Entropy effects on protein hinges: The reaction catalyzed by triosephosphate isomerase

Biochemistry

Volumn 43, Issue 36, 2004, Pages 11436-11445

  Xiang, Jingyi ^a   Jung, Ju Yeon ^a   Sampson, Nicole S ^a  

^a STONY BROOK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOTHERMAL CALORIMETRY; SEGMENTAL MOTIONS;

CALORIMETRY; CATALYST ACTIVITY; CATALYSTS; ENTROPY; ISOTOPES; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEINS;

BIOCHEMISTRY;

2 PHOSPHOGLYCOLATE; GLYCINE; GLYCOLIC ACID; TRIOSEPHOSPHATE ISOMERASE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CALORIMETRY; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CHEMICAL REACTION; CONFORMATIONAL TRANSITION; ENTHALPY; ENTROPY; ENZYME CONFORMATION; ENZYME KINETICS; ISOTHERMAL CALORIMETRY MEASUREMENT; KINETICS; LIGAND BINDING; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PRIMARY KINETIC ISOTOPE EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTON NUCLEAR MAGNETIC RESONANCE; REACTION ANALYSIS; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

ANIMALS; BINDING SITES; CALORIMETRY; CATALYSIS; CHICKENS; DEUTERIUM EXCHANGE MEASUREMENT; ENTROPY; ENZYME INHIBITORS; GLYCINE; GLYCOLATES; KINETICS; LEISHMANIA MEXICANA; MUTAGENESIS, INSERTIONAL; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHOSPHORUS ISOTOPES; PROTEIN CONFORMATION; PROTOZOAN PROTEINS; PYRUVALDEHYDE; RECOMBINANT PROTEINS; TRIOSE-PHOSPHATE ISOMERASE;

GALLUS GALLUS;

EID: 4444321214     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049208d     Document Type: Article

References (40)

1. Gerstein, M., Lesk, A. M., and Chothia, C. (1994) Structural mechanisms for domain movements in proteins, Biochemistry 33, 6739-6749.
2. Leszczynski, J. F., and Rose, G. D. (1986) Loops in globular proteins: A novel category of secondary structure, Science 234, 849-855.
3. Gerstein, M., and Krebs, W. (1998) A database of macromolecular motions, Nucleic Acids Res. 26, 4280-4290.
4. Taylor, J. C., Takusagawa, F., and Markham, G. D. (2002) The active site loop of S-adenosylmethionine synthetase modulates catalytic efficiency, Biochemistry 41, 9358-9369.
5. Gulotta, M., Deng, H., Dyer, R. B., and Callender, R. H. (2002) Toward an understanding of the role of dynamics on enzymatic catalysis in lactate dehydrogenase, Biochemistry 41, 3353-3363.
6. Deng, H., Zheng, J., Clarke, A., Holbrook, J. J., Callender, R., and Burgner, J. W., II (1994) Source of catalysis in the lactate dehydrogenase system. Ground-state interactions in the enzyme-substrate complex, Biochemistry 33, 2297-2305.
7. Pompliano, D. L., Peyman, A., and Knowles, J. R. (1990) Stabilization of a reaction intermediate as a catalytic device: Definition of the functional role of the flexible loop in triosephosphate isomerase, Biochemistry 29, 3186-3194.
8. Sampson, N. S., and Knowles, J. R. (1992) Segmental movement: Definition of the structural requirements for loop closure in catalysis by triosephosphate isomerase, Biochemistry 31, 8482-8487.
9. Sampson, N. S., and Knowles, J. R. (1992) Segmental motion in catalysis: Investigation of a critical hydrogen bond for loop closure in the reaction of triosephosphate isomerase, Biochemistry 31, 8488-8494.
10. Williams, J. C., and McDermott, A. E. (1995) Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand gated, Biochemistry 34, 8309-8319.
11. Rozovsky, S., Jogl, G., Tong, L., and McDermott, A. E. (2001) Solution-state NMR investigations of triosephosphate isomerase active site loop motion: Ligand release in relation to active site loop dynamics, J. Mol. Biol. 310, 271-280.
12. Rozovsky, S., and McDermott, A. E. (2001) The time scale of the catalytic loop motion in triosephosphate isomerase, J. Mol. Biol. 310, 259-270.
13. Joseph, D., Petsko, G. A., and Karplus, M. (1990) Anatomy of a conformational change: hinged "lid" motion of the triosephosphate isomerase loop, Science 249, 1425-1428.
14. Derreumaux, P., and Schlick, T. (1998) The loop opening/closing motion of the enzyme triosephosphate isomerase, Biophys. J. 74, 72.
15. Noble, M. E. M., Wierenga, R. K., Lambeir, A.-M., Opperdoes, R. R., Thunnissen, A.-M. W. H., Kalk, K. H., Groendijk, H., and Hol, W. G. J. (1991) The adaptability of the active site of trypanosomal triosephosphate isomerase as observed in the crystal structures of three different complexes, Proteins: Struct., Funct., Genet. 10, 50-69.
16. DeLano, W. L. (2002) The PyMOL molecular graphics system, http://www.pymol.org.
17. Noble, M. E. M., Zeelen, J. P., and Wierenga, R. K. (1993) Structures of the "open" and "closed" state of trypansomal triosephosphate isomerase, as observed in a new crystal form: Implications for the reaction mechanism, Proteins: Struct., Funct., Genet. 16, 311-326.
18. Kursula, I., Salin, M., Sun, J., Norledge, B., Haapalainen, A., Sampson, N. S., and Wierenga, R. K. (2004) Understanding protein lids: Structural analysis of active hinge mutants in triosephosphate isomerase, Protein Eng., Des., Select. 47, 375-382.
19. Sun, J., and Sampson, N. S. (1998) Determination of the amino acid requirements for a protein hinge in triosephosphate isomerase, Protein Sci. 7, 1495-1505.
20. Xiang, J., Sun, J., and Sampson, N. S. (2001) The importance of hinge sequence for loop function and catalytic activity in the reaction catalyzed by triosephosphate isomerase, J. Mol. Biol. 307, 1103-1112.
21. Wallace, A. C., Laskowski, R. A., and Thornton, J. M. (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions, Protein Eng. 8, 127-134.
22. Kursula, I., and Wierenga, R. K. (2003) Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83 Å resolution, J. Biol. Chem. 278, 9544-9551.
23. Straus, D., and Gilbert, W. (1985) Chicken triosephosphate isomerase complements an Escherichia coli deficiency, Proc. Natl. Acad. Sci. U.S.A. 82, 2014.
24. Hermes, J. D., Parekh, S. M., Blacklow, S. C., Köster, H., and Knowles, J. R. (1989) A reliable method for random mutagenesis: The generation of mutant libraries using spiked oligodeoxyribonucleotide primers, Gene 84, 143.
25. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal. Biochem. 72, 248-254.
26. Plaut, B., and Knowles, J. R. (1972) pH-Dependence of the triosephosphate isomerase reaction, Biochem. J. 129, 311-320.
27. Johnson, L. N., and Wolfenden, R. (1970) Changes in absorption spectrum and crystal structure of triose phosphate isomerase brought about by 2-phosphoglycollate, a potential transition state analogue, J. Mol. Biol. 47, 93-100.
28. Leadlay, P. F., Albery, W. J., and Knowles, J. R. (1976) Energetics of triosephosphate isomerase: Deuterium isotope effects in the enzyme-catalyzed reaction, Biochemistry 15, 5617-5620.
29. Richard, J. P. (1991) Kinetic parameters for the elimination reaction catalyzed by triosephosphate isomerase and an estimation of the reaction's physiological significance, Biochemistry 30, 4581-4585.
30. Putman, S. J., Coulson, A. F. W., Farley, I. R. T., Riddleston, B., and Knowles, J. R. (1972) Specificity and kinetics of triose phosphate isomerase from chicken muscle, Biochem. J. 129, 301-310.
31. Wolfenden, R. (1969) Transition state analogues for enzyme catalysis, Nature 223, 704-705.
32. Sun, J., and Sampson, N. S. (1999) Understanding protein lids: Kinetic analysis of active hinge mutants in triosephosphate isomerase, Biochemistry 38, 11474-11481.
33. Lolis, E., Alber, T., Davenport, R. C., Rose, D., Hartman, F. C., and Petsko, G. A. (1990) Structure of yeast triosephosphate isomerase at 1.9 Å resolution, Biochemistry 29, 6609-6618.
34. Lolis, E., and Petsko, G. A. (1990) Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5 Å resolution: Implications for catalysis, Biochemistry 29, 6619-6625.
35. Fraenkel, D. (1986) Mutants in glucose metabolism, Annu. Rev. Biochem. 55, 317-337.
36. Jogl, G., Rozovsky, S., McDermott, A. E., and Tong, L. (2003) Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2 Å resolution, Proc. Natl. Acad. Sci. U.S.A. 100, 50-55.
37. Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) Contribution of phosphate intrinsic binding energy to the enzymatic rate acceleration for triosephosphate isomerase, J. Am. Chem. Soc. 123, 11325-11326.
38. Dunitz, J. D. (1994) The entropic cost of bound water in crystals and biomolecules, Science 264, 670.
39. Desamero, R., Rozovsky, S., Zhadin, N., McDermott, A., and Callender, R. (2003) Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation, Biochemistry 42, 2941-2951.
40. Taylor, J. C., and Markham, G. D. (2003) Conformational dynamics of the active site loop of 5-adenosylmethionine synthetase illuminated by site-directed spin labeling, Arch Biochem. Biophys. 415, 164-171.