Mass Spectrometry on Segment-Specific Hydrogen Exchange of Dihydrofolate Reductase

Journal of Biochemistry

Volumn 135, Issue 1, 2004, Pages 17-24

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

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

Dihydrofolate reductase; Hydrogen deuterium exchange; Mass spectrometry; Protease digestion; Structural fluctuation

Indexed keywords

DIHYDROFOLATE REDUCTASE; PEPSIN A;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ENZYME STABILITY; ENZYME STRUCTURE; HYDROPHOBICITY; LIGAND BINDING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; PROTEIN CONFORMATION; PROTON TRANSPORT; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; DEUTERIUM EXCHANGE MEASUREMENT; KINETICS; MOLECULAR SEQUENCE DATA; PEPTIDE FRAGMENTS; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TETRAHYDROFOLATE DEHYDROGENASE;

ESCHERICHIA COLI;

EID: 1642463331     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvh002     Document Type: Article

References (26)

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. 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
3. 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
4. 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
5. 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, 839-846
6. Karplus, M. and McCammon, J.A. (1981) The internal dynamics of globular proteins. CRC Crit. Rev. Biochem. 9, 293-349
7. Gekko, K. and Hasegawa, Y. (1986) Compressibility-structure relationship of globular proteins. Biochemistry 25, 6563-6571
8. Wüthrich, K. (1990) Structure and dynamics in proteins of pharmacological interest. Biochem. Pharmacol. 40, 55-62
9. Creighton, T. (1993) Proteins: Structure and Molecular Properties, Freeman and Company, New York
10. Hvidt, A. and Nielsen, S.O. (1966) Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287-386
11. Englander, S.W. and Kallenbach, N.R. (1983) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521-655
12. Nakanishi, M. and Tsuboi, M. (1976) Structure and fluctuation of a Streptomyces subtilisin inhibitor. Biochim. Biophys. Acta 434, 365-376
13. 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
14. 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
15. Zhang, Z. and Smith, D.L. (1993) Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2, 522-531
16. Akashi, S. and Takio, K. (2000) Characterization of the interface structure of enzyme-inhibiter complex by using hydrogen-deuterium exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. Protein Sci. 9, 2497-2505
17. Babu, K.R. and Douglas, D.J. (2000) Methanol-induced conformations of myoglobin at pH 4.0. Biochemistry 39, 14702-14710
18. Powell, K.D., Wales, T.E., and Fitzgerald, M.C. (2002) Thermodynamic stability measurements on multimeric proteins using a new H/D exchange- and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry-based method. Protein Sci. 11, 841-851
19. Englander, J.J., Del Mar, C., Li, W., Englander, S.W., Kim, J.S., Stranz, D.D., Hamuro, Y., and Woods V.L., Jr. (2003) Protein structure change studied by hydrogen-deuterium exchange, functional labeling, and mass spectrometry. Proc. Natl Acad. Sci. USA 100, 7057-7062
20. 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
21. 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
22. Gekko, K., Yamagami, K., Kunori, Y., Ichihara, S., Kodama, M., and Iwakura, M. (1993) Effect of point mutations in a flexible loop on the stability and enzymatic function Escherichia coli dihydrofolate reductase. J. Biochem. 113, 74-80
23. 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
24. 2 of the Linderstrøm-Lang model for protein amide hydrogen exchange. A study of the individual amides in hen egg-white lysozyme. J. Mol. Biol. 230, 651-660
25. 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
26. Epstein, D.M., Benkovic, S.J., and Wright, P.E. (1995) Dynamics of the dihydrofolate reductase-folate complex: catalytic sites and regions known to undergo conformational change exhibit diverse dynamical features. Biochemistry 34, 11037-11048