Dimerization affects collective dynamics of triosephosphate isomerase

Biochemistry

Volumn 47, Issue 5, 2008, Pages 1358-1368

  Cansu, Sertan ^a   Doruker, Pemra ^a  

^a BOGAZICI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; CORRELATION METHODS; DIMERIZATION; DIMERS; MOLECULAR DYNAMICS;

FLUCTUATION DYNAMICS; MONOMERIC STRUCTURE; TRIOSEPHOSPHATE ISOMERASE;

ENZYME KINETICS;

TRIOSEPHOSPHATE ISOMERASE;

ARTICLE; DIMERIZATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME CONFORMATION; ENZYME SUBUNIT; FLUCTUATION DYNAMICS; GLYCOLYSIS; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SIMULATION; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; X RAY ANALYSIS;

ANIMALS; APOENZYMES; CHICKENS; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; MODELS, MOLECULAR; TRIOSE-PHOSPHATE ISOMERASE;

EID: 38849181675     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi701916b     Document Type: Article

References (33)

1. Daniel, R. M., Dunn, R. V., Finney, J. L., and Smith, J. C. (2003) The role of dynamics in enzyme activity, Annu. Rev. Biophys. Biomol. Struct. 32, 69-92.
2. Wang, W., Donini, O., Reyes, C. M., and Kollman, P. A. (2001) Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions, Annu. Rev. Biophys. Biomol. Struct. 30, 211-243.
3. Benkovic, S. J., and Hammes-Schiffer, S. (2003) A perspective on enzyme catalysis, Science 301, 1196-1202.
4. 31P-NMR with reversibly and irreversibly binding substrate analogs, Eur. J. Biochem 199, 231-238.
5. Zhang, Z., Sugio, S., Komives, E. A., Liu, K. D., Knowles, J. R., Petsko, G. A., and Ringe, D. (1994) Crystal structure of recombinant chicken Triosephosphate isomerase-Phosphoglycolohydroxamate complex at 1.8Å resolution, Biochemistry 33, 2830-2837.
6. Williams, J. C., and McDermott, A. E. (1995) Dynamics of the flexible loop of triosephoshate isomerase: the loop motion is not ligand gated, Biochemistry 34, 8309-8319.
7. Xiang, J., Jung, J., and Sampson, N. S. (2004) Entropy effects on protein hinges: the reaction catalyzed by triosephosphate isomerase, Biochemistry 43, 11436-11445.
8. Kempf, J. G., Jung, J. Y., Ragain, C., Sampson, N. S., and Loria, J. P. (2007) Dynamic requirements for a functional protein hinge, J. Mol. Biol. 368, 131-149.
9. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank, Nucleic Acids Res. 28, 235-242.
10. Brown, F. K., and Kollman, P. A. (1987) Molecular dynamics simulations of "loop closing" in the enzyme triose phosphate isomerase, J. Mol. Biol. 198, 533-546.
11. 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.
12. Massi, F., Wang, C., and Palmer, A. G., III (2006) Solution NMR and computer simulation studies of active site loop motion in triosephosphate isomerase, Biochemistry 45, 10787-10794.
13. Derreumaux, P., and Schlick, T. (1998) The loop opening/closing motion of the enzyme triosephosphate isomerase, Biophys. J. 74, 72-81.
14. Kurkcuoglu, O., Jernigan, R. L., and Doruker, P. (2006) Loop motions of triosephosphate isomerase observed with elastic networks, Biochemistry 45, 1173-1182.
15. Case, D. A., Darden, T. A., Cheatham, T. E. I., Simmerling, C. L., Wang, J., Duke, R. E., Luo, R., Merz, K. M., Wang, B., Pearlman, D. A., et al. (2004) AMBER 8, University of California, San Francisco.
16. Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., and Woods, R. (2005) The Amber biomolecular simulation programs, J. Comput. Chem. 26, 1668-1688.
17. Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G., Zhang, W., Yang, R., Cieplak, P., Luo, R., and Lee, T. (2003) A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins, J. Comput. Chem. 24, 1999-2012.
18. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) Comparison of simple potential functions for simulating liquid water, J. Chem. Phys. 79, 926-935.
19. Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., DiNola, A., and Haak, J. R. (1984) Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81, 3684-3690.
20. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes, J. Comput. Phys. 23, 327-341.
21. Essman, U., Perera, L., Berkowitz, M. L., Darden, T. A., Lee, H., and Pedersen, L. G. (1995) A smooth Particle Mesh Ewald method, J. Chem. Phys. 103, 8577-8593.
22. Amadei, A., Linssen, A. B. M., and Berendsen, H. J. C. (1993) Essential dynamics of proteins, Proteins 17, 412-425.
23. Doruker, P., Atilgan, A. R., and Bahar, I. (2000) Dynamics of Proteins Predicted by Molecular Dynamics Simulations and Analytical Approaches: Application to alpha-Amylase Inhibitor, Proteins 40, 512-524.
24. Thanki, N., Zeelen, J. P., Mathieu, M., Jaenicke, R., Abagyan, R. A., Wierenga, R. K., and Schliebs, W. (1997) Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modeling and structure verification of a seven-loop residue, Protein Eng. 10, 159-167.
25. Borchert, T. V., Abagyan, R., Jaenicke, R., and Wierenga, R. K. (1994) Design, creation, and characterization of a stable, monomeric triosephosphate isomerase, Proc. Natl. Acad. Sci. U.S.A. 91, 1515-1518.
26. Rozovsky, S., McDermott., and A. E. (2001) The Time scale of the Catalytic Loop Motion in Triosephosphate Isomerase, J. Mol. Biol. 310, 259-270.
27. 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.
28. Doruker, P., Nilsson, L., and Kurkcuoglu, O. (2006) Collective dynamics of EcoRI-DNA complex by elastic network model and molecular dynamics simulations, J. Biomol Struct. Dyn. 24, 1-15.
29. Van Wynsberghe, A. W., and Cui, Q. (2006) Interpreting correlated motions using normal mode analysis, Structure 14, 1647-1653.
30. Erijman, L., Lorimer, G. H., and Weber, G. (1993) Reversible dissociation and conformational stability of dimeric ribulose biphosphate carboxylase, Biochemistry 32, 5187-5195.
31. Erijman, L., Paladini, A. A., Lorimer, G. H., and Weber, G. (1993) Plurality of protein conformations of ribulose- 1,5- biphosphate carboxylate oxygenase monomers probed by high-pressure electrophoresis, J. Biol Chem. 268, 25914-25919.
32. Weber, G. (1992) Protein Interactions, Chapman & Hall, Inc., New York.
33. Eisenmesser, E. J., Millet, O., Labeikovsky, W., Korzhnev, D. M., Wolf-Watz, M. Bosco, D. A., Skalicky, J. J., Kay, L. E. and Kern, D. (2005) Intrinsic dynamics of an enzyme underlies catalysis, Nature 438, 117-121.