Dynamics of immobilized and native Escherichia coli dihydrofolate reductase by quasielastic neutron scattering

Biophysical Journal

Volumn 90, Issue 3, 2006, Pages 1090-1097

  Tehei, M ^a,c   Smith, J C ^b   Monk, C ^a   Ollivier, J ^c   Oettl, M ^a   Kurkal, V ^b   Finney, J L ^d   Daniel, R M ^a  

^a UNIVERSITY OF WAIKATO   (New Zealand)

^b UNIVERSITY OF HEIDELBERG   (Germany)

^c INSTITUT LAUE LANGEVIN   (France)

^d UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DIHYDROFOLATE REDUCTASE;

ARTICLE; CONTROLLED STUDY; DYNAMICS; ENERGY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME IMMOBILIZATION; ESCHERICHIA COLI; NEUTRON SCATTERING; NONHUMAN; SAMPLING; VIBRATION;

ESCHERICHIA COLI;

EID: 33646254850     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.062182     Document Type: Article

References (44)

1. Tanaka, A., T. Tosa, and T. Kobayashi. 1993. Industrial Applications of Immobilized Biocatalysts. Dekker, New York.
2. Blun, L. J., and P. R. Coulet. 1990. Biosensors: Principles and Applications. Dekker, New York.
3. Klibanov, A. M. 1983. Immobilized enzymes and cells as practical catalysts. Science. 219:722-727.
4. Katchalski-Katzir, E. 1993. Immobilized enzymes-learning from past successes and failures. Trends Biotechnol. 11:471-478.
5. Simpson, H. D., U. R. Haufler, and R. M. Daniel. 1991. An extremely thermostable xylanase from the thermophilic eubacterium Thermotoga. Biochem. J. 277:413-417.
6. Eggers, D. K., and J. S. Valentine. 2001. Molecular confinement influences protein structure and enhances thermal protein stability. Protein Sci. 10:250-261.
7. Zhou, H. X., and K. A. Dill. 2001. Stabilization of proteins in confined spaces. Biochemistry. 40:11289-11293.
8. Huennekens, F. M. 1994. The methotrexate story: a paradigm for development of cancer chemotherapeutic agents. Adv. Enzyme Regul. 34:397-419.
9. Arai, M., M. Kataoka, K. Kuwajima, C. R. Matthews, and M. Iwakura. 2003. Effects of the difference in the unfolded-state ensemble on the folding of Escherichia coli dihydrofolate reductase. J. Mol. Biol. 329:779-791.
10. Baccanari, D., A. Phillips, S. Smith, D. Sinski, and J. Burchall. 1975. Purification and properties of Escherichia coli dihydrofolate reductase. Biochemistry. 14:5267-5273.
11. Fierke, C. A., K. A. Johnson, and S. J. Benkovic. 1987. Construction and evaluation of the kinetic scheme associated with dihydrofolate reductase from Escherichia coli. Biochemistry. 26:4085-4092.
12. Huang, Z., C. R. Wagner, and S. J. Benkovic. 1994. Nonadditivity of mutational effects at the folate binding site of Escherichia coli dihydrofolate reductase. Biochemistry. 33:11576-11585.
13. Sawaya, M. R., and J. Kraut. 1997. Loop and subdomain movements in the mechanism of Escherichia coli dihydrofolate reductase: crystallographic evidence. Biochemistry. 36:586-603.
14. Tehei, M., B. Franzetti, D. Madern, M. Ginzburg, B. Z. Ginzburg, M. T. Giudici-Orticoni, M. Bruschi, and G. Zaccai. 2004. Adaptation to extreme environments: macromolecular dynamics in bacteria compared in vivo by neutron scattering. EMBO Rep. 51:66-70.
15. Tehei, M., D. Madern, C. Pfister, and G. Zaccai. 2001. Fast dynamics of halophilic malate dehydrogenase and BSA measured by neutron scattering under various solvent conditions influencing protein stability. Proc. Natl. Acad. Sci. USA. 98:14356-14361.
16. Brooks, C. L., M. Karplus, and B. M. Pettitt. 1988. Proteins: a theoretical perspective of dynamics, structure and thermodynamics. Adv. Chem. Phys. 71:74-95.
17. Gabel, F., D. Bicout, U. Lehnert, M. Tehei, M. Weik, and G. Zaccai. 2002. Protein dynamics studied by neutron scattering. Q. Rev. Biophys. 35:327-367.
18. Paciaroni, A., S. Cinelli, and G. Onori. 2002. Effect of the environment on the protein dynamical transition: a neutron scattering study. Biophys. J. 83:1157-1164.
19. Bée, M. 1988. Quasielastic Neutron Scattering: Principles and Applications in Solid State Chemistry, Biology and Materials Science. Adam Hilger, Bristol and Philadelphia.
20. Smith, J. C. 1991. Protein dynamics: comparison of simulations with inelastic neutron scattering experiments. Q. Rev. Biophys. 24:227-291.
21. Epstein, D. M., S. J. Benkovic, and P. E. Wright. 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.
22. Osborne, M. J., J. Schnell, S. J. Benkovic, H. J. Dyson, and P. E. Wright. 2001. Backbone dynamics in dihydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism. Biochemistry. 40:9846-9859.
23. Moreno, J. M., and J. V. Sinisterra. 1994. Immobilization of lipase from Candida cylindracea on inorganic supports. J. Mol. Catal. 93:357-369.
24. Sinisterra, J. V. 1997. Immobilization of enzymes on inorganic supports by covalent methods. In Immobilization of Enzymes and Cells. G.F. Bickerstaff, editor. Humana Press, Totowa, NY.
25. Biagioni, S., R. Sisto, A. Ferraro, P. Caiafa, and C. Turano. 1978. A new method for the preparation of DNA-cellulose. Anal. Biochem. 89:616-619.
26. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
27. Volino, F., and A. J. Dianoux. 1980. Neutron incoherent scattering law for diffusion in a potential of spherical symmetry: general formalism and application to diffusion inside a sphere. Mol. Phys. 41:271-279.
28. Receveur, V., P. Calmettes, J. C. Smith, M. Desmadril, G. Coddens, and D. Durand. 1997. Picosecond dynamical changes on denaturation of yeast phosphoglycerate kinase revealed by quasielastic neutron scattering. Proteins. 28:380-387.
29. Bellissent-Funel, M. C., J. Teixeira, K. Bradley, and S. Chen. 1992. Dynamics of hydration water in protein. J. Phys. I. 2:995-1001.
30. Kataoka, M., M. Ferrand, A. V. Goupil-Lamy, H. Kamikubo, J. Yunoki, T. Oka, and J. C. Smith. 1999. Dynamical and structural modifications of staphylococcal nuclease on C-terminal truncation. Physica B (Amsterdam). 266:20-26.
31. Chen, S. H. 1991. Hydrogen Bonded Liquids. J.C. Dore and J. Teixeira, editors. Kluwer Academic, Dordrecht, The Netherlands.
32. Egelstaff, P. A. 1972. Quasielastic Neutron Scattering for the Investigation of Diffusive Motions in Solids and Liquids. Springer, Berlin, Germany.
33. Casalvara, L. P., F. F. De Moraes, and G. M. Zanin. 2001. Comparison of catalytic properties of free and immobilized cellobiase novozym 188. Appl. Biochem. Biotechnol. 91-93:615-626.
34. + ternary complex. Substrate binding and a model for the transition state. Biochemistry. 29:3263-3277.
35. Lee, H., V. M. Reyes, and J. Kraut. 1996. Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4. Biochemistry. 35:7012-7020.
36. Rajagopalan, P. T., and S. J. Benkovic. 2002. Preorganization and protein dynamics in enzyme catalysis. Chem. Rec. 2:24-36.
37. Billeter, S. R., S. P. Webb, P. K. Agarwal, T. Iordanov, and S. Hammes-Schiffer. 2001. Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion. J. Am. Chem. Soc. 123:11262-11272.
38. Agarwal, P. K., S. R. Billeter, P. T. Rajagopalan, S. J. Benkovic, and S. Hammes-Schiffer. 2002. Network of coupled promoting motions in enzyme catalysis. Proc. Natl. Acad. Sci. USA. 99:2794-2799.
39. Watney, J. B., P. K. Agarwal, and S. Hammes-Schiffer. 2003. Effect of mutation on enzyme motion in dihydrofolate reductase. J. Am. Chem. Soc. 125:3745-3750.
40. Hall, P. L., and D. K. Ross. 1981. Incoherent neutron scattering functions for random jump diffusion in bounded and infinite media. Mol. Phys. 42:673-682.
41. Bu, Z., D. A. Neumann, S. H. Lee, C. M. Brown, D. M. Engelman, and C. C. Han. 2000. A view of dynamics changes in the molten globule-native folding step by quasielastic neutron scattering. J. Mol. Biol. 301:525-536.
42. Daniel, R. M., J. L. Finney, V. Reat, R. Dunn, M. Ferrand, and J. C. Smith. 1999. Enzyme dynamics and activity: timescale dependence of dynamical transitions in glutamate dehydrogenase solution. Biophys. J. 77:2184-2190.
43. Dunn, R. V., V. Reat, J. Finney, M. Ferrand, J. C. Smith, and R. M. Daniel. 2000. Enzyme activity and dynamics: xylanase activity in the absence of fast anharmonic dynamics. Biochem. J. 346:355-358.
44. Daniel, R. M., R. V. Dunn, J. L. Finney, and J. C. Smith. 2003. The role of dynamics in enzyme activity. Annu. Rev. Biophys. Biomol. Struct. 32:69-92.