Outline Of Class

Outline of “Protein structure, folding and functions” Wenqing Xu University of Washington Seattle, WA 98195-7420, USA Email: [email protected] September 12: 1. Basic principles of protein structure Protein secondary structures: mainchain H-bonds Organization of protein secondary elements Protein assembly 2. Protein folding: in vitro and in vivo - from sequence to structure Forces that determine protein structure Protein folding thermodynamic landscape: in vitro folding studies Protein folding in the cell: chaperones; folding vs. degradation; sorting etc. Protein misfolding and human diseases 3. Techniques for structural studies X-ray crystallography for a non-crystallographer Other tools for structural studies: NMR, Cryo-EM, Fluoresence/FRET, MS How to display and analyze a know protein structure: Pymol demo September 14: 4. Nucleic acid structures and protein-nucleic acid interactions DNA structure Protein-DNA interactions: specificity and major families Design of specific DNA binding proteins RNA structure 5. Protein-protein interactions Techniques for studying protein-protein interactions Protein-peptide interaction: induced folding Domain-domain interactions Intermolecular interaction vs. intramolecular interaction: Src regulation 6. Protein design and structure-based drug design Protein design and protein engineering: subtiligase Chemical genetics: identification of direct targets of protein kinases Chemical genetics: substrate trapping Structure-based drug design Paper for discussion: Song JJ, Smith SK, Hannon GJ, Joshua-Tor L. (2004). Crystal structure of Argonaute and its implications for RISC slicer activity. Science. 305, 1434-1437.