Design, selection, and characterization of a split chorismate mutase

Protein Science

Volumn 19, Issue 5, 2010, Pages 1000-1010

  Müller, Manuel M ^a   Kries, Hajo ^a   Csuhai, Eva ^a,b   Kast, Peter ^a   Hilvert, Donald ^a  

^a ETH ZURICH   (Switzerland)

^b TRANSYLVANIA UNIVERSITY   (United States)

Author keywords

Directed evolution; Fragment complementation; Helix bundle; Leucine zipper; Protein oligomerization; Split protein

Indexed keywords

CHORISMATE MUTASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; DIMERIZATION; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME STABILITY; IN VIVO STUDY; METHANOCOCCUS JANNASCHII; MUTAGENESIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN PURIFICATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; CHORISMATE MUTASE; COMBINATORIAL CHEMISTRY TECHNIQUES; DIRECTED MOLECULAR EVOLUTION; ESCHERICHIA COLI; LEUCINE ZIPPERS; METHANOCOCCUS; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PROTEIN ENGINEERING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT;

METHANOCALDOCOCCUS JANNASCHII;

EID: 77951570155     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.377     Document Type: Article

References (50)

1. Richards FM (1958) On the enzymic activity of subtilisin-modified ribonuclease. Proc Nat Acad Sci USA 44: 162-166.
2. Anfinsen CB (1973) Principles that govern folding of protein chains. Science 181:223-230.
3. Finn FM, Hofmann K (1965) Studies on polypeptides. XXXIII. Enzymic properties of partially synthetic ribonucleases. J Am Chem Soc 87:645-651.
4. Hamachi I, Hiraoka T, Yamada Y, Shinkai S (1998) Photoswitching of the enzymatic activity of semisynthetic ribonuclease S' bearing phenylazophenylalanine at a specific site. Chem Lett 27:537-538.
5. Nitz M, Mezo AR, Ali MH, Imperiali B (2002) Enantio-selective synthesis and application of the highly fluorescent and environment-sensitive amino acid 6-(2-dimethylaminonaphthoyl) alanine (DANA). Chem Commun 2002:1912-1913. (Pubitemid 36139003)
6. Wildemann D, Schiene-Fischer C, Aumüller T, Bachmann A, Kiefhaber T, Lücke C, Fischer G (2007) A nearly isosteric photosensitive amide-backbone substitution allows enzyme activity switching in ribonuclease S. J Am Chem Soc 129:4910-4918. (Pubitemid 46651368)
7. Michnick SW (2001) Exploring protein interactions by interaction-induced folding of proteins from complementary peptide fragments. Curr Opin Struct Biol 11: 472-477.
8. Pelletier JN, Arndt KM, Plückthun A, Michnick SW (1999) An in vivo library-versus-library selection of optimized protein-protein interactions. Nat Biotechnol 17:683-690. (Pubitemid 29316147)
9. Magliery TJ, Wilson CGM, Pan WL, Mishler D, Ghosh I, Hamilton AD, Regan L (2005) Detecting protein-protein interactions with a green fluorescent protein fragment reassembly trap: Scope and mechanism. J Am Chem Soc 127:146-157. (Pubitemid 40094379)
10. Campbell-Valois F-X, Michnick SW, Synthesis of degenerated libraries of the Ras-binding domain of Raf and rapid selection of fast-folding and stable clones with the dihydrofolate reductase protein fragment complementation assay. In: Arndt K., Müller K., Eds. (2007) Protein Engineering Protocols. Totowa (NJ): Humana Press, pp 249-274.
11. Leveson-Gower DB, Michnick SW, Ling V (2004) Detection of TAP family dimerizations by an in vivo assay in mammalian cells. Biochemistry 43:14257-14264.
12. Remy I, Wilson IA, Michnick SW (1999) Erythropoietin receptor activation by a ligand-induced conformation change. Science 283:990-993. (Pubitemid 129505219)
13. Laser H, Bongards C, Schuller J, Heck S, Johnsson N, Lehming N (2000) A new screen for protein interactions reveals that the Saccharomyces cerevisiae high mobility group proteins Nhp6A/B are involved in the regulation of the GAL1 promoter. Proc Nat Acad Sci USA 97:13732-13737.
14. Raquet X, Eckert JH, Müller S, Johnsson N (2001) Detection of altered protein conformations in living cells. J Mol Biol 305:927-938. (Pubitemid 33030036)
15. Ozawa T, Sako Y, Sato M, Kitamura T, Umezawa Y (2003) A genetic approach to identifying mitochondrial proteins. Nat Biotechnol 21:287-293. (Pubitemid 36314813)
16. Ear PH, Michnick SW (2009) A general life-death selection strategy for dissecting protein functions. Nat Methods 6:813-816.
17. Bloom JD, Labthavikul ST, Otey CR, Arnold FH (2006) Protein stability promotes evolvability. Proc Nat Acad Sci USA 103:5869-5874.
18. MacBeath G, Kast P, Hilvert D (1998) Redesigning enzyme topology by directed evolution. Science 279: 1958-1961. (Pubitemid 28168654)
19. Qiu JX, Petersson EJ, Matthews EE, Schepartz A (2006) Toward beta-amino acid proteins: a cooperatively folded beta-peptide quaternary structure. J Am Chem Soc 128:11338-11339.
20. Horne WS, Price JL, Keck JL, Gellman SH (2007) Helix bundle quaternary structure from alpha/beta-peptide foldamers. J Am Chem Soc 129:4178-4180.
21. MacBeath G, Kast P, Hilvert D (1998) Probing enzyme quaternary structure by combinatorial mutagenesis and selection. Protein Sci 7:1757-1767. (Pubitemid 29133180)
22. Vamvaca K, Butz M, Walter KU, Taylor SV, Hilvert D (2005) Simultaneous optimization of enzyme activity and quaternary structure by directed evolution. Protein Sci 14:2103-2114. (Pubitemid 41132376)
23. Bittker JA, Le BV, Liu JM, Liu DR (2004) Directed evolution of protein enzymes using nonhomologous random recombination. Proc Nat Acad Sci USA 101: 7011-7016.
24. Jäckel C, Kast P, Hilvert D (2008) Protein design by directed evolution. Annu Rev Biophys 37:153-173.
25. Lee AY, Karplus PA, Ganem B, Clardy J (1995) Atomic structure of the buried catalytic pocket of Escherichia coli chorismate mutase. J Am Chem Soc 117:3627-3628.
26. Pervushin K, Vamvaca K, Vögeli B, Hilvert D (2007) Structure and dynamics of a molten globular enzyme. Nat Struct Mol Biol 14:1202-1206. (Pubitemid 350223332)
27. MacBeath G, Kast P (1998) UGA read-through artifacts - when popular gene expression systems need a pATCH. Biotechniques 24:789-794. (Pubitemid 28211342)
28. Sasso S, Ramakrishnan C, Gamper M, Hilvert D, Kast P (2005) Characterization of the secreted chorismate mutase from the pathogen Mycobacterium tuberculosis. FEBS J 272:375-389.
29. Kast P, Asif-Ullah M, Jiang N, Hilvert D (1996) Exploring the active site of chorismate mutase by combinatorial mutagenesis and selection: The importance of electrostatic catalysis. Proc Nat Acad Sci USA 93:5043-5048. (Pubitemid 26162867)
30. Ghosh I, Hamilton AD, Regan L (2000) Antiparallel leucine zipper-directed protein reassembly: Application to the green fluorescent protein. J Am Chem Soc 122: 5658-5659. (Pubitemid 30431094)
31. Liu DR, Cload ST, Pastor RM, Schultz PG (1996) Analysis of active site residues in Escherichia coli chorismate mutase by site-directed mutagenesis. J Am Chem Soc 118:1789-1790. (Pubitemid 26092325)
32. MacBeath G, Kast P, Hilvert D (1998) A small, thermostable, and monofunctional chorismate mutase from the archaeon Methanococcus jannaschii. Biochemistry 37:10062-10073. (Pubitemid 28366360)
33. Vamvaca K, Vögeli B, Kast P, Pervushin K, Hilvert D (2004) An enzymatic molten globule: Efficient coupling of folding and catalysis. Proc Nat Acad Sci USA 101: 12860-12864. (Pubitemid 39167548)
34. Woycechowsky KJ, Choutko A, Vamvaca K, Hilvert D (2008) Relative tolerance of an enzymatic molten globule and its thermostable counterpart to point mutation. Biochemistry 47:13489-13496.
35. Stryer L (1968) Fluorescence spectroscopy of proteins. Science 162:526-533.
36. Roderer K, Kast P (2009) Evolutionary cycles for pericyclic reactions - or why we keep mutating mutases. Chimia 63:313-317.
37. Lee AY, Stewart JD, Clardy J, Ganem B (1995) New insight into the catalytic mechanism of chorismate mutases from structural studies. Chem Biol 2: 195-203.
38. Sasso S, Ökvist M, Roderer K, Gamper M, Codoni G, Krengel U, Kast P (2009) Structure and function of a complex between chorismate mutase and DAHP synthase: efficiency boost for the junior partner. EMBO J 28:2128-2142.
39. Porter JR, Stains CI, Jester BW, Ghosh I (2008) A general and rapid cell-free approach for the interrogation of protein-protein, protein-DNA, and protein-RNA interactions and their antagonists utilizing split-protein reporters. J Am Chem Soc 130:6488-6497.
40. Neuenschwander M, Butz M, Heintz C, Kast P, Hilvert D (2007) A simple selection strategy for evolving highly efficient enzymes. Nat Biotechnol 25:1145-1147. (Pubitemid 47538117)
41. Pelletier JN, Campbell-Valois F-X, Michnick SW (1998) Oligomerization domain-directed reassembly of active dihydrofolate reductase from rationally designed fragments. Proc Nat Acad Sci USA 95:12141-12146.
42. Kent KP, Oltrogge LM, Boxer SG (2009) Synthetic control of green fluorescent protein. J Am Chem Soc 131: 15988-15989.
43. Garcia-Viloca M, Gao J, Karplus M, Truhlar DG (2004) How enzymes work: Analysis by modern rate theory and computer simulations. Science 303:186-195. (Pubitemid 38057561)
44. Kienhöfer A, Kast P, Hilvert D (2003) Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor. J Am Chem Soc 125:3206-3207. (Pubitemid 36512450)
45. Müller MM, Windsor MA, Pomerantz WC, Gellman SH, Hilvert D (2009) A rationally designed aldolase foldamer. Angew Chem Int Ed Engl 48:922-925.
46. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
47. Gamper M, Hilvert D, Kast P (2000) Probing the role of the C-terminus of Bacillus subtilis chorismate mutase by a novel random protein-termination strategy. Biochemistry 39:14087-14094.
48. Laue TM, Shah BD, Ridgeway TM, Pelletier SL (1992) Analytical ultracentrifugation in biochemistry and polymer science. Cambridge, UK: Royal Society of Chemistry.
49. Demeler B, Ultrascan - a comprehensive data analysis software package for analytical ultracentrifugation experiments. In: Scott DJ, Harding SE, Rowe AJ, Eds. (2005) Modern Analytical Ultracentrifugation: Techniques and Methods. Cambridge, UK: Royal Society of Chemistry, pp 210-229.
50. Nozaki Y (1972) The preparation of guanidine hydrochloride. Methods Enzymol 26:43-50.