Mass spectrometry on hydrogen/deuterium exchange of dihydrofolate reductase: Effects of ligand binding

Journal of Biochemistry

Volumn 135, Issue 6, 2004, Pages 663-671

  Yamamoto, Tatsuya ^a   Izumi, Shunsuke ^a   Gekko, Kunihiko ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

Dihydrofolate reductase; Hydrogen deuterium exchange; Ligand binding; Mass spectrometry; Structural fluctuation

Indexed keywords

DEUTERIUM; DIHYDROFOLATE REDUCTASE; DIHYDROFOLIC ACID; FOLIC ACID; HYDROGEN; LIGAND; METHOTREXATE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; PEPSIN A; PROTEINASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; TETRAHYDROFOLIC ACID;

ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ELECTROSPRAY MASS SPECTROMETRY; ENERGY; ENZYME KINETICS; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; ISOTOPE ANALYSIS; LIGAND BINDING; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR WEIGHT; NONHUMAN; RADIOISOTOPE EXCHANGE;

BACTERIAL PROTEINS; DEUTERIUM; ESCHERICHIA COLI; HYDROGEN; LIGANDS; MACROMOLECULAR SUBSTANCES; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; TETRAHYDROFOLATE DEHYDROGENASE;

ESCHERICHIA COLI; NEGIBACTERIA;

EID: 3142552375     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvh080     Document Type: Article

References (29)

1. Sawaya, M.R. and Kraut, J. (1997) Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry 36, 586-603
2. Lumry, R. (1995) The new paradigm for protein research in Protein-Solvent Interactions (Gregory, R.B., ed.), pp. 1-141, Marcel Dekker, New York
3. Bystroff, C. and Kraut, J. (1991) Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding. Biochemistry 30, 2227-2239
4. Kitahara, R., Sareth, S., Yamada, H., Ohmae, E., Gekko, K., and Akasaka, K. (2000) High pressure NMR reveals active-site hinge motion of folate-bound Escherichia coli dihydrofolate reductase. Biochemistry 39, 12789-12795
5. Gekko, K., Kunori, Y., Takeuchi, H., Ichihara, S., and Kodama, M. (1994) Point mutations at glycine-121 of Escherichia coli dihydrofolate reductase: important roles of a flexible loop in the stability and function. J. Biochem. 116, 34-41
6. Ohmae, E., Iriyama, K., Ichihara, S., and Gekko, K. (1996) Effects of point mutations at the flexible loop glycine-67 of Escherichia coli dihydrofolate reductase on its stability and function. J. Biochem. 119, 703-710
7. Ohmae, E., Ishimura, K., Iwakura, M., and Gekko, K. (1998) Effects of point mutations at the flexible loop alanine-145 of Escherichia coli dihydrofolate reductase on its stability and function. J. Biochem. 123, 839-884
8. Karplus, M. and McCammon, J.A. (1981) The internal dynamics of globular proteins. CRC Crit. Rev. Biochem. 9, 293-349.
9. Gekko, K. and Hasegawa, Y. (1986) Compressibility-structure relationship of globular proteins. Biochemistry 25, 6563-6571
10. Wüthrich, K. (1990) Structure and dynamics in proteins of pharmacological interest. Biochem. Pharmacol. 40, 55-62
11. Creighton, T. (1993) Proteins: Structure and Molecular Properties. Freeman and Company, New York
12. Hvidt, A. and Nielsen, S.O. (1966) Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287-386
13. Englander, S.W. and Kallenbach, N.R. (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521-655
14. Nakanishi, M. and Tsuboi, M. (1976) Structure and fluctuation of a Streptomyces subtilisin inhibitor. Biochim. Biophys. Acta 434, 365-376
15. Wagner, G. and Wüthrich, K. (1982) Amide proton exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance. J. Mol. Biol. 160, 343-361
16. Akasaka, K., Inoue, T., Hatano, H., and Woodward, C.K. (1985) Hydrogen exchange kinetics of core peptide protons in Streptomyces subtilisin inhibitor. Biochemistry 24, 2973-2979
17. Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F., and Whitehouse, C.M. (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246, 64-71
18. Tanaka, K., Waki, H., Ido, H., Akita, S., and Yoshida T. (1988) Protein and polymer analyses up to m/z 100000 by laser ionization time-of-flight mass spectrometry. Rapid. Commun. Mass Spectrom. 2, 151-153
19. Karas, M. and Hillenkamp, F. (1988) Laser desorption ionization of proteins with molecular masses exceeding 10, 000 daltons. Anal. Chem. 60, 2299-2301
20. Yamamoto, T., Izumi, S., and Gekko, K. (2004) Mass spectrometry on segment-specific hydrogen exchange of dihydrofolate reductase. J. Biochem. 135, 17-24
21. Yamamoto, T., Izumi, S., Ohmae, E., and Gekko, K. (2004) Mass spectrometry of hydrogen/deuterium exchange of Escherichia coli dihydrofolate reductase: Effects of loop mutations. J. Biochem. 135, 487-494
22. Iwakura, M., Jones, B.E., Luo, J., and Matthews, C.R. (1995) A strategy for testing the suitability of cysteine replacements in dihydrofolate reductase from Escherichia coli. J. Biochem. 117, 480-488
23. Fierke, C.A., Johnson, K.A., and Benkovic, S.J. (1987) Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry 26, 4085-4092
24. Williams, E.A. and Morrison, J.F. (1991) Characterization of tightly bound substrates in pure preparations of dihydrofolate reductase: implications for studies on enzymes. Biochim. Biophys. Acta 1078, 47-55
25. Kamiyama, T. and Gekko, K. (2000) Effect of ligand binding on the flexibility of dihydrofolate reductase as revealed by compressibility. Biochim. Biophys. Acta 1478, 257-266
26. Takahashi, T., Nakanishi, M., and Tsuboi, M. (1978) Hydrogen-deuterium exchange rate between a peptide group and an aqueous solvent as determined by a stopped flow ultraviolet spectrophotometry. Bull. Chem. Soc. Jpn. 51, 1988-1990
27. Miller, G.P. and Benkovic, S.J. (1998) Deletion of a highly motional residue affects formation of the Michaelis complex for Escherichia coli dihydrofolate reductase. Biochemistry 37, 6327-6335
28. Miller, G.P. and Benkovic, S.J. (1998) Strength of an interloop hydrogen bond determines the kinetic pathway in catalysis by Escherichia coli dihydrofolate reductase. Biochemistry 37, 6336-6342
29. Osborne, M.J., Schnell, J., Benkovic, S.J., Dyson, H.J., and Wright, P.E. (2001) Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism. Biochemistry 40, 9846-9859