Slow solvation dynamics at the active site of an enzyme: Implications for catalysis

Biochemistry

Volumn 44, Issue 25, 2005, Pages 8940-8947

  Guha, Soumi ^a   Sahu, Kalyanasis ^b   Roy, Durba ^b   Mondal, Sudip Kumar ^b   Roy, Siddhartha ^a,c   Bhattacharyya, Kankan ^b  

^a BOSE INSTITUTE   (India)

^b DEPARTMENT OF MATERIALS SCIENCE   (India)

^c INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; ENZYMES; FLUORESCENCE; MUTAGENESIS; PROBES; RELAXATION PROCESSES; RNA; SOLVENTS; SUBSTRATES;

CYSTEINE; FLUORESCENCE PROBES; SOLVATION DYNAMICS; STOKES SHIFT;

ENZYME KINETICS;

ADENOSINE TRIPHOSPHATE; CYSTEINE; GLUTAMINE TRANSFER RNA LIGASE; GLYCINE; TRANSFER RNA;

ARTICLE; CIRCULAR DICHROISM; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME MECHANISM; ENZYME SPECIFICITY; GENE MUTATION; PRIORITY JOURNAL; SOLVATION; WILD TYPE;

AMINO ACYL-TRNA SYNTHETASES; BINDING SITES; CATALYSIS; CIRCULAR DICHROISM; CYSTEINE; GLUTAMINE; HYDROGEN SULFIDE; KINETICS; MODELS, MOLECULAR; MUTATION; PROTEIN STRUCTURE, TERTIARY; RNA, TRANSFER; RNA, TRANSFER, GLN; SOLVENTS; SPECTROMETRY, FLUORESCENCE; SUBSTRATE SPECIFICITY; TYROSINE;

EID: 21744438306     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0473915     Document Type: Article

References (50)

1. Simonson, T., Archontis, G., and Karplus, M. (2002) Free energy simulations come of age: Protein-ligand recognition, Acc. Chem. Res. 35, 430-437.
2. Makarov, V., Petit, B. M., and Feig, M. (2002) Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment, Acc. Chem. Res. 35, 376-384.
3. Warshel, A. (2003) Computer simulations of enzyme catalysis: Methods, progress, and insights, Annu. Rev. Biophys. Biomol. Struct. 32, 425-443.
4. Jencks, W. P. (1997) From chemistry to biochemistry to catalysis to movement, Annu. Rev. Biochem. 66, 1-18.
5. Cannon, W. R., and Benkovic, S. J. (1998) Solvation, reorganization energy, and biological catalysis. J. Biol. Chem. 273, 26257-26260.
6. Eisenmesser, E. Z., Bosco, D. A., Akke, M., and Kern, D. (2002) Enzyme dynamics during catalysis, Science 295, 1520-1523.
7. Dellerue, S., and Bellisent-Funnel, M.-C. (2000) Relaxational dynamics of water molecules at protein surface, Chem. Phys. 258, 315-325.
8. Modig, K., Liepinsh, E., Otting, G., and Halle, B. (2004) Dynamics of protein and peptide hydration, J. Am. Chem. Soc. 126, 102-114.
9. Denisov, V. P., Jonsson, B.-H., and Halle, B. (1999) Hydration of denatured and molten globule proteins, Nat. Struct. Biol. 6, 253-260.
10. Jordanides, X. J., Lang, M. J., Song, X., and Fleming, G. R. (1999) Solvation dynamics in protein environments studied by photon echo spectroscopy, J. Phys. Chem. B 103, 7995-8005.
11. Lundgren, J. S., Heitz, M. P., and Bright. F. V. (1995) Dynamics of acrylodan-labeled bovine and human serum albumin sequestered within aerosol-OT reverse micelles, Anal. Chem. 67, 3775-3781.
12. Nandi, N., Bhattacharyya, K., and Bagchi, B. (2000) Dielectric relaxation and solvation dynamics of water in complex chemical and biological systems, Chem. Rev. 100, 2013-2046.
13. Bhattacharyya, K. (2003) Solvation dynamics and proton transfer in supramolecular assemblies, Acc. Chem. Res. 36, 95-101.
14. Pal, S. K., and Zewail, A. H. (2004) Dynamics of Water in Biological Recognition, Chem. Rev. 104, 2099-2124.
15. Changenet-Barret, P., Choma, C. T., Gooding, E. F., Degrade, W. F., and Hochstrasser, R. M. (2000) Ultrafast dielectric response of proteins from dynamic Stokes shifting of coumarin in calmodulin, J. Phys. Chem. B 104, 9322-9329.
16. Glc protein, J. Phys. Chem. B 105, 2043-2055.
17. Gearheart, L. A., Somoza, M. M., Rivers, W. E., Murphy, C. J., Coleman, R. S., and Berg, M. A. (2003) Sodium-ion binding to DNA: Detection by ultrafast time-resolved stokes-shift spectroscopy, J. Am. Chem. Soc. 125, 11812-11813.
18. Brauns, E. B., Madaras, M. L., Coleman, R. S., and Berg, M. (2002) Complex local dynamics in DNA on the picosecond and nanosecond time scales, Phys. Rev. Lett. 88, 158101-1-4.
19. Sen, P., Mukherjee, S., Dutta, P., Halder, A., Mandal, D., Banerjee, R., Roy, S., and Bhattacharyya, K. (2003) Solvation dynamics in the molten globule state of a protein, J. Phys. Chem. B 107, 14563-14568.
20. Mandal, D., Sen, S., Sukul, D., Bhattacharyya, K., Mandal, A. K., Banerjee, R., and Roy, S. (2002) Solvation dynamics of a probe covalently bound to a protein and in an AOT microemulsion: 4-(N-Bromoacetylamino)phthalimide. J. Phys. Chem. B 106, 10741-10747.
21. Dutta, P., Sen, P., Halder, A., Mukherjee, S., Sen, S., and Bhattacharyya, K. (2003) Solvation dynamics in a protein-surfactant complex. Chem. Phys. Lett. 377, 229-235.
22. Nandi, N., and Bagchi, B. (1997) Dielectric relaxation of biological water, J. Phys. Chem. B 101, 10954-10961.
23. Marchi, M., Sterpone, F., and Ceccarelli, M. (2002) Water rotational relaxation and diffusion in hydrated lysozyme. J. Am. Chem. Soc. 124, 6787-6791.
24. Sterpone, F., Ceccarelli, M., and Marchi, M. (2001) Dynamics of hydration in hen egg white lysozyme, J. Mol. Biol. 311, 409-419.
25. Balasubramanian, S., Pal, S., and Bagchi, B. (2002) Hydrogen bond dynamics near a miceller surface: Origin of the universal slow relaxation at complex aqueous interfaces, Phys. Rev. Lett. 89, 115505-1-4.
26. Pal, S., Balasubramanian, S., and Bagchi, B. (2003) Identity, energy, and environment of interfacial water molecules in a micellar solution, J. Phys. Chem. B 107, 5194-5202.
27. Bruce, C. D., Senapatil S., Berkowitz, M. L., Perera, L., and Forbes, M. D. E. (2002) Molecular dynamics simulations of sodium dodecyl sulfate micelle in water: The behavior of water, J. Phys. Chem. B 106, 10902-10907.
28. Faeder, J., Albert, M. V., and Ladanyi, B. M. (2003) Molecular dynamics simulations of the interior of aqueous reverse micelles: A comparison between sodium and potassium counterions, Langmuir 19, 2514-2520.
29. Senapati, S., and Chandra, A. (2001) Dielectric constant of water confined in a nanocavity, J. Phys. Chem. B 105, 5106-5109.
30. Michael, D., and Benjamin, I. (2001) Molecular dynamics computer simulations of solvation dynamics at liquid/liquid interfaces, J. Chem. Phys. 114, 2817-2824.
31. Fecko, C. J., Eaves, J. D., Loparo, J. J., Tokmakoff, A., and Geissler, P. L. (2003) Ultrafast hydrogen-bond dynamics in the infrared spectroscopy of water, Science 301, 1698-1702.
32. Jimenez, R., Fleming, G. R., Kumar, P. V., and Maroncelli, M. (1994) Femtosecond solvation dynamics of water, Nature 369, 471-473.
33. Nandi, N., Roy, S., and Bagchi, B. (1995) Ultrafast solvation dynamics in water: Isotope effects and comparison with experimental results, J. Chem. Phys. 102, 1390-1397.
34. Jarzeba, W., Walker, G. C., Johnson, A. E., Kahlow, M. A., and Barbara, P. F. (1988) Femtosecond microscopic solvation dynamics of aqueous solutions, J. Phys. Chem. 92, 7039-7041.
35. Sherlin, L. D., and Perona, J. J. (2003) tRNA-dependent active site assembly in a class I aminoacyl-tRNA synthetase. Structure 11, 591-603.
36. Gln and ATP at 2.8 angstrom resolution. Science 246, 1135-1142.
37. Uter, N. T., and Perona, J. J. (2004) Long-range intramolecular signaling in a tRNA synthetase complex revealed by pre-steady-state kinetics, Proc. Natl. Acad. Sci. U.S.A. 101, 14396-14401.
38. Bhattacharyya, T., and Roy S. (1993) A fluorescence spectroscopic study of substrate-induced conformational changes in glutaminyl-tRNA synthetase, Biochemistry 32, 9268-9273.
39. Bhattacharyya, T., Bhattacharyya, A., and Roy, S. (1991) A fluorescence spectroscopic study of glutaminyl-tRNA synthetase from Escherichia coli and its implications for the enzyme mechanism, Eur. J. Biochem. 200, 739-745.
40. Aiyar, A., Xiang, Y., and Leis, J. (1996) Site-directed mutagenesis using overlap extension PCR, Methods Mol. Biol. 57, 177-191.
41. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy, Chapter 7, Kluwer/Plenum, New York.
42. Maroncelli, M., and Fleming, G. R. (1987) Picosecond solvation dynamics of coumarin 153: The importance of molecular aspects of solvation, J. Chem. Phys. 86, 6221-6239.
43. Fee, R. S., and Maroncelli, M. (1994) Estimating the time-zero spectrum in time-resolved emission measurements of solvation dynamics, Chem. Phys. 183, 235-247.
44. Kropman, M. F., and Bakker, H. J. (2001) Dynamics of water molecules in aqueous solvation shells, Science 291, 2118-2120.
45. Chandra, A. (2000) Effects of ion atmosphere on hydrogen-bond dynamics in aqueous electrolyte solutions, Phys. Rev. Lett. 85, 768-771.
46. Xu, H., and Berne, B. J. (2001) Hydrogen-bond kinetics in the solvation shell of a polypeptide, J. Phys. Chem. B 105, 11929-11932.
47. Reddy, G. B., Srinivas, V. R., Ahmad, N., and Surolia, A. (1999) Molten globule-like state of peanut lectin monomer retains its carbohydrate specificity. Implications in protein folding and legume lectin oligomerization. J. Biol. Chem. 274, 4500-4503.
48. Ibba, M., and Soll, D. (1999) Quality control mechanisms during translation, Science 286, 1893-1897.
49. Jahn, M., Rogers, M. J., and Soll, D. (1991) Anticodon and acceptor stem nucleotides in tRNA(Gln) are major recognition elements for E. coli glutaminyl-tRNA synthetase, Nature 352, 258-260.
50. Gln mediates tRNA-dependent amino acid recognition by glutaminyl-tRNA synthetase, Biochemistry 37, 9836-9842.