Single amino acid substitutions in flexible loops can induce large compressibility changes in dihydrofolate reductase

Journal of Biochemistry

Volumn 128, Issue 1, 2000, Pages 21-27

  Gekko, Kunihiko ^a   Kamiyama, Tadashi ^a   Ohmae, Eiji ^a   Katayanagi, Katsuo ^a  

^a HIROSHIMA UNIVERSITY   (Japan)

Author keywords

Amino acid substitution; Compressibility; Dihydrofolate reductase; Flexible loops; Structural flexibility

Indexed keywords

DIHYDROFOLATE REDUCTASE;

AMINO ACID SUBSTITUTION; ARTICLE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME DENATURATION; ENZYME STABILITY; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; STRUCTURE ANALYSIS;

ESCHERICHIA COLI; FELIS CATUS;

EID: 0033929162     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/oxfordjournals.jbchem.a022726     Document Type: Article

References (39)

1. Farnum, M.F., Magde, D., Howell, E.E., Hirai, J.T., Warren, M.S., Grimsley, J.K., and Kraut, J. (1991) Analysis of hydride transfer and cofactor fluorescence decay in mutants of dihydrofolate reductase: possible evidence for participation of enzyme molecular motions in catalysis. Biochemistry 30, 11567-11579
2. Yu, A., Ballard, L., Smillie, L., Pearlstone, J., Foguel, D., Silva, J., Jonas, A., and Jonas, J. (1999) Effects of high pressure and temperature on the wild-type and F29W mutant forms of the N-domain of avian troponin C. Biochim. Biophys. Acta 1431, 53-63
3. Consonni, R., Santomo, L., Fusi, P., Tortora, P., and Zetta, L. (1999) A single-point mutation in the extreme heat- and pressure-resistant sso7d sulfolobus solfataricus leads to a major rearrangement of the hydrophobic core. Biochemistry 38, 12709-12717
4. Karplus, M. and McCammon, J.A. (1981) The internal dynamics of globular proteins. CRC Crit. Rev. Biochem. 9, 293-349
5. Wüthrich, K. (1990) Structure and dynamics in proteins of pharmacological interest. Biochem. Pharmacol. 40, 55-62
6. Creiton, T.E. (1993) Proteins - Structures and Molecular Properties - , W.H. Freeman and Company, New York
7. Li, H., Yamada, H., and Akasaka, K. (1999) Effect of pressure on the tertiary structure and dynamics of folded basic pancreatic trypsin inhibitor Biophys. J. 77, 2801-2812
8. Cooper, A. (1976) Thermodynamic fluctuations in protein molecules. Proc. Natl Acad. Sci. USA 73, 2740-2741
9. Gekko, K. and Noguchi, H. (1979) Compressibility of globular proteins in water at 25°C. J. Phys. Chem. 83, 2706-2714
10. Gekko, K. and Hasegawa, Y. (1986) Compressibility-structure relationship of globular proteins. Biochemistry 25, 6563-6571
11. Chalikian, T.V., Totrov, M., Abagyan, R., and Breslauer, K.J. (1996) The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J. Mol. Biol. 260, 588-603
12. Tamura, Y. and Gekko, K. (1995) Compactness of thermally and chemically denatured ribonuclease A as revealed by volume and compressibility. Biochemistry 34, 1878-1884
13. Chalikian, T.V., Gindikin, V.S., and Breslauer, K.J. (1995) Volumetric characterizations of the native, molten globule and unfolded states of cytochrome c at acidic pH. J. Mol. Biol. 250, 291-306
14. Kharakoz, D.P. (1997) Partial volumes and compressibilities of extended polypeptide chains in aqueous solution: additivity scheme and implication of protein unfolding at normal and high pressure. Biochemistry 36, 10276-10285
15. Nikitin, S.Ia., Sarvazian, A.P., and Kravchenko, N.A. (1984) Ultrasound velocimetry of lysozyme solutions. Mol. Biol. (Mosk) 18, 831-838
16. Gekko, K. and Yamagami, K. (1998) Compressibility and volume changes of lysozyme due to inhibitor binding. Chem. Lett. 839-840
17. 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
18. Gekko, K., Tamura, Y., Ohmae, E., Hayashi, H., Kagamiyama, H., and Ueno, H. (1996) A large compressibility change of protein induced by a single amino acid substitution. Protein Sci. 5, 542-545
19. 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
20. 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
21. Gekko, K., Yamagami, K., Kunori, Y., Ichihara, S., Kodama, M., and Iwakura, M. (1993) Effects of point mutation in a flexible loop on the stability and enzymatic function of Escherichia coli dihydrofolate reductase. J. Biochem. 113, 74-80
22. 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
23. 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
24. 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
25. Ohmae, E., Iriyama, K., Ichihara, S., and Gekko, K. (1998) Nonadditive effects of double mutations at the flexible loops, glycine-67 and glycine-121, of Escherichia coli dihydrofolate reductase on its stability and function. J. Biochem. 123, 33-41
26. Iwakura, M. and Tanaka, T. (1992) Dihydrofolate reductase from Bacillus subtilis and its artificial derivatives: expression, purification, and characterization. J. Biochem. 111, 638-642
27. 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
28. 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
29. Kauzmann, W. (1959) Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14, 1-63
30. Gekko, K. and Yamagami, K. (1991) Flexibility of food proteins as revealed by compressibility. J. Agric. Food. Chem. 39, 57-62
31. Pakula, A.A. and Sauer, R.T. (1990) Reverse hydrophobic effects relieved by amino-acid substitutions at a protein surface. Nature 344, 363-364
32. Bowler, B.E., May, K., Zaragoza, T., York, P., Dong, A., and Caughey, W.S. (1993) Destabilizing effects of replacing a surface lysine of cytochrome c with aromatic amino acids: implications for the denatured state. Biochemistry 32, 183-190
33. Schellman, J.A. (1978) Solvent denaturation. Biopolymers 17, 1305-1322
34. Shortle, D. (1995) Staphylococcal nuclease: a showcase of m-value effects. Adv. Protein Chem. 46, 217-247
35. Ahrweiler, P.M. and Frieden, C. (1991) Effects of point mutations in a hinge region on the stability, folding, and enzymatic activity of Escherichia coli dihydrofolate reductase. Biochemistry 30, 7801-7809
36. Li, L., Falzone, C.J., Wright, P.E., and Benkovic, S.J. (1992) Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization. Biochemistry 31, 7826-7833
37. Cameron, C.E. and Benkovic, S.J. (1997) Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. Biochemistry 36, 15792-15800
38. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950
39. Zamyatnin, A.A. (1984) Amino acid, peptide, and protein volume in solution. Annu. Rev. Biophys. Bioeng. 13, 145-165