Engineering transcriptional regulator effector specificity using computational design and in vitro rapid prototyping: Developing a vanillin sensor

Synthetic Biology: Engineering, Evolution, and Design Conference 2015, SEED 2015

Volumn 2, Issue , 2015, Pages 852-880

  De Los Santos, E L C ^a   Meyerowitz, J T ^a   Mayo, S L ^a   Murray, R M ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Cell free systems; Computational protein design; In vitro biological circuit prototyping; Protein engineering; Synthetic biology

Indexed keywords

BIOCHEMICAL ENGINEERING; CELL ENGINEERING; MOLECULES; PROTEINS; RECONFIGURABLE HARDWARE; TRANSCRIPTION;

CELL-FREE SYSTEM; COMPUTATIONAL PROTEIN DESIGN; IN-VITRO; PROTEIN ENGINEERING; SYNTHETIC BIOLOGY;

BIOLOGY;

EID: 84964714807     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. Purnick, P. E. M., and Weiss, R. (2009) The second wave of synthetic biology: from modules to systems. Nature reviews. Molecular cell biology 10, 410â?422.
2. Ramos, J. L., Martinez-Bueno, M., Molina-Henares, A. J., TerÃjn, W., Watanabe, K., Zhang, X. D., Gallegos, M. T., Brennan, R., and Tobes, R. (2005) The TetR family of transcriptional repressors. Microbiology and Molecular Biology Reviews 69, 326â?+.
3. Elowitz, M. B., and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403, 335â?338.
4. Gardner. T. S. Cantor. C. R. and Collins. J. J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339â?342.
5. Grkovic, S., and Hardie, K. M., Brown, M. H., and Skurray, R. A. (2003) Interactions of the QacR multidrug-binding protein with structurally diverse ligands: implications for the evolution of the binding pocket. Biochemistry 42, 15226â?15236. 16
6. Schumacher, M. A., Miller, M. C, Grkovic, S., and Brown, M. H., Skurray, R. A., and Brennan, R. G. (2001) Structural mechanisms of QacR induction and multidrug recognition. Science 294, 2158â?2163.
7. Schumacher, M. A., and Brennan, R. G. (2003) Deciphering the molecular basis of multidrug recognition: Crystal structures of the Staphylococcus aureus multidrug binding transcription regulator QacR. Research in Microbiology 154, 69â?77.
8. Peters, K. M., and Brooks, B. E., Schumacher, M. A., Skurray, R. A., and Brennan, R. G., and Brown, M. H. (2011) A single acidic residue can guide binding site selection but does not govern QacR cationic-drug affinity. PLoS ONE 6, e15974.
9. Klinke, H. B., Thomsen, ABâ? and Ahring, B. K. (2004) Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomass. Applied Microbiology and Biotechnology 66, 10â?26.
10. Bochevarov, A. D., Harder, E., Hughes, T. F., and Greenwood, J. R., Braden, D. A., Philipp, D. M., Rinaldo, D., and Halls, M. D., Zhang, J., and Friesner, R. A. (2013) Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences. International Journal of Quantum Chemistry 113, 2110â?2142.
11. Lassila, J. K., and Privett, H. K., Allen, B. D., and Mayo, S. L. (2006) Combinatorial methods for small-molecule placement in computational enzyme design. Proceedings of the National Academy of Sciences of the United States of America 103, 16710â?16715.
12. Kuhlman, B., Dantas, G., Ireton, G. C, Varani, G., and Stoddard, B. L., and Baker, D. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302, 1364â?1368.
13. Allen, B. D., and Mayo, S. L. (2006) Dramatic performance enhancements for the FASTER optimization algorithm. Journal of Computational Chemistry 27, 1071â?1075. 17
14. Allen, B. D., and Mayo, S. L. (2010) An efficient algorithm for multistate protein design based on FASTER. Journal of Computational Chemistry 31, 904â?916.
15. Sun, Z. Z., and Hayes, C. A., Shin, J., Caschera, F., Murray, R. M., and Noireaux, V. (2013) Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology. Journal of visualized experiments: JoVE e50762.
16. Stanton, B. C., Siciliano, V., Ghodasara, A., Wroblewska, L., Clancy, K., Trefzer, A. C., and Chesnut, J. D., Weiss, R., and Voigt, C. A. (2014) Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian Cells. ACS synthetic biology
17. Lutz, R., and Bujard, H. (1997) Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/Il-I2 regulatory elements. Nucleic Acids Research 25, 1203â?1210. 18