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. 2000 May;78(5):2191–2200. doi: 10.1016/S0006-3495(00)76768-3

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

G H Peters 1, T M Frimurer 1, J N Andersen 1, O H Olsen 1
PMCID: PMC1300813  PMID: 10777720

Abstract

Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme and substrate flexibility for binding, 3) the electrostatic properties of the enzyme, and 4) the contribution from solvation. The simulations were performed for 1 ns, using explicit water molecules. The last 700 ps of the trajectories was used for analysis determining enthalpic and entropic contributions to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. In particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24)-Ser(28), Pro(38)-Arg(47), and Glu(115)-Gly(117). These motions are correlated to the C- and N-terminal motions of the substrate. Relatively small fluctuations are observed in the region of the consensus active site motif (H/V)CX(5)R(S/T) and in the region of the WPD loop, which contains the general acid for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein surface is characterized by a predominantly negative electrostatic field. This positive electrostatic field attracts negatively charged substrates and could explain the experimentally observed preference of PTP1B for negatively charged substrates like the DADEpYL peptide.

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Selected References

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  1. Ajay, Murcko M. A. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem. 1995 Dec 22;38(26):4953–4967. doi: 10.1021/jm00026a001. [DOI] [PubMed] [Google Scholar]
  2. Amadei A., Linssen A. B., Berendsen H. J. Essential dynamics of proteins. Proteins. 1993 Dec;17(4):412–425. doi: 10.1002/prot.340170408. [DOI] [PubMed] [Google Scholar]
  3. Antosiewicz J., McCammon J. A., Gilson M. K. Prediction of pH-dependent properties of proteins. J Mol Biol. 1994 May 6;238(3):415–436. doi: 10.1006/jmbi.1994.1301. [DOI] [PubMed] [Google Scholar]
  4. Barford D., Flint A. J., Tonks N. K. Crystal structure of human protein tyrosine phosphatase 1B. Science. 1994 Mar 11;263(5152):1397–1404. [PubMed] [Google Scholar]
  5. Barford D. Protein phosphatases. Curr Opin Struct Biol. 1995 Dec;5(6):728–734. doi: 10.1016/0959-440x(95)80004-2. [DOI] [PubMed] [Google Scholar]
  6. Bernstein F. C., Koetzle T. F., Williams G. J., Meyer E. F., Jr, Brice M. D., Rodgers J. R., Kennard O., Shimanouchi T., Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 1977 May 25;112(3):535–542. doi: 10.1016/s0022-2836(77)80200-3. [DOI] [PubMed] [Google Scholar]
  7. Boylan J. M., Brautigan D. L., Madden J., Raven T., Ellis L., Gruppuso P. A. Differential regulation of multiple hepatic protein tyrosine phosphatases in alloxan diabetic rats. J Clin Invest. 1992 Jul;90(1):174–179. doi: 10.1172/JCI115833. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cool D. E., Fischer E. H. Protein tyrosine phosphatases in cell transformation. Semin Cell Biol. 1993 Dec;4(6):443–453. doi: 10.1006/scel.1993.1052. [DOI] [PubMed] [Google Scholar]
  9. Denu J. M., Dixon J. E. A catalytic mechanism for the dual-specific phosphatases. Proc Natl Acad Sci U S A. 1995 Jun 20;92(13):5910–5914. doi: 10.1073/pnas.92.13.5910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Eckstein J. W., Beer-Romero P., Berdo I. Identification of an essential acidic residue in Cdc25 protein phosphatase and a general three-dimensional model for a core region in protein phosphatases. Protein Sci. 1996 Jan;5(1):5–12. doi: 10.1002/pro.5560050102. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Fauman E. B., Saper M. A. Structure and function of the protein tyrosine phosphatases. Trends Biochem Sci. 1996 Nov;21(11):413–417. doi: 10.1016/s0968-0004(96)10059-1. [DOI] [PubMed] [Google Scholar]
  12. Fauman E. B., Yuvaniyama C., Schubert H. L., Stuckey J. A., Saper M. A. The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications. J Biol Chem. 1996 Aug 2;271(31):18780–18788. doi: 10.1074/jbc.271.31.18780. [DOI] [PubMed] [Google Scholar]
  13. Fischer E. H., Charbonneau H., Tonks N. K. Protein tyrosine phosphatases: a diverse family of intracellular and transmembrane enzymes. Science. 1991 Jul 26;253(5018):401–406. doi: 10.1126/science.1650499. [DOI] [PubMed] [Google Scholar]
  14. Frangioni J. V., Oda A., Smith M., Salzman E. W., Neel B. G. Calpain-catalyzed cleavage and subcellular relocation of protein phosphotyrosine phosphatase 1B (PTP-1B) in human platelets. EMBO J. 1993 Dec;12(12):4843–4856. doi: 10.1002/j.1460-2075.1993.tb06174.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gilson M. K. Multiple-site titration and molecular modeling: two rapid methods for computing energies and forces for ionizable groups in proteins. Proteins. 1993 Mar;15(3):266–282. doi: 10.1002/prot.340150305. [DOI] [PubMed] [Google Scholar]
  16. Goddette D. W., Christianson T., Ladin B. F., Lau M., Mielenz J. R., Paech C., Reynolds R. B., Yang S. S., Wilson C. R. Strategy and implementation of a system for protein engineering. J Biotechnol. 1993 Mar;28(1):41–54. doi: 10.1016/0168-1656(93)90124-6. [DOI] [PubMed] [Google Scholar]
  17. Honig B., Nicholls A. Classical electrostatics in biology and chemistry. Science. 1995 May 26;268(5214):1144–1149. doi: 10.1126/science.7761829. [DOI] [PubMed] [Google Scholar]
  18. Hunter T. Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell. 1995 Jan 27;80(2):225–236. doi: 10.1016/0092-8674(95)90405-0. [DOI] [PubMed] [Google Scholar]
  19. Ichiye T., Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins. 1991;11(3):205–217. doi: 10.1002/prot.340110305. [DOI] [PubMed] [Google Scholar]
  20. Ide R., Maegawa H., Kikkawa R., Shigeta Y., Kashiwagi A. High glucose condition activates protein tyrosine phosphatases and deactivates insulin receptor function in insulin-sensitive rat 1 fibroblasts. Biochem Biophys Res Commun. 1994 May 30;201(1):71–77. doi: 10.1006/bbrc.1994.1670. [DOI] [PubMed] [Google Scholar]
  21. Jencks W. P. Binding energy, specificity, and enzymic catalysis: the circe effect. Adv Enzymol Relat Areas Mol Biol. 1975;43:219–410. doi: 10.1002/9780470122884.ch4. [DOI] [PubMed] [Google Scholar]
  22. Jia Z., Barford D., Flint A. J., Tonks N. K. Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1B. Science. 1995 Jun 23;268(5218):1754–1758. doi: 10.1126/science.7540771. [DOI] [PubMed] [Google Scholar]
  23. Koshland D. E. Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci U S A. 1958 Feb;44(2):98–104. doi: 10.1073/pnas.44.2.98. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Krystek S., Stouch T., Novotny J. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures. J Mol Biol. 1993 Dec 5;234(3):661–679. doi: 10.1006/jmbi.1993.1619. [DOI] [PubMed] [Google Scholar]
  25. Lammers R., Bossenmaier B., Cool D. E., Tonks N. K., Schlessinger J., Fischer E. H., Ullrich A. Differential activities of protein tyrosine phosphatases in intact cells. J Biol Chem. 1993 Oct 25;268(30):22456–22462. [PubMed] [Google Scholar]
  26. McGuire M. C., Fields R. M., Nyomba B. L., Raz I., Bogardus C., Tonks N. K., Sommercorn J. Abnormal regulation of protein tyrosine phosphatase activities in skeletal muscle of insulin-resistant humans. Diabetes. 1991 Jul;40(7):939–942. doi: 10.2337/diab.40.7.939. [DOI] [PubMed] [Google Scholar]
  27. Montserat J., Chen L., Lawrence D. S., Zhang Z. Y. Potent low molecular weight substrates for protein-tyrosine phosphatase. J Biol Chem. 1996 Mar 29;271(13):7868–7872. doi: 10.1074/jbc.271.13.7868. [DOI] [PubMed] [Google Scholar]
  28. Møller N. P., Møller K. B., Lammers R., Kharitonenkov A., Hoppe E., Wiberg F. C., Sures I., Ullrich A. Selective down-regulation of the insulin receptor signal by protein-tyrosine phosphatases alpha and epsilon. J Biol Chem. 1995 Sep 29;270(39):23126–23131. doi: 10.1074/jbc.270.39.23126. [DOI] [PubMed] [Google Scholar]
  29. Peters G. H., Frimurer T. M., Andersen J. N., Olsen O. H. Molecular dynamics simulations of protein-tyrosine phosphatase 1B. I. ligand-induced changes in the protein motions. Biophys J. 1999 Jul;77(1):505–515. doi: 10.1016/S0006-3495(99)76907-9. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Peters G. H., Frimurer T. M., Olsen O. H. Electrostatic evaluation of the signature motif (H/V)CX5R(S/T) in protein-tyrosine phosphatases. Biochemistry. 1998 Apr 21;37(16):5383–5393. doi: 10.1021/bi971187i. [DOI] [PubMed] [Google Scholar]
  31. Peters G. H., Toxvaerd S., Olsen O. H., Svendsen A. Computational studies of the activation of lipases and the effect of a hydrophobic environment. Protein Eng. 1997 Feb;10(2):137–147. doi: 10.1093/protein/10.2.137. [DOI] [PubMed] [Google Scholar]
  32. Posner B. I., Faure R., Burgess J. W., Bevan A. P., Lachance D., Zhang-Sun G., Fantus I. G., Ng J. B., Hall D. A., Lum B. S. Peroxovanadium compounds. A new class of potent phosphotyrosine phosphatase inhibitors which are insulin mimetics. J Biol Chem. 1994 Feb 11;269(6):4596–4604. [PubMed] [Google Scholar]
  33. Pot D. A., Dixon J. E. A thousand and two protein tyrosine phosphatases. Biochim Biophys Acta. 1992 Jul 22;1136(1):35–43. doi: 10.1016/0167-4889(92)90082-m. [DOI] [PubMed] [Google Scholar]
  34. Ruíz P., Pulido J. A., Martínez C., Carrascosa J. M., Satrústegui J., Andrés A. Effect of aging on the kinetic characteristics of the insulin receptor autophosphorylation in rat adipocytes. Arch Biochem Biophys. 1992 Jul;296(1):231–238. doi: 10.1016/0003-9861(92)90567-g. [DOI] [PubMed] [Google Scholar]
  35. Salemme F. R., Spurlino J., Bone R. Serendipity meets precision: the integration of structure-based drug design and combinatorial chemistry for efficient drug discovery. Structure. 1997 Mar 15;5(3):319–324. doi: 10.1016/s0969-2126(97)00189-5. [DOI] [PubMed] [Google Scholar]
  36. Schubert H. L., Fauman E. B., Stuckey J. A., Dixon J. E., Saper M. A. A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase. Protein Sci. 1995 Sep;4(9):1904–1913. doi: 10.1002/pro.5560040924. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Stone R. L., Dixon J. E. Protein-tyrosine phosphatases. J Biol Chem. 1994 Dec 16;269(50):31323–31326. [PubMed] [Google Scholar]
  38. Streuli M., Krueger N. X., Thai T., Tang M., Saito H. Distinct functional roles of the two intracellular phosphatase like domains of the receptor-linked protein tyrosine phosphatases LCA and LAR. EMBO J. 1990 Aug;9(8):2399–2407. doi: 10.1002/j.1460-2075.1990.tb07415.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Tonks N. K., Flint A. J., Gebbink M. F., Sun H., Yang Q. Signal transduction and protein tyrosine dephosphorylation. Adv Second Messenger Phosphoprotein Res. 1993;28:203–210. [PubMed] [Google Scholar]
  40. Vajda S., Weng Z., Rosenfeld R., DeLisi C. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry. 1994 Nov 29;33(47):13977–13988. doi: 10.1021/bi00251a004. [DOI] [PubMed] [Google Scholar]
  41. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph. 1990 Mar;8(1):52-6, 29. doi: 10.1016/0263-7855(90)80070-v. [DOI] [PubMed] [Google Scholar]
  42. Walton K. M., Dixon J. E. Protein tyrosine phosphatases. Annu Rev Biochem. 1993;62:101–120. doi: 10.1146/annurev.bi.62.070193.000533. [DOI] [PubMed] [Google Scholar]
  43. Wiener J. R., Kassim S. K., Yu Y., Mills G. B., Bast R. C., Jr Transfection of human ovarian cancer cells with the HER-2/neu receptor tyrosine kinase induces a selective increase in PTP-H1, PTP-1B, PTP-alpha expression. Gynecol Oncol. 1996 May;61(2):233–240. doi: 10.1006/gyno.1996.0131. [DOI] [PubMed] [Google Scholar]
  44. Wlodek S. T., Antosiewicz J., McCammon J. A. Prediction of titration properties of structures of a protein derived from molecular dynamics trajectories. Protein Sci. 1997 Feb;6(2):373–382. doi: 10.1002/pro.5560060213. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Zanke B., Squire J., Griesser H., Henry M., Suzuki H., Patterson B., Minden M., Mak T. W. A hematopoietic protein tyrosine phosphatase (HePTP) gene that is amplified and overexpressed in myeloid malignancies maps to chromosome 1q32.1. Leukemia. 1994 Feb;8(2):236–244. [PubMed] [Google Scholar]
  46. Zhang Z. Y., Maclean D., McNamara D. J., Sawyer T. K., Dixon J. E. Protein tyrosine phosphatase substrate specificity: size and phosphotyrosine positioning requirements in peptide substrates. Biochemistry. 1994 Mar 1;33(8):2285–2290. doi: 10.1021/bi00174a040. [DOI] [PubMed] [Google Scholar]
  47. Zhang Z. Y., Thieme-Sefler A. M., Maclean D., McNamara D. J., Dobrusin E. M., Sawyer T. K., Dixon J. E. Substrate specificity of the protein tyrosine phosphatases. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4446–4450. doi: 10.1073/pnas.90.10.4446. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Zhang Z. Y., Wang Y., Dixon J. E. Dissecting the catalytic mechanism of protein-tyrosine phosphatases. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1624–1627. doi: 10.1073/pnas.91.5.1624. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Zhang Z. Y., Wu L. 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. 1997 Feb 11;36(6):1362–1369. doi: 10.1021/bi9624043. [DOI] [PubMed] [Google Scholar]
  50. Zheng X. M., Wang Y., Pallen C. J. Cell transformation and activation of pp60c-src by overexpression of a protein tyrosine phosphatase. Nature. 1992 Sep 24;359(6393):336–339. doi: 10.1038/359336a0. [DOI] [PubMed] [Google Scholar]

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