Active TEM-1 β-lactamase mutants with random peptides inserted in three contiguous surface loops

Protein Science

Volumn 15, Issue 10, 2006, Pages 2323-2334

  Mathonet, Pascale ^a   Deherve, Julie ^a   Soumillion, Patrice ^a   Fastrez, Jacques ^a  

^a UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

Author keywords

lactamase; In vivo selection; Insertion tolerance; Loop engineering

Indexed keywords

BETA LACTAMASE; BETA LACTAMASE TEM 1; DISULFIDE; LIGAND; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARTICLE; BETA SHEET; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CORRELATION ANALYSIS; ENZYME ACTIVITY; ENZYME BINDING; ENZYME ENGINEERING; ENZYME STRUCTURE; GENE INSERTION; HYDROPHOBICITY; MUTATION; PRIORITY JOURNAL;

AMINO ACID SEQUENCE; BETA-LACTAMASES; CYSTEINE; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; HYDROPHOBICITY; MUTAGENESIS; MUTATION; PEPTIDE LIBRARY; PEPTIDES; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY;

EID: 33749357740     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1110/ps.062303606     Document Type: Article

References (45)

1. Ambler, R.P., Coulson, A.F.W., Frere, J.-M., Ghuysen, J.M., Joris, B., Forsman, M., Levesque, R.C., Tiraby, G., and Waley, S.G. 1991. A standard numbering scheme for the Class A β-lactamases. Biochem. J. 276: 269-270.
2. Barany, F. 1985. Two-codon insertion mutagenesis of plasmid genes by using single-stranded hexameric oligonucleotides. Proc. Natl. Acad. Sci. 82: 4202-4206.
3. Batori, V., Koide, A., and Koide, S. 2002. Exploring the potential of the monobody scaffold: Effects of loop elongation on the stability of a fibronectin type III domain. Protein Eng. 15: 1015-1020.
4. Binz, K.P., Amstutz, P., and Plückthun, A. 2005. Engineering novel binding proteins from nonimmunoglobulin domains. Nat. Biotechnol. 23: 1257-1268.
5. Brennan, C.A., Christianson, K., La Fleur, M.A., and Mandecki, W. 1995. Engineering novel binding proteins from nonimmunoglobulin domains. Proc. Natl. Acad. Sci. 92: 5783-5787.
6. Cantu III, C., Huang, W., and Palzkill, T. 1996. Selection and characterization of amino acid substitutions at residues 237-240 of TEM-1 β-lactamase with altered substrate specificity for aztreonam and ceftazidime. J. Biol. Chem. 271: 22538-22545.
7. Collinet, B., Garcia, P., Minard, P., and Desmadril, M. 2001. Intrachain loops in polymers: Effects of excluded volume. Eur. J. Biochem. 268: 5107-5118.
8. Combet, C., Blanchet, C., Geourjon, C., and Deléage, G. 2000. NPS@: Network protein sequence analysis. Trends Biochem. Sci. 25: 147-150.
9. Feliu, J.X. and Villaverde, A. 1998. Engineering of solvent-exposed loops in Escherichia coli β-galactosidase. FEBS Lett. 434: 23-27.
10. Ferrer-Miralles, N., Feliu, J.X., Vandevuer, S., Muller, A., Cabrera-Crespo, J., Ortmans, I., Hoffmann, F., Cazorla, D., Rinas, U., Prevost, M., et al. 2001. Engineering regulable Escherichia coli β-galactosidases as biosensors for anti-HIV antibody detection in human sera. J. Biol. Chem. 276: 40087-40095.
11. Gu, H., Kim, D., and Baker, D. 1997. Contrasting roles for symmetrically disposed β-turns in the folding of a small protein. J. Mol. Biol. 274: 588-596.
12. Guex, N. and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
13. Hallet, B., Sherratt, D.J., and Hayes, F. 1997. Pentapeptide scanning mutagenesis: Random insertion of a variable five amino acid cassette in a target protein. Nucleic Acids Res. 25: 1866-1867.
14. Hamers-Casterman, C., Atarhouch, T., Muyldermans, S., Robinson, G., Hamers, C., Songa, E.B., Bendahman, N., and Hamers, R. 1993. Naturally occurring antibodies devoid of light chains. Nature 363: 446-448.
15. Hayes, F., Hallet, B., and Cao, Y. 1997. Insertion mutagenesis as a tool in the modification of protein function. Extended substrate specificity conferred by pentapeptide insertions in the Ω-loop of TEM-1 β-lactamase. J. Biol. Chem. 272: 28833-28836.
16. Horn, J.R. and Shoichet, B.K. 2004. Allosteric inhibition through core disruption. J. Mol. Biol. 336: 1283-1291.
17. Huang, W., Petrosino, J., Hirsch, M., Shenkin, P.S., and Palzkill, T. 1996. Amino acid sequence determinants of β-lactamase structure and activity. J. Mol. Biol. 258: 688-703.
18. Jelsch, C., Mourey, L., Masson, J.M., and Samama, J.P. 1993. Crystal structure of Escherichia coli TEM1 β-lactamase at 1.8 Å resolution. Proteins 16: 364-383.
19. Kay, B.K., Adey, N.B., He, Y.S., Manfredi, J.P., Mataragnon, A.H., and Fowlkes, D.M. 1993. An M13 phage library displaying random 38-amino-acid peptides as a source of novel sequences with affinity to selected targets. Gene 128: 59-65.
20. Ladurner, A.G. and Fersht, A.R. 1997. Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. J. Mol. Biol. 273: 330-337.
21. Lee, K.Y., Hopkins, J.D., O'Brien, T.F., and Syvanen, M. 1991. Gly-238-Ser substitution changes the substrate specificity of the SHV Class A β-lactamases. Proteins 11: 45-51.
22. Legendre, D., Soumillion, P., and Fastrez, J. 1999. Engineering a regulatable enzyme for homogeneous immunoassays. Nat. Biotechnol. 17: 67-72.
23. Legendre, D., Vucic, B., Hougardy, V., Girboux, A.-L., Henrioul, C., Van Haute, J., Soumillion, P., and Fastrez, J. 2002. TEM-1 β-lactamase as a scaffold for protein recognition and assay. Protein Sci. 11: 1506-1518.
24. Lu, Z., Murray, K.S., Van Cleave, V., LaVallie, E.R., Stahl, M.L., and McCoy, J.M. 1995. Expression of thioredoxin random peptide libraries on the Escherichia coli cell surface as functional fusions to flagellin: A system designed for exploring protein-protein interactions. Bio/Technology 13: 366-372.
25. Matagne, A. and Frere, J.-M. 1995. Contribution of mutant analysis to the understanding of enzyme catalysis. The case of class A β-lactamases. Biochim. Biophys. Acta 1246: 109-127.
26. Matagne, A., Lamotte-Brasseur, J., and Frere, J.-M. 1998. Catalytic properties of class A β-lactamases: Efficiency and diversity. Biochem.J. 330: 581-598.
27. Mathonet, P. and Fastrez, J. 2004. Engineering of non-natural receptors. Curr. Opin. Struct. Biol. 14: 505-511.
28. Mathonet, P., Barrios, H., Soumillion, P., and Fastrez, J. 2006. Selection of allosteric β-lactamase mutants featuring an activity regulation by transition metal ions. Protein Sci. 15: (this issue).
29. Nagi, A.D. and Regan, L. 1997. An inverse correlation between loop length and stability in a four-helix-bundle protein. Fold. Des. 2: 67-75.
30. Pal, M. and Dasgupta, S. 2003. The nature of the turn in Ω loops of proteins. Proteins 51: 591-606.
31. Palzkill, T. and Botstein, D. 1992. Identification of amino acid substitutions that alter the substrate specificity of TEM-1 β-lactamase. J. Bacteriol. 174: 5237-5243.
32. Petyuk, V., McDermott, J., Cook, M., and Sauer, B. 2004. Functional mapping of Cre recombinase by pentapeptide insertional mutagenesis. J. Biol. Chem. 279: 37040-37048.
33. Prakash, S. and Matouschek, A. 2004. Protein unfolding in the cell. Trends Biochem. Sci. 29: 593-600.
34. Raquet, X., Lamotte-Brasseur, J., Fonze, E., Goussard, S., Courvalin, P., and Frere, J.M. 1994. TEM β-lactamase mutants hydrolyzing third-generation cephalosporins. A kinetic and molecular modeling analysis. J. Mol. Biol. 244: 625-639.
35. Raquet, X., Vanhove, M., Lamotte-Brasseur, J., Goussard, S., Courvalin, P., and Frère, J.M. 1995. Stability of TEM β-lactamase mutants hydrolyzing third generation cephalosporins. Proteins 23: 63-72.
36. Skerra, A. 2000. Engineered protein scaffolds for molecular recognition. J. Mol. Recognit. 13: 167-187.
37. Soumillion, P., Jespers, L., Bouchet, M., Marchand-Brynaert, J., Winter, G., and Fastrez, J. 1994. Selection of β-lactamase on filamentous bacteriophage by catalytic activity. J. Mol. Biol. 237: 415-422.
38. Tramontano, A., Chothia, C., and Lesk, A.M. 1989. Structural determinants of the conformations of medium-sized loops in proteins. Proteins 6: 382-394.
39. Vanhove, M., Guillaume, G., Ledent, P., Richards, J.H., Pain, R.H., and Frere, J.-M. 1997. Kinetic and thermodynamic consequences of the removal of the Cys-77-Cys-123 disulfide bond for the folding of TEM-1 β-lactamase. Biochem. J. 321: 413-417.
40. Vanwetswinkel, S., Avalle, B., and Fastrez, J. 2000. Selection of β-lactamases and penicillin binding mutants from a library of phage displayed TEM-1 β-lactamase randomly mutated in the active site Ω-loop. J. Mol. Biol. 295: 527-540.
41. Venkatachalam, K.V., Huang, W., LaRocco, M., and Palzkill, T. 1994. Characterization of TEM-1 β-lactamase mutants from positions 238 to 241 with increased catalytic efficiency for ceftazidine. J. Biol. Chem. 269: 23444-23450.
42. Vetter, I.R., Baase, W.A., Heinz, D.W., Xiong, J.-P., Snow, S., and Matthews, B.W. 1996. Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme. Protein Sci. 5: 2399-2415.
43. Viguera, A.-R. and Serrano, L. 1997. Loop length, intramolecular diffusion and protein folding. Nat. Struct. Biol. 4: 939-946.
44. Zebala, J. and Barany, F. 1991. Mapping catalytically important regions of an enzyme using two-codon insertion mutagenesis: A case study correlating β-lactamase mutants with the three-dimensional structure. Gene 100: 51-57.
45. Zhou, H.X., Hoess, R.H., and DeGrado, W.F. 1996. In vitro evolution of thermodynamically stable turns. Nat. Struct. Biol. 3: 446-451.