20.109(S08):Student presentations (M2D8)

Instructions
The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to the primary research articles on this list. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Search pubmed yourself to find articles of interest to you. Once you have decided on a paper for your presentation, please email the citation to astachow AT mit DOT edu, and also "reserve" it by putting your (initials/lab section/team color) next to the listing here. As you prepare your talk be sure to follow the specific guidelines for oral presentations in this class.

For visibility, please use the following format to sign up if possible, substituting in your own initials and team colour: [ANS/WF/Purple]. Thanks!

Note: If you have trouble accessing your article directly, go to http://libraries.mit.edu/vera, which is MIT's collection of journals online. Try selecting "exact title" from the search pulldown menu if the name of your journal is a common word such as Science. For older articles, you need to choose the JSTOR rather than Highwire interface.

Rational design

 * 1) Kaplan, J. & DeGrado, W. F. (2004) De novo design of catalytic proteins. Proc Natl Acad Sci U S A 101, 11566-70. [ZBBH/WF/Green]
 * 2) Leatherbarrow, R. J., Fersht, A. R. & Winter, G. (1985) Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering. Proc Natl Acad Sci U S A 82, 7840-4. PubMed link [EJO/TR/Purple]
 * 3) Looger, L. L., Dwyer, M. A., Smith, J. J. & Hellinga, H. W. (2003) Computational design of receptor and sensor proteins with novel functions. Nature 423, 185-90. PubMed link [JIG/WF/Pink]
 * 4) Pomerantz, J. L., Sharp, P. A. & Pabo, C. O. (1995) Structure-based design of transcription factors. Science 267, 93-6. PubMed link [JJ/WF/Blue] #Sarkar, C. A., Lowenhaupt, K., Horan, T., Boone, T. C., Tidor, B. & Lauffenburger, D. A. (2002) Rational cytokine design for increased lifetime and enhanced potency using pH-activated "histidine switching". Nat Biotechnol 20, 908-13. PubMed link [KAA/TR/Yellow]
 * 5) Serrano, L., Neira, J. L., Sancho, J. & Fersht, A. R. (1992) Effect of alanine versus glycine in alpha-helices on protein stability. Nature 356, 453-5. PubMed link [MLM/TR/Pink]
 * 6) Shifman, J. M. & Mayo, S. L. (2003) Exploring the origins of binding specificity through the computational redesign of calmodulin. Proc Natl Acad Sci U S A 100, 13274-9. PubMed link [JJQ/TR/Blue] [EL/WF/Green]
 * 7) Spencer, D. M., Wandless, T. J., Schreiber, S. L. & Crabtree, G. R. (1993) Controlling signal transduction with synthetic ligands. Science 262, 1019-24. PubMed link [BE/TR/Red]

Review Articles (for reference only)

 * 1) Brannigan, J. A. & Wilkinson, A. J. (2002) Protein engineering 20 years on. Nat Rev Mol Cell Biol 3, 964-70. PubMed link
 * 2) Peisajovich, S. G. & Tawfik, D. S. (2007) Protein engineers turned evolutionists. Nat Methods 4, 991-4. PubMed link

High throughput and directed evolution approaches

 * 1) Boder, E. T. & Wittrup, K. D. (1997) Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol 15, 553-7. PubMed link
 * 2) Ellington, A. D. & Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-22. PubMed link [KBP/WF/Yellow] [SM/WF/Purple].
 * Li, Y., Drummond, D. A., Sawayama, A. M., Snow, C. D., Bloom, J. D. & Arnold, F. H. (2007) A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments. Nat Biotechnol 25, 1051-6. PubMed link]
 * 1) Lowman, H. B., Bass, S. H., Simpson, N. & Wells, J. A. (1991) Selecting high-affinity binding proteins by monovalent phage display. Biochemistry 30, 10832-8. PubMed link [MEC/TR/Yellow]
 * 2) Masip, L., Pan, J. L., Haldar, S., Penner-Hahn, J. E., DeLisa, M. P., Georgiou, G., Bardwell, J. C. & Collet, J. F. (2004) An engineered pathway for the formation of protein disulfide bonds. Science 303, 1185-9.  PubMed link
 * 3) Mazor, Y., Van Blarcom, T., Mabry, R., Iverson, B. L. & Georgiou, G. (2007) Isolation of engineered, full-length antibodies from libraries expressed in Escherichia coli. Nat Biotechnol 25, 563-5. PubMed link [CM/TR/Purple]  [YG/WF/Yellow]
 * 4) Pollack, S. J., Jacobs, J. W. & Schultz, P. G. (1986) Selective chemical catalysis by an antibody. Science 234, 1570-3. PubMed link [EBH/WF/Red]
 * 5) Whaley, S. R., English, D. S., Hu, E. L., Barbara, P. F. & Belcher, A. M. (2000) Selection of peptides with semiconductor binding specificity for directed nanocrystal assembly. Nature 405, 665-8. PubMed link [AMR/TR/Blue].

Imaging and sensors

 * 1) Fernandez-Suarez, M., Baruah, H., Martinez-Hernandez, L., Xie, K. T., Baskin, J. M., Bertozzi, C. R. & Ting, A. Y. (2007) Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes. Nat Biotechnol 25, 1483-7. PubMed link [YH/TR/Green]
 * 2) Galarneau, A., Primeau, M., Trudeau, L. E. & Michnick, S. W. (2002) Beta-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions. Nat Biotechnol 20, 619-22. PubMed link [WJG/TR/Pink]
 * 3) Heim, N., Garaschuk, O., Friedrich, M. W., Mank, M., Milos, R. I., Kovalchuk, Y., Konnerth, A. & Griesbeck, O. (2007) Improved calcium imaging in transgenic mice expressing a troponin C-based biosensor. Nat Methods 4, 127-9.PubMed link [SP/TR/Green] [RM/WF/blue]
 * 4) Loening, A. M., Wu, A. M. & Gambhir, S. S. (2007) Red-shifted Renilla reniformis luciferase variants for imaging in living subjects. Nat Methods 4, 641-3.  PubMed link
 * 5) Miyawaki, A., Llopis, J., Heim, R., McCaffery, J. M., Adams, J. A., Ikura, M. & Tsien, R. Y. (1997) Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388, 882-7. PubMed link
 * 6) Ohki, K., Chung, S., Ch'ng, Y. H., Kara, P. & Reid, R. C. (2005) Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature 433, 597-603. PubMed link [RR/WF/Purple]
 * 7) Orger, M. B., Kampff, A. R., Severi, K. E., Bollmann, J. H. & Engert, F. (2008) Control of visually guided behavior by distinct populations of spinal projection neurons. Nat Neurosci 11, 327-33. PubMed link [EK/WF/Pink]
 * 8) Tour, O., Adams, S. R., Kerr, R. A., Meijer, R. M., Sejnowski, T. J., Tsien, R. W. & Tsien, R. Y. (2007) Calcium Green FlAsH as a genetically targeted small-molecule calcium indicator. Nat Chem Biol 3, 423-31. PubMed link

Review Articles (for reference only)

 * 1) Tsien, R. Y. (2003) Imagining imaging's future. Nat Rev Mol Cell Biol Suppl, SS16-21.

For next time

 * 1) Complete the final, short assignment in your portfolio: Part 4.
 * 2) An awareness of your own strengths and weaknesses can often help you improve your future work. After you give your presentation today, write a brief self-evaluation. Specifically, describe (in a short phrase or sentence each) two things that you thought you did well, and two that could use improvement. Feel free to include both big-picture and detail-oriented comments.