The reading assignments listed below show what you should read before coming to class. You are expected to come to class prepared to discuss the assigned articles.
| SES # | TOPICS | READINGS |
|---|---|---|
| 1 | Introduction | |
| 2 | Library generation by point mutation |
Cadwell, R. C., and G. F. Joyce. "Randomization of Genes by PCR Mutagenesis." PCR Methods Applic 2 (1992): 28-33. Kegler-Ebo, D. M., C. M. Docktor, and D. DiMaio. "Codon Cassette Mutagenesis: A General Method to Insert or Replace Individual Codons by using Universal Mutagenic Cassettes." Nuc Acids Res 22 (1994): 1593-1599. |
| 3 | Library generation by recombination |
Zhao, H., L. Giver, A. Shao, J. A. Affholter, and F. A. Arnold. "Molecular Evolution by Staggered Extension Process (StEP) in vitro Recombination." Nature Biotechnol 16 (1998): 258-261. Stemmer, W. P. C. "Rapid Evolution of a Protein in vitro by DNA Shuffling." Nature 370 (1994): 389-391. |
| 4 | Alternative methods for library generation |
Lai, Y.-P, J. Huang, L.-F. Wang, J. Li, and Z.-J. Wu. "A New Approach to Random Mutagenesis in vitro." Biotech Bioeng 86 (2004): 622-627. Coia, G., A. Ayres, G. G. Lilley, P. J. Hudson, and R. A. Irving. "Use of Mutator Cells as a Means for Increasing Production Levels of a Recombinant Antibody Directed Against Hepatitis B." Gene 201 (1997): 203-209. |
| 5 | Enzyme evolution by genetic complementation |
Yano, T., S. Oue, and H. Kagamiyama. "Directed Evolution of an Aspartate Aminotransferase with New Substrate Specificities." PNAS 95 (1998): 5511-5515. Otten, L. G., C. F. Sio, J. Vrielink, R. H. Cool, and W. J. Quax. "Altering the Substrate Specificity of Cephalosporin Acylase by Directed Evolution of the β-Subunit." J Biol Chem 277 (2002): 42121-42127. |
| 6 | Enzyme evolution by chemical complementation |
Baker, K., C. Bleczinski, H. Lin, G. Salazar-Jimenez, D. Sengupta, S. Krane, and V. W. Cornish. "Chemical Complementation: A Reaction-independent Genetic Assay for Enzyme Catalysis." PNAS 99 (2002): 16537-16542. Azizi, B., E. I. Chang, and D. F. Doyle. "Chemical Complementation: Small-Molecule-Based Genetic Selection in Yeast." Biochem Biophys Res Commun 306 (2003): 774-780. Lin, H., H. Tao, and V. W. Cornish. "Directed Evolution of a Glycosynthase via Chemical Complementation." J Am Chem Soc 126 (2004): 15051-15059. |
| 7 | Enzyme evolution using phage display |
Smith, G. P. "Filamentous Fusion Phage: Novel Expression Vectors that Display Cloned Antigens on the Virion Surface." Science 228 (1985): 1315-1317. Ponsard, I., M. Galleni, P. Soumillion, and J. Fastrez. "Selection of Metalloenzymes by Catalytic Activity using Phage Display and Catalytic Elution." Chembiochem 2 (2001): 253-259. |
| 8 | Enzyme evolution using phage display (cont.) |
Strobel, H., D. Ladant, and J. L. Jestin. "In vitro Selection for Enzymatic Activity: A Model Study using Adenylate Cyclase." J Mol Biol 332 (2003): 1-7. Pedersen, H., S. Holder, D. P. Sutherlin, U. Schwitter, D. S. King, and P. G. Schultz. "A Method for the Directed Evolution and Functional Cloning of Enzymes." Proc Natl Acad Sci USA 95 (1998): 10523-10528. |
| 9 | Enzyme evolution using bacterial cell surface display |
Olsen, M. J., D. Stephens, D. Griffiths, P. Daughtery, G. Georgiou, and B. L. Iverson. "Function-Based Isolation of Novel Enzymes from a Large Library." Nat Biotechnol 18 (2000): 1071-1074. Kim, Y.-S., H.-C. Jung, and J.-G. Pan. "Bacterial Cell Surface Display of an Enzyme Library for Selective Screening of Improved Cellulose Variants." App Environ Microbiol 66 (2000): 788-793. |
| 10 | Enzyme evolution using yeast surface display |
Boder, E. T., and K. D. Wittrup. "Yeast Surface Display for Screening Combinatorial Polypeptide Libraries." Nat Biotechnol 15 (1997): 553-557. Shiraga, S., M. Kawakami, M. Ishiguro, and M. Ueda. "Enhanced Reactivity of Rhizopus Oryzae Lipase Displayed on Yeast Cell Surfaces in Organic Solvents: Potential as a Whole-cell Biocatalyst in Organic Solvents." App Environ Microbiol 71 (2005): 4335-4338. |
| 11 | Enzyme evolution using ribosome display |
Amstutz, P., J. N. Pelletier, A. Guggisberg, L. Jermutus, S. Cesaro-Tadic, C. Zahnd, and A. Pluckthun. "In vitro Selection for Catalytic Activity with Ribosome Display." JACS 124 (2002): 9396-9403. Takahashi, F., H. Funabashi, M. Mie, Y. Endo, T. Sawasaki, M. Aizawa, and E. Kobatake. "Activity-based in vitro Selection of T4 DNA Ligase." Biochem Biophys Res Commun 336 (2005): 987-993. |
| 12 | Enzyme evolution by in vitro compartmentalization |
Tawfik, D. S., and A. D. Griffiths. "Man-Made Cell-like Compartments for Molecular Evolution." Nat Biotechnol 16 (1998): 652-656. ———. "Directed Evolution of an Extremely Fast Phosphotriesterase by in vitro Compartmentalization." EMBO J 22 (2003): 24-35. |
| 13 | Alternative methods for enzyme/catalyst design |
Hill, C. M., W.-S. Li, J. B. Thoden, H. M. Holden, and F. M. Raushel. "Enhanced Degradation of Chemical Warfare Agents through Molecular Engineering of the Phosphotriesterase Active Site." JACS 125 (2003): 8990-8991. Williams, G. J., T. Woodhall, A. Nelson, and A. Berry. "Structure-guided Saturation of N-Acetylneuraminic Acid Lyase for the Synthesis of Sialic Acid Mimetics." Prot Eng Des Select 18 (2005): 239-246. Reetz, M. T., M. Bocola, J. D. Carballeira, D. Zha, and A. Vogel. "Expanding the Range of Substrate Acceptance of Enzymes: Combinatorial Active-Site Saturation Test." Angew Chem Int Ed 44 (2005): 4192-4196. |
| 14 | Student presentations |