Kinetic analysis and ligand-induced conformational changes in dimeric and tetrameric forms of human thymidine kinase 2

Biochemistry

Volumn 44, Issue 12, 2005, Pages 4886-4896

  Barroso, João Filipe ^a   Carvalho, Raquel Negrão ^a   Flatmark, Torgeir ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DIMERIZATION; ESCHERICHIA COLI; FLUORESCENCE; MATHEMATICAL MODELS; PHOSPHATES; PURIFICATION;

ARRHENIUS EQUATIONS; CIRCULAR DICHROISM (CD); LIGANDS; NUCLEOSIDE MONOPHOSPHATE KINASE FAMILY;

ENZYMES;

DEOXYRIBONUCLEOSIDE TRIPHOSPHATE; DIMER; LIGAND; NUCLEOSIDE MONOPHOSPHATE KINASE; TETRAMER; THYMIDINE KINASE; THYMIDINE KINASE 2; UNCLASSIFIED DRUG;

ARTICLE; CIRCULAR DICHROISM; DENATURATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME BINDING; ENZYME CONFORMATION; ENZYME IMMOBILIZATION; ENZYME INDUCTION; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE; ESCHERICHIA COLI; FLUORESCENCE ANALYSIS; LIGAND BINDING; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FAMILY; STOICHIOMETRY; STRUCTURE ANALYSIS; SURFACE PLASMON RESONANCE; THERMAL ANALYSIS;

CIRCULAR DICHROISM; DEOXYRIBONUCLEOTIDES; DIMERIZATION; ENZYME INHIBITORS; HUMANS; HYDROLYSIS; ISOENZYMES; KINETICS; LIGANDS; PROTEIN CONFORMATION; PROTEIN DENATURATION; RECOMBINANT PROTEINS; SPECTROMETRY, FLUORESCENCE; SURFACE PLASMON RESONANCE; THYMIDINE KINASE; TRYPSIN; TRYPTOPHAN;

EID: 15444367617     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi047766m     Document Type: Article

References (49)

1. Arnér, E. S., and Eriksson, S. (1995) Mammalian deoxyribonucleoside kinases, Pharmacol. Ther. 67, 155-186.
2. Kit, S., and Leung, W. C. (1974) Submitochondrial localization and characteristics of thymidine kinase molecular forms in parental and kinase-deficient HeLa cells, Biochem. Genet. 11, 231-247.
3. 32P]dTTP of the enzyme from spleen, liver, heart and brain, Eur. J. Biochem. 206, 485-490.
4. Wettin, K., Johansson, M., Zheng, X., Zhu, C., and Karlsson, A. (1999) Cloning of mouse mitochondrial thymidine kinase 2 cDNA, FEBS Lett. 460, 103-106.
5. Wang, L., and Eriksson, S. (2000) Cloning and characterization of full-length mouse thymidine kinase 2: The N-terminal sequence directs import of the precursor protein into mitochondria, Biochem. J. 351, 469-476.
6. Wang, L., Saada, A., and Eriksson, S. (2003) Kinetic properties of mutant human thymidine kinase 2 suggest a mechanism for mitochondrial DNA depletion myopathy, J. Biol. Chem. 278, 6963-6968.
7. Söderlund, J. C., and Arnér, E. S. (1994) Mitochondrial versus cytosolic activities of deoxyribonucleoside salvage enzymes, Adv. Exp. Med. Biol. 370, 201-204.
8. Johansson, M., and Karlsson, A. (1997) Cloning of the cDNA and chromosome localization of the gene for human thymidine kinase 2, J. Biol. Chem. 272, 8454-8458.
9. Johansson, M., Brismar, S., and Karlsson, A. (1997) Human deoxycytidine kinase is located in the cell nucleus, Proc. Natl. Acad. Sci. U.S.A. 94, 11941-11945.
10. Elholm, M., Hollås, H., Issalene, C., Barroso, J. F., Berge, R. K., and Flatmark, T. (2001) Transient up-regulation of liver mitochondrial thymidine kinase activity in proliferating mitochondria, IUBMB Life 51, 99-104.
11. Barroso, J. F., Elholm, M., and Flatmark, T. (2003) Tight binding of deoxyribonucleotide triphosphates to human thymidine kinase 2 expressed in Escherichia coli. Purification and partial characterization of its dimeric and tetrameric forms, Biochemistry 42, 15158-15169.
12. Saada, A., Shaag, A., Mandel, H., Nevo, Y., Eriksson, S., and Elpeleg, O. (2001) Mutant mitochondrial thymidine kinase in mitochondrial DNA depletion myopathy, Nat. Genet. 29, 342-344.
13. Carrozzo, R., Bornstein, B., Lucioli, S., Campos, Y., de la Pena, P., Petit, N., Dionisi-Vici, C., Vilarinho, L., Rizza, T., Bertini, E., Garesse, R., Santorelli, F. M., and Arenas, J. (2003) Mutation analysis in 16 patients with mtDNA depletion, Hum. Mutat. 21, 453-454.
14. Mancuso, M., Salviati, L., Sacconi, S., Otaegui, D., Camano, P., Marina, A., Bacman, S., Moraes, C. T., Carlo, J. R., Garcia, M., Garcia-Alvarez, M., Monzon, L., Naini, A. B., Hirano, M., Bonilla, E., Taratuto, A. L., DiMauro, S., and Vu, T. H. (2002) Mitochondrial DNA depletion: Mutations in thymidine kinase gene with myopathy and SMA, Neurology 59, 1197-1202.
15. Vila, M. R., Segovia-Silvestre, T., Gamez, J., Marina, A., Naini, A. B., Meseguer, A., Lombes, A., Bonilla, E., DiMauro, S., Hirano, M., and Andreu, A. L. (2003) Reversion of mtDNA depletion in a patient with TK2 deficiency, Neurology 60, 1203-1205.
16. Saada, A., Ben-Shalom, E., Zyslin, R., Miller, C., Mandel, H., and Elpeleg, O. (2003) Mitochondrial deoxyribonucleoside triphosphate pools in thymidine kinase 2 deficiency, Biochem. Biophys. Res. Commun. 310, 963-966.
17. Ikeda, S., Chakravarty, R., and Ives, D. H. (1986) Multisubstrate analogs for deoxynucleoside kinases. Triphosphate end products and synthetic bisubstrate analogs exhibit identical modes of binding and are useful probes for distinguishing kinetic mechanisms, J. Biol. Chem. 261, 15836-15843.
18. Kim, M. Y., and Ives, D. H. (1989) Human deoxycytidine kinase: Kinetic mechanism and end product regulation, Biochemistry 28, 9043-9047.
19. Johansson, K., Ramaswamy, S., Ljungcrantz, C., Knecht, W., Piškur, J., Munch-Petersen, B., Eriksson, S., and Eklund, H. (2001) Structural basis for substrate specificities of cellular deoxyribonucleoside kinases, Nat. Struct. Biol. 8, 616-620.
20. Mikkelsen, N. E., Johansson, K., Karlsson, A., Knecht, W., Andersen, G., Piškur, J., Munch-Petersen, B., and Eklund, H. (2003) Structural basis for feedback inhibition of the deoxyribonucleoside salvage pathway: Studies of the Drosophila deoxyribonucleoside kinase, Biochemistry 42, 5706-5712.
21. Andrade, M. A., Chacon, P., Merelo, J. J., and Moran, F. (1993) Evaluation of secondary structure of proteins from UV circular dichroism spectra using an unsupervised learning neural network, Protein Eng. 6, 383-390.
22. Kurganov, B. I., Lyubarev, A. E., Sanchez-Ruiz, J. M., and Shnyrov, V. L. (1997) Analysis of differential scanning calorimetry data for proteins. Criteria of validity of one-step mechanism of irreversible protein denaturation, Biophys. Chem. 69, 125-135.
23. Jönsson, U., Fägerstam, L., Ivarsson, B., Johnsson, B., Karlsson, R., Lundh, K., Löfås, S., Persson, B., Roos, H., Rönnberg, I., Sjölander, S., Stenberg, E., Ståhlberg, R., Urbaniczky, C., Östlin, H., and Malmqvist, M. (1991) Real-time biospecific interaction analysis using surface plasmon resonance and a sensor chip technology, BioTechniques 11, 620-627.
24. Hubbard, S. J. (1998) The structural aspects of limited proteolysis of native proteins, Biochim. Biophys. Acta 1382, 191-206.
25. Wurth, C., Kessler, U., Vogt, J., Schulz, G. E., Folkers, G., and Scapozza, L. (2001) The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase, Protein Sci. 10, 63-73.
26. Sabini, E., Ort, S., Monnerjahn, C., Konrad, M., and Lavie, A. (2003) Structure of human dCK suggests strategies to improve anticancer and antiviral therapy, Nat. Struct. Biol. 10, 513-519.
27. Myszka, D. G. (2004) Analysis of small-molecule interactions using Biacore S51 technology, Anal. Biochem. 329, 316-323.
28. Lumry, R., and Eyring, E. (1954) Conformation changes of proteins, J. Phys. Chem. 58, 110-120.
29. Sanchez-Ruiz, J. M. (1992) Theoretical analysis of Lumry-Eyring models in differential scanning calorimetry, Biophys. J. 61, 921-935.
30. Plaza del Pino, I. M., Ibarra-Molero, B., and Sanchez-Ruiz, J. M. (2000) Lower kinetic limit to protein thermal stability: A proposal regarding protein stability in vivo and its relation with misfolding diseases, Proteins 40, 58-70.
31. Milardi, D., La Rosa, C., and Grasso, D. (1994) Extended theoretical analysis of irreversible protein thermal unfolding, Biophys. Chem. 52, 183-189.
32. Lyubarev, A. E., and Kurganov, B. I. (1998) Modeling of irreversible thermal protein denaturation at varying temperature. I. The model involving two consecutive irreversible steps, Biochemistry (Moscow) 63, 434-440.
33. Lyubarev, A. E., and Kurganov, B. I. (1999) Modeling of irreversible thermal protein denaturation at varying temperature. II. The complete kinetic model of Lumry and Eyring, Biochemistry (Moscow) 64, 832-838.
34. Schulz, G. E., Müller, C. W., and Diederichs, K. (1990) Induced-fit movements in adenylate kinases, J. Mol. Biol. 213, 627-630.
35. Vonrhein, C., Schlauderer, G. J., and Schulz, G. E. (1995) Movie of the structural changes during a catalytic cycle of nucleoside monophosphate kinases, Structure 3, 483-490.
36. Suzuki, N. N., Koizumi, K., Fukushima, M., Matsuda, A., and Inagaki, F. (2004) Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase, Structure 12, 751-764.
37. Perozzo, R., Jelesarov, I., Bosshard, H. R., Folkers, G., and Scapozza, L. (2000) Compulsory order of substrate binding to herpes simplex virus type 1 thymidine kinase. A calorimetric study, J. Biol. Chem. 275, 16139-16145.
38. Lee, L. S., and Cheng, Y. (1976) Human deoxythymidine kinase II: Substrate specificity and kinetic behavior of the cytoplasmic and mitochondrial isozymes derived from blast cells of acute myelocytic leukemia, Biochemistry 15, 3686-3690.
39. Munch-Petersen, B., Cloos, L., Tyrsted, G., and Eriksson, S. (1991) Diverging substrate specificity of pure human thymidine kinases 1 and 2 against antiviral dideoxynucleosides, J. Biol. Chem. 266, 9032-9038.
40. Salamon, Z., Wang, Y., Brown, M. F., Macleod, H. A., and Tollin, G. (1994) Conformational changes in rhodopsin probed by surface plasmon resonance spectroscopy, Biochemistry 33, 13706-13711.
41. Sota, H., Hasegawa, Y., and Iwakura, M. (1998) Detection of conformational changes in an immobilized protein using surface plasmon resonance, Anal. Chem. 70, 2019-2024.
42. Flatmark, T., Stokka, A. J., and Berge, S. V. (2001) Use of surface plasmon resonance for real-time measurements of the global conformational transition in human phenylalanine hydroxylase in response to substrate binding and catalytic activation, Anal. Biochem. 294, 95-101.
43. Gestwicki, J. E., Hsieh, H. V., and Pitner, J. B. (2001) Using receptor conformational change to detect low molecular weight analytes by surface plasmon resonance, Anal. Chem. 73, 5732-5737.
44. Munch-Petersen, B. (1984) Differences in the kinetic properties of thymidine kinase isoenzymes in unstimulated and phytohemagglutinin-stimulated human lymphocytes, Mol. Cell. Biochem. 64, 173-185.
45. Munch-Petersen, B., Völker, C., Cloos, L., Hofbauer, R., Mortensen, B. T., and Tyrsted, G. (1994) Altered substrate and inhibitor specificity of purified human adult thymidine kinases (TK2) from leukemic cells, Adv. Exp. Med. Biol. 370, 253-256.
46. Wang, L., Munch-Petersen, B., Herrström Sjöberg, A., Hellman, U., Bergman, T., Jörnvall, H., and Eriksson, S. (1999) Human thymidine kinase 2: Molecular cloning and characterisation of the enzyme activity with antiviral and cytostatic nucleoside substrates, FEBS Lett. 443, 170-174.
47. Munch-Petersen, B., Piškur, J., and Søndergaard, L. (1998) The single deoxynucleoside kinase in Drosophila melanogaster, Dm-dNK, is multifunctional and differs from the mammalian deoxynucleoside kinases, Adv. Exp. Med. Biol. 431, 465-469.
48. Munch-Petersen, B., Piškur, J., and Søndergaard, L. (1998) Four deoxynucleoside kinase activities from Drosophila melanogaster are contained within a single monomeric enzyme, a new multifunctional deoxynucleoside kinase, J. Biol. Chem. 273, 3926-3931.
49. Johansson, M., van Rompay, A. R., Degrève, B., Balzarini, J., and Karlsson, A. (1999) Cloning and characterization of the multisubstrate deoxyribonucleoside kinase of Drosophila melanogaster, J. Biol. Chem. 274, 23814-23819.