De novo designed proteins from a library of artificial sequences function in Escherichia Coli and enable cell growth

PLoS ONE

Volumn 6, Issue 1, 2011, Pages

  Fisher, Michael A ^a,b   McKinley, Kara L ^a,c   Bradley, Luke H ^a,d   Viola, Sara R ^a,e   Hecht, Michael H ^a  

^a PRINCETON UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^d UNIVERSITY OF KENTUCKY   (United States)

^e NewYork Presbyterian Hospital   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CELL GROWTH; COMBINATORIAL LIBRARY; CONTROLLED STUDY; ESCHERICHIA COLI; GENE DELETION; IN VIVO STUDY; NONHUMAN; PROTEIN EXPRESSION; PROTEIN FUNCTION; GENE INACTIVATION; GENE LIBRARY; GENE TARGETING; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; MICROBIAL VIABILITY; NUCLEOTIDE SEQUENCE; PROTEIN ENGINEERING; SYNTHETIC BIOLOGY;

ESCHERICHIA COLI;

BACTERIAL PROTEINS; BASE SEQUENCE; ESCHERICHIA COLI; GENE KNOCK-IN TECHNIQUES; GENE KNOCKOUT TECHNIQUES; GENE LIBRARY; MICROBIAL VIABILITY; PROTEIN ENGINEERING; SYNTHETIC BIOLOGY;

EID: 79251539227     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0015364     Document Type: Article

References (25)

1. Pereto J, Catala J (2007) The renaissance of synthetic biology. Biol Theor 2: 128-130.
2. Cello J, Paul AV, Wimmer E (2002) Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science 297: 1016-1018.
3. Gibson DG, Glass JI, Lartigue C, Noskov VN, Chuang R-Y, et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329: 52-56.
4. Beasley JR, Hecht MH (1997) Protein design: The choice of de novo sequences. J Biol Chem 272: 2031-2034.
5. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: The Keio collection. Mol Syst Biol 2: 2006.0008.
6. International Human Genome Sequencing Consortium (2004) Finishing theeuchromatic sequence of the human genome. Nature 431: 931-945.
7. Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH (1993) Protein design by binary patterning of polar and nonpolar amino acids. Science 262: 1680-1685.
8. Hecht MH, Das A, Go A, Bradley LH, Wei Y (2004) De novo proteins from designed combinatorial libraries. Protein Sci 13: 1711-1723.
9. Nelson DL, Cox MM (2008) Lehninger, Principles of Biochemistry 5th ed. New York, W.H. Worth Publishers.
10. Xiong H, Buckwalter BL, Shieh HM, Hecht MH (1995) Periodicity of polar and nonpolar amino acids is the major determinant of secondary structure in selfassembling oligomeric peptides. Proc Natl Acad Sci USA 92: 6349-6353.
11. Bradley LH, Kleiner RE, Wang AF, Hecht MH, Wood DW (2005) An inteinbased genetic selection allows the construction of a high-quality library of binary patterned de novo protein sequences. Protein Eng Des Sel 18: 201-207.
12. Bradley LH, Wang AF, Platt J, Fisher MA, Korolev M, Hecht MH. A designed artificial proteome for high throughput screens and selections. In preparation.
13. Patel S, Bradley LH, Jinadasa S, Hecht MH (2009) Cofactor binding and enzymatic activity in an unevolved superfamily of de novo designed 4-helix bundle proteins. Protein Sci 18: 1388-1400.
14. Kitagawa M, Ara T, Arifuzzaman M, Ioka-Nakamichi T, Inamoto E, et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A complete Set of E. coli K-12 ORF Archive): Unique resources for biological research. DNA Res 12: 291-299.
15. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
16. Raymond KN, Dertz EA, Kim SS (2003) Enterobactin: An archetype formicrobial iron transport. Proc Natl Acad Sci USA 100: 3584-3588.
17. Patrick WM, Quandt E, Swartzlander D, Matsumura I (2007) Multicopysuppression underpins metabolic evolvability. Mol Biol Evol 24: 2716-2722.
18. Umbarger HE, Brown B (1957) Threonine deaminase in Escherichia coli:Evidence for two L- threonine deaminases. J Bacteriol 73: 105-112.
19. Wei Y, Kim S, Fela D, Baum J, Hecht MH (2003) Solution structure of a de novo protein from a designed combinatorial library. Proc Natl Acad Sci USA 100: 13270-13273.
20. Go A, Kim S, Baum J, Hecht MH (2008) Structure and dynamics of de novo proteins from a designed superfamily of 4-helix bundles. Protein Sci 17: 821-832.
21. Morett E, Saab-Rincón G, Olvera L, Olvera M, Flores H, et al. (2008) Sensitive Genome-Wide Screen for Low Secondary Enzymatic Activities: The YjbQFamily Shows Thiamin Phosphate Synthase Activity. J Mol Biol 376: 839-853.
22. Patrick WM, Matsumura I (2008) A study in molecular contingency: Glutamine phosphoribosylpyrophosphate amidotransferase is a promiscuous and evolvable phosphoribosylanthranilate isomerase. J Mol Biol 377, 323-336.
23. Scheich C, Kummel D, Soumailakakis D, Heinemann U, Bussow K (2007) Vectors for co-expression of an unrestricted number of proteins. Nucleic Acids Res 35: e43.
24. Rudd KE (2000) EcoGene: A genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28: 60-64.
25. Wei Y, Liu T, Sazinsky SL, Moffet DA, Pelczer I, et al. (2003) Stably folded de novo proteins from a designed combinatorial library. Protein Sci 12: 92-112.