Foldability, enzymatic activity, and interacting ability of barnase mutants obtained by permutation of secondary structure units

Biochemistry

Volumn 43, Issue 22, 2004, Pages 6968-6975

  Tsuji, Toru ^a   Yanagawa, Hiroshi ^a  

^a KEIO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; ESCHERICHIA COLI; GENETIC ENGINEERING; RNA;

FUNCTIONAL PROTEINS; RNA ACTIVITY;

BIOCHEMISTRY;

ALANINE; AMINO ACID; BARNASE; DNA; HISTIDINE; RIBONUCLEASE;

AMINO ACID SUBSTITUTION; ARTICLE; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE MUTATION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; ULTRAVIOLET SPECTROPHOTOMETRY;

ALANINE; AMINO ACID SUBSTITUTION; ESCHERICHIA COLI; HISTIDINE; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT FUSION PROTEINS; RIBONUCLEASES; UREA;

ESCHERICHIA COLI;

EID: 2642577536     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049882v     Document Type: Article

References (30)

1. Tsuji, T., Onimaru, M., and Yanagawa, H. (2001) Random multi-recombinant PCR for the construction of combinatorial protein libraries, Nucleic Acids Res. 29, E97.
2. Kitamura, K., Kinoshita, Y., Narasaki, S., Nemoto, N., Husimi, Y., and Nishigaki, K. (2002) Construction of block-shuffled libraries of DNA for evolutionary protein engineering: Y-ligation-based block shuffling, Protein Eng. 15, 843-853.
3. Shiba, K., Hatada, T., Takahashi, Y., and Noda, T. (2002) Guide oligonucleotide-dependent DNA linkage that facilitates controllable polymerization of microgene blocks, J Biochem. (Tokyo) 132, 689-696.
4. Tsuji, T., Onimaru, M., Kitagawa, M., Kojoh, K., Tabata, N., and Yanagawa, H. Random Multi-recombinant PCR (RM-PCR). Methods Enzymol., in press.
5. Go, M., and Nosaka, M. (1987) Protein architecture and the origin of introns, Cold Spring Harbor Symp. Quant. Biol. 52, 915-924.
6. Wakasugi, K., Ishimori, K., Imai, K., Wada, Y., and Morishima, I. (1994) "Module" substitution in hemoglobin subunits. Preparation and characterization of a "chimera beta alpha-subunit". J. Biol. Chem. 269, 18750-18756.
7. Inaba, K., Wakasugi, K., Ishimori, K., Konno, T., Kataoka, M., and Morishima, I. (1997) Structural and functional roles of modules in hemoglobin. Substitution of module M4 in hemoglobin subunits, J. Biol. Chem. 272, 30054-30060.
8. Hartley, R. W. (1989) Barnase and barstar: two small proteins to fold and fit together. Trends Biochem. Sci. 14, 450-454.
9. Matouschek, A., Serrano, L., and Fersht, A. R. (1994) Analysis of protein folding by protein engineering, in Mechanisms of Protein Folding (Pain, R. H., Ed) pp 137-159, Oxford University Press, New York.
10. Daggett, V., and Fersht, A. R. (2003) The present view of the mechanism of protein folding, Nat. Rev. Mol. Cell Biol. 4, 497-502.
11. Yanagawa, H., Yoshida, K., Torigoe, C., Park, J. S., Sato, K., Shirai, T., and Go, M. (1993) Protein anatomy: functional roles of bamase module, J. Biol. Chem. 268, 5861-5865.
12. Ikura, T., Go, N., Kohda, D., Inagaki, F., Yanagawa, H., Kawabata, M., Kawabata, S., Iwanaga, S., Noguti, T., and Go, M. (1993) Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation, Proteins 16, 341-356.
13. Yoshida, K., Shibata, T., Masai, J., Sato, K., Noguti, T., Go, M., and Yanagawa, H. (1993) Protein anatomy: spontaneous formation of filamentous helical structures from the N-terminal module of barnase, Biochemistry 32, 2162-2166.
14. Tsuji, T., Yoshida, K., Satoh, A., Kohno, T., Kobayashi, K., and Yanagawa, H. (1999) Foldability of barnase mutants obtained by permutation of modules or secondary structure units, J. Mol. Biol. 286, 1581-1596.
15. Tsuji, T., Kobayashi, K., and Yanagawa, H. (1999) Permutation of modules or secondary structure units creates proteins with basal enzymatic properties, FEBS Lett. 453, 145-150.
16. Hartley, R. W. (1988) Barnase and barstar. Expression of its cloned inhibitor permits expression of a cloned ribonuclease, J. Mol. Biol. 202, 913-915.
17. Mossakowska, D. E., Nyberg, K., and Fersht, A. R. (1989) Kinetic characterization of the recombinant ribonuclease from Bacillus amyloliquefaciens (barnase) and investigation of key residues in catalysis by site-directed mutagenesis, Biochemistry 28, 3843-3850.
18. Studier, F. W. (1991) Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system, J. Mol. Biol. 219, 37-44.
19. Gill, S. C., and von Hippel, P. H. (1989) Calculation of protein extinction coefficients from amino acid sequence data, Anal. Biochem. 182, 319-326.
20. Vuilleumier, S., Sancho, J., Loewenthal, R., and Fersht, A. R. (1993) Circular dichroism studies of barnase and its mutants: Characterization of the contribution of aromatic side chains, Biochemistry, 32, 10303-10313.
21. Guillet, V., Lapthorn, A., and Mauguen, Y. (1993) Three-dimensional structure of a barnase-3′GMP complex at 2.2 Å resolution, FEBS Lett. 330, 137-140.
22. Meiering, E. M., Bycroft, M., Lubienski, M. J., and Fersht, A. R. (1993) Structure and dynamics of barnase complexed with 3′-GMP studied by NMR spectroscopy, Biochemistry 32, 10975-10987.
23. Meiering, E. M., Serrano, L., and Fersht, A. R. (1992) Effect of active site residues in barnase on activity and stability, J. Mol. Biol. 255, 585-589.
24. Axe, D. D., Foster, N. W., and Fersht, A. R. (1998) A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease, Biochemistry 37, 7157-7166.
25. Iwakura, M., Takenawa, T., and Nakamura, T. (1998) Topological mutation of Escherichia coli dihydrofolate reductase, J. Biochem. (Tokyo) 124, 769-777.
26. Schlunegger, M. P., Bennett, M. J., and Eisenberg, D. (1997) Oligomer formation by 3D domain swapping: a model for protein assembly and misassembly, Adv. Protein Chem. 50, 61-122.
27. Zegers, I., Deswarte, J., and Wyns, L. (1999) Trimeric domain-swapped barnase, Proc. Natl. Acad. Sci. U.S.A. 96, 818-822.
28. Shiraki, K., Nishikawa, K., and Goto, Y. (1995) Trifluoroethanol-induced stabilization of the α-helical structure of β-lactoglobulin: Implication for non-hierarchical protein folding, J. Mol. Biol. 245, 180-194.
29. Waterhous, D. V., and Johnson, W. C., Jr. (1994) Importance of environment in determining secondary structure in proteins, Biochemistry 33, 2121-2128.
30. Minor, D. L., Jr., and Kim, P. S. (1996) Context-dependent secondary structure formation of a designed protein sequence, Nature 380, 730-734.