Carboxylic Acids. Potential Tyrosine Hydroxylase Inhibitors. J. Med. Chem. 1971, 14, 892-893.
10. Darula, Z.; Köver, K. E., Monory, K.; Borsodi, A.; Mako, E.; Ronai, A.; Tourwé, D.; Péter, A.; Toth, G. Deltorphin II Analogues with 6-Hydroxy-2-aminotetralin-2-carboxylic Acid in Position 1. J. Med. Chem. 2000, 43, 1359-1366.
11. Lecointe, L.; Rolland, V.; Pappalardo, L.; Roumestant, M. L.; Viallefont, P.; Martinez, J. Diastereoselective Synthesis of Non-Proteinogenic Alpha-Amino Acids. J. Peptide Res. 2000, 55, 300-307.
12. Wellings, D. A.; Atherton, E. Standard Fmoc Protocols. In Methods in Enzymology; Fields, G. B., Ed.; Academic Press Inc.: San Diego, 1997; Vol. 289, pp 44-67.
13. Ruzza, P.; Calderan, A.; Cavaggion, F.; Borin, G. Solid-Phase Synthesis of an Htc-Containing Dimer Analog of the Autophosphorylation Site of pp60(src) PTK: Effective Acylation Conditions for Htc Residues. Lett. Pept. Sci. 2000, 7, 79-83.
14. Wüthrich, K. NMR of Proteins and Nucleic Acids; John Wiley & Sons: New York, 1986; pp 162-175.
15. Bystrov, V. F. Spin-Spin Coupling and the Conformational States of Peptide Systems. Prog. NMR Spectrosc. 1976, 10, 41-81.
16. Kessler, H.; Bermel, W.; Müller. A.; Pook, K. H. The Peptides: Analysis, Synthesis, Biology; Hruby, V. J., Ed.; Academic Press Inc.: Orlando, 1985; Vol. 7, pp 437-473.
17. IUPAC-IUB commission on biochemical nomenclature. Biochemistry 1970, 9, 3471-3479.
18. Basus, V. J. Proton Nuclear Magnetic Resonance Assignments. In Methods in Enzymology, Oppenheimer, N. J., James, T. L., Eds.; Academic Press Inc.: San Diego, 1989; Vol. 177, pp 132-149.
19. Kessler, H.; Griesinger, C.; Wagner, K. Peptide Conformations. 42. Conformation of Side Chains in Peptides Using Heteronuclear Coupling Constants Obtained by Two-Dimensional NMR Spectroscopy. J. Am. Chem. Soc. 1987, 109, 6927-6933.
20. Schiller, P. W.; Weltrowska, G.; Mai Dung, N. T.; Lemieux, C.; Chung, N. N.; Marsden, B. J.; Wilkes, B. C. Conformational Restriction of the Phenylalanine Residue in a Cyclic Opioid Peptide Analog: Effects On Receptor Selectivity and Stereospecificity. J. Med. Chem. 1991, 34, 3125-3132.
21. Hruby, V. J.; Botejn, L. V. Encyclopedia of molecular biology and molecular medicine; Meyers, R. A., Ed.; VCH: Weinhein, 1996; Vol. 4, pp 371-382.
22. Hruby, V. J.; Li, G.; Haskett-Luevano, C.; Shenderovich, M. Design of Peptides, Proteins, and Peptidomimetics in Chi Space. Biopolymers 1997, 43, 219-266.
23. Atwell, S.; Adams, J. M.; Badger, J.; Buchanan, M. D.; Feil, I. K.; Froning, K. J.; Gao, X.; Hendle, J.; Keegan, K.; Leon, B. C.; Muller-Dieckmann, H. J.; Nienaber, V. L.; Noland, B. W.; Post, K.; Rajashankar, K. R.; Ramos, A.; Russell, M.; Burley, S. K.; Buchanan, S. G. A Novel Mode of Gleevec Binding is Revealed by the Structure of Spleen Tyrosine Kinase. J. Biol. Chem. 2004, 279, 55827-55832.
24. Parang, K.; Till, J. H.; Ablooglu, A. J.; Kohanski, R. A.; Hubbard. S. R.; Cole, P. A. Mechanism-Based Design of a Protein Kinase Inhibitor. Nat. Struct. Biol. 2001, 8, 37-41.
25. Nolen, B.; Taylor, S.; Ghosh, G. Regulation of Protein Kinases: Controlling Activity Through Activation Segment Conformation. Mol. Cell 2004, 15, 661-675.
26. Johnson, L. N.; Lewis, R. J. Structural Basis for Control by Phosphorylation Chem. Rev. 2001, 101, 2209-2242.
27. Hubbard, S. R. Crystal Structure of the Activated Insulin Receptor Tyrosine Kinase in Complex with Peptide Substrate and ATP Analog. EMBO J. 1997, 16, 5572-5581.
28. Gaul, B. S.; Harrison, M. L.; Geahlen, R. L.; Burton, R. A.; Post, C. B. Substrate Recognition by the Lyn Protein Tyrosine Kinase. NMR Structure of the Immunoreceptor Tyrosine-Based Activation Motif Signaling Region of the B Cell J. Biol. Chem. 2000, 275, 16174-16182.
29. Ren, P. Y.; Ponder, J. W. Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation. J. Phys. Chem. B 2003, 107, 5933-5947.
30. Marshall, G. R.; Bosshard, H. E. Angiotensin II: Studies on the Biologically Active Conformation. Circ. Res. 1972, 30, 11-143.
31. Pals, D. T.; Thaisrivongs, S.; Lawson, J. A.; Kati, W. M.; Turner, S. R.; DeGraaf, G. L.; Harris, D. W.; Johnson, G. A. An Orally Active Inhibitor of Renin. Hypertension 1986, 8, 1105-1112.
32. Thaisrivongs, S.; Pals, D. T.; Lawson, J. A.; Turner, S. R.; Harris, D. W. Alpha-Methylproline-Containing Renin Inhibitory Peptides: In Vivo Evaluation in an Anesthetized, Ganglion-Blocked, Hog Renin Infused Rat Model. J. Med. Chem. 1987, 30, 536-541.
33. Cheng, A. M.; Chan, A. C. Protein Tyrosine Kinases In Thymocyte Development. Curr. Opin. Immunol. 1997, 9, 528-533.
34. Kurosaki, T. Molecular Mechanism in B Cell Antigen Receptor Signaling. Curr. Opin. Immunol. 1997, 9, 309-318.
35. Chu, D. H.; Morita, C. T.; Weiss, A. The Syk Family of Protein Tyrosine Kinases in T-Cell Activation and Development. Immunol. Rev. 1998, 165, 167-180.
36. Indik, Z. K.; Park, J. G.; Pan, X. Q.; Schreiber, A. D. Induction of Phagocytosis by Aprotein Tyrosine Kinase. Blood 1995, 85, 1175-1180.
37. Miyazawa, T. Enzymatic Resolution of Amino Acids Via Ester Hydrolysis. Amino Acids 1999, 16, 191-213.
38. Chan, W. C.; White, P. D. Basic Procedures. In Fmoc Solid Phase Peptide Synthesis. A Practical Approach; Chan, W. C.; White, P. D., Eds.; Oxford University Press: Oxford, 2000; pp 41-76.
39. Marion, D.; Wüthrich, K. Application of Phase Sensitive Two-Dimensional Correlated Spectroscopy (COSY) for Measurements of 1H-1H Spin Coupling Constants in Proteins. Biochem. Biophys. Res. Commun. 1983, 113, 967-971.
40. Bax, A.; Davis, D. G. MLEV-17 Based Two-Dimensional Homonuclear Magnetization Transfer Spectroscopy. J. Magn. Reson. 1985, 65, 355-360.
41. Bax, A.; Davis, D. G. Practical Aspect of Two-Dimensional Transverse NOE Spectroscopy. J. Magn. Reson. 1985, 63, 207-213.
42. Macura, S.; Ernst, R. R. Elucidation of Cross-Relaxation in Liquids by Two-Dimensional NMR Spectroscopy. Mol. Phys. 1980, 41, 95-117.
43. Griesinger, C.; Sorensen, O. W.; Ernst, R. R. Practical Aspects of the E.COSY Technique. Measurements of Scalar Spin-Spin Coupling Constants In Peptides. J. Magn. Reson. 1987, 75, 474-492.
44. Bax, A.; Summers, M. F. Proton and Carbon-13 Assignments from Sensitivity-Enhanced Detection of Heteronuclear Multiple-Bond Connectivity by 2D Multiple Quantum NMR. J. Am. Chem. Soc. 1986, 108, 2093-2094.
45. Williamson, R. T.; Marquez, B. L.; Gerwick, W. H.; Kover, K. E. One- and Two-Dimensional Gradient-Selected HSQMBC NMR Experiments for the Efficient Analysis of Long-Range Heteronuclear Coupling Constants. Magn. Reson. Chem. 2000, 38, 265-273.
46. Donella-Deana, A.; Marin, O.; Brunati, A. M.; Pinna, L. A. Selective Effect of Poly(lysine) on the Enhancement of the Lyn Tyrosine Protein Kinase Activity. Increased Specificity Toward Src Peptides. Eur. J. Biochem. 1992, 204, 1159-1163.
47. Brunati, A. M.; James, P.; Donella-Deana, A.; Matoskova, B.; Robbins, K. C.; Pinna, L. A. Isolation and Identification of 2 Protooncogene Products Related to c-Fgr and Fyn in a Tyrosine Protein Kinase Fraction of Rat Spleen. Eur. J. Biochem. 1993, 216, 323-327.
48. Brunati, A. M.; Allee, G.; Marin, O.; Donella-Deana, A.; Cesaro, L.; Bougeret, C.; Fagard, R.; Benarous, R.; Fischer, S.; Pinna; L. A. Spleen Protein Tyrosine Kinases Tpk-IIB and Csk Display Different Immunoreactivity and Opposite Specificites Toward c-Src-Derived Peptides. FEBS Lett. 1992, 313, 291-294.
49. 32P-Phosphoryl Group of ATP into Phosphoproteins and Phosphopeptides. Anal. Biochem. 1976, 71, 583-587.
50. Glass, D. B.; Masaracchia, R. A.; Feramisco, J. R.; Kemp, D. E. Isolation of Phosphorylated Peptides and Proteins on Ion Exchange Papers. Anal. Biochem. 1978, 87, 566-575.