9/1 Introduction
- Syllabus for Chem 401
- Instructions for final paper
- Sign up sheet for food and presentations
9/8 Competing Protocells
- Chen et al. (2004) The Emergence of Competition Between Model Protocells. Science 305, 1474.
- Adamala and Szostak (2013) Competition between model protocells driven by an encapsulated catalyst. Nat. Chem., 5, 495.
- Guiding questions for this week's readings.
- Nice introduction to FRET.
9/15 Stapled Helices
- Schafmeister et al. (2000) An All-Hydrocarbon Cross-Linking System for Enhancing the Helicity and Metabolic Stability of Peptides. JACS, 122, 5891.
- Walensky et al. (2004) Activation of Apoptosis in Vivo by a Hydrocarbon-Stapled BH3 Helix. Science 305, 1466.
9/22* Prions
- Smirnovas et al. (2011) Structural organization of brain-derived mammalian prions examined by hydrogen-deuterium exchange Nat. Struct. Mol. Biol. 18, 504.
- Chattopadhyay et al. (2008) Initiation and elongation in fibrillation of ALS-linked superoxide dismutase PNAS, 105, 18663.
- Paul et al. (2015) Generating new prions by targeted mutation or segment duplication PNAS, 112, 8584.
9/29* Alternate Nucleic Acids
- Kolganova et al. (2012) Targeting duplex DNA with chimeric a,b-triplex-forming oligonucleotides. NAR 40, 8187.
- Yang et al. (2011) Amplification, Mutation, and Sequencing of a Six-Letter Synthetic Genetic System JACS, 133, 38.
- Malyshev et al. (2013) A semi-synthetic organism with an expanded genetic alphabet Nature, 509, 385.
10/6 CRISPR
- Haurwitz et al. (2010) Sequence- and Structure-Specific RNA Processing by a CRISPR Endonuclease Science 329, 1355.
- Jinek et al. (2012) A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity Science, 337, 816.
10/13 Olfaction
- Gane et al. (2003) Molecular Vibration-Sensing Component in Human Olfaction PLOSone DOI: 10.1371/journal.pone.0055780
- Block et al. (2015) Implausibility of the vibrational theory of olfaction PNAS, 112, E2766.
10/27* Engineering Membrane Proteins
- Joh et al. (2014) De novo design of a transmembrane Zn2+-transporting four-helix bundleScience, 346, 1520.
- Slovic et al. (2004) Computational design of water-soluble analogues of the potassium channel KcsA PNAS, 101, 1828.
11/3* Modification of the Cell Surface
- Shieh et al. (2012) Fluorogenic Azidofluoresceins for Biological Imaging JACS, 134, 17428.
- Li et al. (2011) Spatial control of cell fate using synthetic surfaces to potentiate TGF-β signaling PNAS 108, 11745.
- Porterfield et al. (2011) A "Caged" Luciferin for Imaging Cell-Cell Contacts JACS 137, 8656.
11/10* Chemical Control of Cellular Signalling
- Shah et al. (1997) Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates PNAS, 94, 3565.
- Garske et al. (2011) Chemical genetic strategy for targeting protein kinases based on covalent complementarity PNAS, 108, 15046.
- Hobert et al. (2012) Rewiring Kinase Specificity with a Synthetic Adaptor Protein JACS 134, 3976.
11/17 Ketosteroid Isomerase
- Schwans et al. (2011) Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase. J Am Chem Soc 133, 20052–20055.
- Fried et al. (2014) Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science 346, 1510.
- Comments and Responses related to "Extreme electric fields power catalysis in the active site of ketosteroid isomerase."
11/24 Redox Chemistry in Transcriptional Regulation
- Gorodetsky et al. (2008) DNA binding shifts the redox potential of the transcription factor SoxR. PNAS 105, 3684.
- Lee et al. (2009) DNA-mediated redox signaling for transcriptional activation of SoxR. PNAS 106, 13164.
12/1 Unnatural Amino Acids
- Wang et al. (2001) Expanding the Genetic Code of Escherichia coli. Science 292, 498.
- Xiao et al. (2015) Exploring the potential impact of an expanded genetic code on protein function. PNAS 112, 6961.
