Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. Substrate-enzyme interactions and dynamics

Biophysical Journal

Volumn 78, Issue 5, 2000, Pages 2191-2200

  Peters, Günther H ^b   Frimurer, Thomas M ^a   Andersen, Jannik N ^a   Olsen, Ole H ^a  

^a NOVO NORDISK A S   (Denmark)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; GLUTAMINE; GLYCINE; PROLINE; PROTEIN TYROSINE PHOSPHATASE; SERINE;

ARTICLE; CATALYSIS; CHEMICAL INTERACTION; ELECTRICITY; ENZYME ACTIVE SITE; ENZYME SUBSTRATE COMPLEX; MOLECULAR DYNAMICS; SIMULATION;

EID: 0034026757     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76768-3     Document Type: Article

References (56)

1. Ajay, and M. A. Murcko. 1995. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 38:4953-4967.
2. Amadei, A., A. B. M. Linssen, and H. J. C. Berendsen. 1993. Essential dynamics of proteins. Proteins Struct. Funct. Genet. 17:412-425.
3. Antosiewicz, J., J. A. McCammon, and M. K. Gilson. 1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415-436.
4. Barford, D. 1995. Protein phosphatases. Curr. Opin. Struct. Biol. 5:728-734.
5. Barford, D., A. J. Flint, and N. K. Tonks. 1994. Crystal structure of human protein tyrosine phosphatase IB. Science. 263:1397-1404.
6. Bernstein, F. C., T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rogers, O. Kennard, T. Shimanouchi, and M. Tasumi. 1977. The Protein Data Bank: a computer based archival file for macromolecular structure. J. Mol. Biol. 112:535-542.
7. Boylan, J. M., D. L. Brautigan, J. Madden, T. Raven, L. Ellis, and P. A. Gruppuso. 1992. Differential regulation of multiple hepatic protein tyrosine phosphatases in alloxan diabetic rats. J. Clin. Invest. 90: 174-179.
8. Cool, D. E., and E. H. Fischer. 1993. Protein tyrosine phosphatases in cell transformation. Semin. Cell Biol. 4:443-453.
9. Davis, M. E., J. D. Madura, B. A. Luty, and J. A. McCammon. 1991. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comp. Phys. Comm. 62:187-197.
10. Denu, J. M., and J. E. Dixon. 1995. A catalytic mechanism for the dual-specific phosphatases. Proc. Natl. Acad. Sci. USA. 92:5910-5914.
11. Eckstein, J. W., P. Beer-Romero, and I. Berdo. 1996. Identification of an essential acidic residue in Cdc25 protein phosphatase and a general three-dimensional model for the core region in protein phosphatases. Protein Sci. 5:5-12.
12. Fauman, E. B., and M. A. Saper. 1996. Structure an function of the protein tyrosine phosphatases. Trends Biochem. Sci. 21:413-417.
13. Fauman, E. B., C. Yuvaniyama, H. L. Schubert, J. A. Stuckey, and M. A. Saper. 1996. The x-ray crystal structure of Yersinia tyrosine phosphatase with bound tungstate and nitrate. J. Biol. Chem. 271:18780-18788.
14. Fisher, E. H., H. Charbonneau, and N. K. Tonks. 1991. Protein tyrosine phosphatases. Science. 253:401-406.
15. Frangioni, J. V., M. Smith, E. W. Salzman, A. Oda, and B. G. Neel. 1993. Calpain-catalyzed cleavage and subcellular relocation of protein phosphotyrosine phosphatase 1B (FTP-1B) in human platelets. EMBO J. 12:4843-4849.
16. Gilson, M. K. 1993. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins Struct. Funct. Genet. 15:266-282.
17. Goddette, D. W., T. Christianson, B. F. Ladin, M. Lau, J. R. Mielenz, C. Paech, R. B. Reynolds, S. S. Yang, and C. R. Wilson. 1993. Strategy and implementation of a system for protein engineering. J. Biotechnol. 28:41-54.
18. Honig, B., and A. Nicholls. 1995. Classical electrostatics in biology and chemistry. Science. 268:1144-1149.
19. Hunter, T. 1995. Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell. 80:225-235.
20. Ichiye, T., and M. Karplus. 1991. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Protein Struct. Funct. Genet. 11:205-217.
21. Ide, R., H. Maegawa, R. Kikkawa, Y. Shigeta, and A. Kashiwagi. 1994. High glucose condition activates protein tyrosine phosphatases and deactivates insulin receptor function in insulin-sensitive rat 1 fibroblasts. Biochem. Biophys. Res. Commun. 201:71-77.
22. Jencks, W. P. 1975. Binding energy, specificity, and enzymic catalysis: the Circe effect. Adv. Enzymol. Relat. Areas Mol. Biol. 219-410.
23. Jia, Z., D. Barford, A. J. Flint, and N. K. Tonks. 1995. Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase IB. Science. 268:1754-1758.
24. Koshland, D. E., Jr. 1958. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA. 44:98-106.
25. Krystek, S., T. Stouch, and J. Novotny. 1993. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. J. Mol. Biol. 234: 661-679.
26. Ku, T. W., F. E. Ali, and L. S. Barton. 1993. Direct design of a potent non-peptide fibrinogen receptor antagonist based on the structure and conformation of a highly constrained cyclic rigid peptide. J. Am. Chem. Soc. 115:8861-8862.
27. Lammers, R., B. Bossenmaier, D. E. Cool, N. K. Tonks, J. Schlessinger, E. H. Fischer, and A. Ullrich. 1993. Differential activities of protein tyrosine phosphatases in intact cells. J. Biol. Chem. 268:22456-22462.
28. Madura, J. D., J. M. Briggs, R. C. Wade, M. E. Davis, B. A. Luty, A. Hin, J. Antosiewicz, M. K. Gilson, B. Bagheri, L. R. Scott, and J. A. McCammon. 1995. Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian dynamics program. Comp. Phys. Comm. 91:57-67.
29. McGuire, M., R. M. Fields, B. L. Nyomba, I. Raz, C. Bogardus, N. K. Tonks, and J. Sommercon. 1991. Abnormal regulation of protein tyrosine phosphatase activities in skeletal muscle of insulin-resistant humans. Diabetes. 40:939-942.
30. Møller, N. P. H., K. B. Møller, R. Lammers, A. Kharitonenkov, E. Hoppe, F. C. Wiberg, I. Sures, and A. Ullrich. 1995. Selective down-regulation of the insulin receptor signal by protein-tyrosine phosphatases α and ε *. J. Biol. Chem. 270:23126-23131.
31. Montsera, J., L. Chen, D. S. Lawrence, and Z.-Y. Zhang. 1996. Potent low molecular weight substrates for protein-tyrosine phosphatase. J. Biol. Chem. 271:7868-7872.
32. Peters, G. H., T. M. Frimurer, J. N. Andersen, and O. H. Olsen. 1999. Molecular dynamics simulations of protein-tyrosine phosphatase IB. I. Ligand-induced changes in protein motions. Biophys. J. 77:505-515.
33. 5R(S/T) in protein-tyrosine phosphatases. Biochemistry. 37:5383-5393.
34. Peters, G. H., S. Toxvaerd, O. H. Olsen, and A. Svendsen. 1997a. Computational studies of activation of lipases and the effect of a hydrophobic environment. Protein Eng. 10:137-147.
35. Peters, G. H., D. M. F. van Aalten, A. Svendsen, and R. Bywater. 1997b. Essential motions in enzyme binding sites and bound inhibitors: the effect of inhibitors of different chain length. Protein Eng. 10:148-156.
36. Posner, B. I., R. Fauer, J. Burgess, A. P. Bevan, D. Lachance, G. ZhangSun, G. Fantus, A. D. Hai, B. S. Lum, and A. Shaver. 1994. Peroxvanadium compounds: a new class of potent phosphotyrosine phosphatase inhibitors which are insulin mimetic. J. Biol. Chem. 269:4596-4604.
37. Pot, D. A., and J. E. Dixon. 1992. A thousand and two protein tyrosine phosphatases. Biochim. Biophys. Acta. 1136:35-43.
38. Ruiz, P., J. A. Pulido, C. Martinez, J. M. Carrascosa, J. Satrustegi, and A. Andres. 1992. Effect of aging on the kinetic characteristics of the insulin receptor autophosphorylation in rat adipocytes. Arch. Biochem. Biophys. 296:231-238.
39. Salemme, F. R., J. Spurlino, and R. Bone. 1997. Serendipity meets precision: the integration of structure-based drug design and combinatorial chemistry for efficient drug discovery. Structure. 5:319-324.
40. Schubert, H. L., E. B. Fauman, J. A. Stuckey, J. E. Dixon, and M. A. Saper. 1995. A substrate-induced conformational change in the Yersinia protein tyrosine phosphatase. Protein Sci. 4:1904-1913.
41. Stone, R. L., and J. E. Dixon. 1994. Protein-tyrosine phosphatases. J. Biol. Chem. 269:31323-31326.
42. Streuli, K., N. X. Krueger, T. Thai, M. Tang, and H. Saito. 1990. Distinct functional roles of the two intracellular phosphatase like domains of the receptor-linked protein tyrosine phosphatases LCA and LAR. EMBO J. 9:2399-2407.
43. Tonks, N. K., A. J. Flint, M. F. B. G. Gebbink, H. Sun, and Q. Yang. 1993. Transduction and protein tyrosine dephosphorylation. Second Messengers Phosphoproteins. 28:203-210.
44. Vajda, S., Z. Weng, R. Rosenfeld, and C. DeLisi. 1994. Effect of conformational flexibility and solvation on receptor-substrate binding free energies. Biochemistry. 33:13977-13988.
45. Van Gunsteren, W. F., and H. J. C. Berendsen. 1987. GROMOS: Groningen Molecular Simulation Computer Program Package. University of Groningen, Groningen, the Netherlands.
46. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
47. Walton, K. M., and J. E. Dixon. 1993. Protein tyrosine phosphatases. Annu. Rev. Biochem. 62:101-120.
48. Weber, P. C., J. J. Wendoloski, M. W. Pantoliano, and F. R. Salemme. 1992. Crystallographic and thermodynamic comparison of natural and synthetic substrates bound to streptavidin. J. Am. Chem. Soc. 114: 3197-3200.
49. Wiener, J. R., S. K. Kassim, Y. Yu, G. B. Mills, and R. C. Bast. 1996. Transfection of human ovarian cancer with the HER-2/neu receptor tyrosine kinase induces a selective increase in PTPH1, PTP1B, and PTPα expression. Gynecol. Oncol. 61:233-240.
50. Wlodek, S. T., J. Antosiewicz, J. A. McCammon. 1997. Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci. 6:373-382.
51. Zanke, B., J. Squire, H. Griesser, M. Henry, H. Suzuki, B. Patterson, M. Minden, and T. W. Mak. 1994. A hematopoietic protein tyrosine phosphatase (HePTP) gene that is amplified and overexpressed in myeloid malignancies maps to chromosome Iq32.1. Leukemia. 8:236-244.
52. Zhang, Z.-Y., D. Maclean, D. J. McNamara, T. K. Sawyer, and J. E. Dixon. 1994a. Protein tyrosine phosphatase substrate specificity: size and phosphotyrosine positioning requirements in peptide substrates. Biochemistry. 33:2285-2290.
53. Zhang, Z.-Y., A. M. Thieme-Sefler, D. Maclean, D. J. Mcnamara, E. M. Dobrusin, T. K. Sawyer, and J. E. Dixon. 1993. Substrate specificity of the protein tyrosine phosphatases. Proc. Natl. Acad. Sci. USA. 90: 4446-4450.
54. Zhang, Z.-Y., Y. Wang, and J. E. Dixon. 1994b. Dissecting the catalytic mechanism of protein-tyrosine phosphatases. Proc. Natl. Acad. Sci. USA. 91:1624-1627.
55. Zhang, Z.-Y., and L. Wu. 1997. The single sulfur to oxygen substitution in the active site nucleophile of the Yersinia protein-tyrosine phosphatase leads to substantial structural and functional perturbations. Biochemistry. 36:1362-1369.
56. Zheng, X. M., Y. Wang, and J. C. Pallen. 1992. Cell transformation and activation of pp60c-src by overexpression of a protein tyrosine phosphatase. Nature. 359:336-339.