A link between hinge-bending domain motions and the temperature dependence of catalysis in 3-isopropylmalate dehydrogenase

Biophysical Journal

Volumn 96, Issue 12, 2009, Pages 5003-5012

  Hajdú, István ^a   Szilágyi, András ^a   Kardos, József ^a,b   Závodszky, Péter ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

^b EÖTVÖS LORÁND UNIVERSITY   (Hungary)

Author keywords

[No Author keywords available]

Indexed keywords

3 ISOPROPYLMALATE DEHYDROGENASE; DEUTERIUM; HYDROGEN;

ARTICLE; CONTROLLED STUDY; DISSOCIATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME SUBSTRATE; ESCHERICHIA COLI; FLUORESCENCE RESONANCE ENERGY TRANSFER; HIGH TEMPERATURE; ISOTHERMAL TITRATION CALORIMETRY; LIGAND BINDING; NONHUMAN; PARAMETER; PROTEIN FUNCTION; TEMPERATURE DEPENDENCE; THERMODYNAMICS; TRANSITION TEMPERATURE;

ESCHERICHIA COLI;

EID: 68949144754     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.04.014     Document Type: Article

References (35)

1. Eisenthal, R., M. J. Danson, and D. W. Hough. 2007. Catalytic efficiency and kcat/KM: a useful comparator? Trends Biotechnol. 25:247-249.
2. Londesborough, J. 1980. The causes of sharply bent or discontinuous Arrhenius plots for enzyme-catalyzed reactions. Eur. J. Biochem. 105:211-215.
3. Truhlar, D., and A. Kohen. 2001. Convex Arrhenius plots and their interpretation. Proc. Natl. Acad. Sci. USA. 98:848-851.
4. Demchenko, A. P. 1997. Breaks in Arrhenius plots for enzyme reactions: the switches between different protein dynamics regimes? Comments Mol. Cell Biophys. 9:87-112.
5. Datta, K., A. J. Wowor, A. Richard, and V. J. LiCata. 2006. Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA. Biophys. J. 90:1739-1751.
6. Kuo, L. Y., and T. R. Cech. 1996. Conserved thermochemistry of guanosine nucleophile binding for structurally distinct group I ribozymes. Nucleic Acids Res. 24:3722-3727.
7. Lonhienne, T., J. Zoidakis, C. E. Vorgias, G. Feller, C. Gerday, et al. 2001. Modular structure, local flexibility and cold-activity of a novel chitobiose from a psychrophilic Antarctic bacterium. J. Mol. Biol. 310:291-297.
8. Ciardiello, M. A., L. Camardella, and G. di Prisco. 1995. Glucose-6-phosphate dehydrogenase from the blood cells of two Antarctic teleosts: correlation with cold adaptation. Biochim. Biophys. Acta. 1250:76-82.
9. Szeltner, Z., D. Rea, V. Renner, L. Juliano, V. Fülop, et al. 2003. Electrostatic environment at the active site of prolyl oligopeptidase is highly influential during substrate binding. J. Biol. Chem. 278:48786-48793.
10. Ayala, Y. M., and E. Di Cera. 2000. A simple method for the determination of individual rate constants for substrate hydrolysis by serine proteases. Protein Sci. 9:1589-1593.
11. Svingor, A., J. Kardos, I. Hajdú, A. Németh, and P. Závodszky. 2001. A better enzyme to cope with cold. Comparative flexibility studies on psychrotrophic, mesophilic, and thermophilic IPMDHs. J. Biol. Chem. 276:28121-28125.
12. Imada, K., M. Sato, N. Tanaka, Y. Katsube, Y. Matsuura, et al. 1991. Three-dimensional structure of a highly thermostable enzyme, 3-isopropylmalate dehydrogenase of Thermus thermophilus at 2.2 a resolution. J. Mol. Biol. 222:725-738.
13. Imada, K., K. Inagaki, H. Matsunami, H. Kawaguchi, H. Tanaka, et al. 1998. Structure of 3-isopropylmalate dehydrogenase in complex with 3-isopropylmalate at 2.0 a resolution: the role of Glu-88 in the unique substrate-recognition mechanism. Structure. 6:971-982.
14. Tsuchiya, D., T. Sekiguchi, and A. Takenaka. 1997. Crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile, Bacillus coagulans: two strategies for thermostabilization of protein structures. J. Biochem. (Tokyo). 122:1092-1104.
15. Wallon, G., K. Yamamoto, H. Kirino, A. Yamagishi, S. T. Lovett, et al. 1997. Purification, catalytic properties and thermostability of 3-isopropylmalate dehydrogenase from Escherichia coli. Biochim. Biophys. Acta. 1337:105-112.
16. Singh, R. K., G. Kefala, R. Janowski, C. Mueller-Dieckmann, J. P. von Kries, et al. 2005. The high-resolution structure of Leub (Rv2995c) from Mycobacterium tuberculosis. J. Mol. Biol. 346:1-11.
17. Wallon, G., G. Kryger, S. T. Lovett, T. Oshima, D. Ringe, et al. 1997. Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. J. Mol. Biol. 266:1016-1031.
18. Závodszky, P., J. Kardos, A. Svingor, and G. A. Petsko. 1998. Adjustment of conformational flexibility is a key event in the thermal adaptation of proteins. Proc. Natl. Acad. Sci. USA. 95:7406-7411.
19. Graczer, E., A. Varga, I. Hajdú, B. Melnik, A. Szilagyi, et al. 2007. Rates of unfolding, rather than refolding, determine thermal stabilities of thermophilic, mesophilic, and psychrotrophic 3-isopropylmalate dehydrogenases. Biochemistry. 46:11536-11549.
20. Privalov, P. L., and T. N. Tsalkova. 1979. Micro- and macro-stabilities of globular proteins. Nature. 280:693-696.
21. Kilár, F., and P. Závodszky. 1987. Non-covalent interactions between Fab and Fc regions in immunoglobulin G molecules. Hydrogen-deuterium exchange studies. Eur. J. Biochem. 162:57-61.
22. Dean, A. M., and L. Dvorak. 1995. The role of glutamate 87 in the kinetic mechanism of Thermus thermophilus isopropylmalate dehydrogenase. Protein Sci. 4:2156-2167.
23. Stryer, L. 1978. Fluorescence energy transfer as a spectroscopic ruler. Annu. Rev. Biochem. 47:819-846.
24. + and NADH allows the transcriptional corepressor carboxyl-terminal binding protein to serve as a metabolic sensor. Proc. Natl. Acad. Sci. USA. 100:9202-9207.
25. Grant, G. A., Z. Hu, and X. L. Xu. 2002. Cofactor binding to Escherichia coli d-3-phosphoglycerate dehydrogenase induces multiple conformations which alter effector binding. J. Biol. Chem. 277:39548-39553.
26. +: ligand-induced loop closing and mechanism for cofactor specificity. Structure. 2:1007-1016.
27. Kadono, S., M. Sakurai, H. Moriyama, M. Sato, Y. Hayashi, et al. 1995. Ligand-induced changes in the conformation of 3-isopropylmalate dehydrogenase from Thermus thermophilus. J. Biochem. (Tokyo). 118:745-752.
28. Massey, V., B. Curti, and H. Ganther. 1966. A temperature-dependent conformational change in d-amino acid oxidase and its effect on catalysis. J. Biol. Chem. 241:2347-2357.
29. Cooper, A. 1981. Spurious conformational transitions in proteins? Proc. Natl. Acad. Sci. USA. 78:3551-3553.
30. Sturtevant, J. M., and P. L. Mateo. 1978. Proposed temperature-dependent conformational transition in d-amino acid oxidase: a differential scanning microcalorimetric study. Proc. Natl. Acad. Sci. USA. 75:2584-2587.
31. Eftink, M. R., A. C. Anusiem, and R. L. Biltonen. 1983. Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions: general thermodynamic models and data for the binding of nucleotides to ribonuclease A. Biochemistry. 22:3884-3896.
32. Somogyi, B., J. Matkó, S. Papp, J. Hevessy, G. R. Welch, et al. 1984. Förster-type energy transfer as a probe for changes in local fluctuations of the protein matrix. Biochemistry. 23:3403-3411.
33. Ross, J. B., C. J. Schmidt, and L. Brand. 1981. Time-resolved fluorescence of the two tryptophans in horse liver alcohol dehydrogenase. Biochemistry. 20:4369-4377.
34. Steinberg, I. Z. 1971. Long-range nonradiative transfer of electronic excitation energy in proteins and polypeptides. Annu. Rev. Biochem. 40:83-114.
35. Sanner, M. F. 1999. Python: a programming language for software integration and development. J. Mol. Graph. Model. 17:57-61.