Using directed evolution to improve the solubility of the C-terminal domain of Escherichia coli aminopeptidase P: Implications for metal binding and protein stability

FEBS Journal

Volumn 274, Issue 18, 2007, Pages 4742-4751

  Liu, Jian Wei ^a   Hadler, Kieran S ^b   Schenk, Gerhard ^b   Ollis, David ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

^b UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Directed evolution; Domain; Fusion; Metalloprotein; Protein solubility

Indexed keywords

AMINOPEPTIDASE P;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DIRECTED MOLECULAR EVOLUTION; ESCHERICHIA COLI; METAL BINDING; NONHUMAN; PHYSIOLOGY; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN BINDING; PROTEIN STRUCTURE; SOLUBILITY;

AMINOPEPTIDASES; BINDING SITES; DIRECTED MOLECULAR EVOLUTION; ESCHERICHIA COLI; METALS; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN RENATURATION; PROTEIN STRUCTURE, TERTIARY; SOLUBILITY;

ESCHERICHIA COLI;

EID: 34548421622     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2007.06022.x     Document Type: Article

References (29)

1. Graham SC, Bond CS, Freeman HC Guss JM (2005) Structural and functional implications of metal ion selection in aminopeptidase P, a metalloprotease with a dinuclear metal center. Biochemistry 44, 13820 13836.
2. Wilce MC, Bond CS, Dixon NE, Freeman HC, Guss JM, Lilley PE Wilce JA (1998) Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli. Proc Natl Acad Sci USA 95, 3472 3477.
3. Bazan JF, Weaver LH, Roderick SL, Huber R Matthews BW (1994) Sequence and structure comparison suggest that methionine aminopeptidase, prolidase, aminopeptidase P, and creatinase share a common fold. Proc Natl Acad Sci USA 91, 2473 2477.
4. Liu JW, Boucher Y, Stokes HW Ollis DL (2006) Improving protein solubility: the use of the Escherichia coli dihydrofolate reductase gene as a fusion reporter. Protein Expr Purif 47, 258 263.
5. Neylon C (2004) Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: library construction methods for directed evolution. Nucleic Acids Res 32, 1448 1459.
6. Schenk G, Boutchard CL, Carrington LE, Noble CJ, Moubaraki B, Murray KS, de Jersey J, Hanson GR Hamilton S (2001) A purple acid phosphatase from sweet potato contains an antiferromagnetically coupled binuclear Fe-Mn center. J Biol Chem 276, 19084 19088.
7. Larrabee JA, Leung CH, Moore RL, Thamrong-Nawasawat T Wessler BS (2004) Magnetic circular dichroism and cobalt(II) binding equilibrium studies of Escherichia coli methionyl aminopeptidase. J Am Chem Soc 126, 12316 12324.
8. Mitic N, Smith SJ, Neves A, Guddat LW, Gahan LR Schenk G (2006) The catalytic mechanisms of binuclear metallohydrolases. Chem Rev 106, 3338 3363.
9. Xu Y, Wen D, Clancy P, Carr PD, Ollis DL Vasudevan SG (2004) Expression, purification, crystallization, and preliminary X-ray analysis of the N-terminal domain of Escherichia coli adenylyl transferase. Protein Expr Purif 34, 142 146.
10. Kerr ID, Berridge G, Linton KJ, Higgins CF Callaghan R (2003) Definition of the domain boundaries is critical to the expression of the nucleotide-binding domains of P-glycoprotein. Eur Biophys J 32, 644 654.
11. Rigden DJ (2002) Use of covariance analysis for the prediction of structural domain boundaries from multiple protein sequence alignments. Protein Eng 15, 65 77.
12. Dumontier M, Yao R, Feldman HJ Hogue CW (2005) Armadillo: domain boundary prediction by amino acid composition. J Mol Biol 350, 1061 1073.
13. Liu J Rost B (2004) Sequence-based prediction of protein domains. Nucleic Acids Res 32, 3522 3530.
14. Galzitskaya OV Melnik BS (2003) Prediction of protein domain boundaries from sequence alone. Protein Sci 12, 696 701.
15. Holland TA, Veretnik S, Shindyalov IN Bourne PE (2006) Partitioning protein structures into domains: why is it so difficult? J Mol Biol 361, 562 590.
16. Severinova E, Severinov K, Fenyo D, Marr M, Brody EN, Roberts JW, Chait BT Darst SA (1996) Domain organization of the Escherichia coli RNA polymerase sigma 70 subunit. J Mol Biol 263, 637 647.
17. Christ D Winter G (2006) Identification of protein domains by shotgun proteolysis. J Mol Biol 358, 364 371.
18. Hart DJ Tarendeau F (2006) Combinatorial library approaches for improving soluble protein expression in Escherichia coli. Acta Crystallogr D Biol Crystallogr 62, 19 26.
19. Cornvik T, Dahlroth SL, Magnusdottir A, Flodin S, Engvall B, Lieu V, Ekberg M Nordlund P (2006) An efficient and generic strategy for producing soluble human proteins and domains in E. coli by screening construct libraries. Proteins 65, 266 273.
20. Wittung-Stafshede P (2004) Role of cofactors in folding of the blue-copper protein azurin. Inorg Chem 43, 7926 7933.
21. Wilson CJ, Apiyo D Wittung-Stafshede P (2004) Role of cofactors in metalloprotein folding. Q Rev Biophys 37, 285 314.
22. Proudfoot AE, Goffin L, Payton MA, Wells TN Bernard AR (1996) In vivo and in vitro folding of a recombinant metalloenzyme, phosphomannose isomerase. Biochem J 318 (2 437 442.
23. Villaverde A Carrio MM (2003) Protein aggregation in recombinant bacteria: biological role of inclusion bodies. Biotechnol Lett 25, 1385 1395.
24. Henikoff S (1987) Unidirectional digestion with exonuclease III in DNA sequence analysis. Methods Enzymol 155, 156 165.
25. Ostermeier M, Nixon AE, Shim JH Benkovic SJ (1999) Combinatorial protein engineering by incremental truncation. Proc Natl Acad Sci USA 96, 3562 3567.
26. Stemmer WP (1994) DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci USA 91, 10747 10751.
27. Graham SC, Lilley PE, Lee M, Schaeffer PM, Kralicek AV, Dixon NE Guss JM (2006) Kinetic and crystallographic analysis of mutant Escherichia coli aminopeptidase P: insights into substrate recognition and the mechanism of catalysis. Biochemistry 45, 964 975.
28. Yang H, Carr PD, McLoughlin SY, Liu JW, Horne I, Qiu X, Jeffries CM, Russell RJ, Oakeshott JG Ollis DL (2003) Evolution of an organophosphate- degrading enzyme: a comparison of natural and directed evolution. Protein Eng 16, 135 145.
29. Kim HK, Liu JW, Carr PD Ollis DL (2005) Following directed evolution with crystallography: structural changes observed in changing the substrate specificity of dienelactone hydrolase. Acta Crystallogr D Biol Crystallogr 61, 920 931.