Biology 5325:    Protein Structure and Function                    Fall 2006

Class Meetings:  Tuesday and Thursday, 8:15-9:45, 521 Medical Library
Coursemaster:    Jay Ponder  (CCB 208, 362-4195, ponder@dasher.wustl.edu)

Aug 31  Taxonomy I: Primary & Secondary Structure                   Ponder
Sep 5   Taxonomy II: Motifs & Supersecondary Structure              Ponder
Sep 7   Taxonomy III: Tertiary Structure & Fold Types               Ponder
Sep 12  Folding I: Forces that Determine Protein Structure          Ponder
Sep 14  Folding II: Mechanisms of Protein Folding                   Ponder
Sep 19  Folding III: Characterization of Folding Pathways           Ponder
Sep 21  Folding IV: Mutagenesis Studies                             Ponder
Sep 26  Special Topics I: Multiscale Modeling of Electrostatics     Baker
Sep 28  Spectroscopy I: Background and Basic Principles             Pryse
Oct 3   Spectroscopy II: Absorption and Fluorescence                Elson
Oct 5   Spectroscopy III: Circular Dichroism and Optical Rotation   Elson
Oct 10  Spectroscopy IV: Fluctuation Spectroscopy                   Elson
Oct 12  Spectroscopy V: Mass Spectrometry                           Chivers
Oct 17  Protein Design I: Structural Scaffolds                      Chivers
Oct 19  Protein Design II: Enzymatic Function                       Chivers
Oct 24  Mid-Term Examination
Oct 26  NMR I: Basic NMR Principles and Parameters                  Cistola
Oct 31  NMR II: Vector & Product Operator Formalisms                Cistola
Nov 2   NMR III: Heteronuclear Correlation Experiments              Cistola
Nov 7   NMR IV: Resonance Assignment Strategies                     Cistola
Nov 9   NMR V: Protein Structure Determination                      Cistola
Nov 14  Special Topics II: 19F NMR Studies of Protein Folding       Frieden
Nov 16  Special Topics III: GPCR Signal Transduction                Marshall
Nov 21  NMR VI: Ligand-Protein Interactions                         Cistola
Nov 23  Thanksgiving Break ­ No Class Meeting
Nov 28  X-Ray I: Crystals, Symmetry & Diffraction Patterns          Ellenberger
Nov 30  X-Ray II: Reciprocal Space, Bragg's Law, Laue's Equations   Ellenberger
Dec 5   X-Ray III: Structure Factors, Density & Patterson Maps      Ellenberger
Dec 7   X-Ray IV: Phase Determination Methods & Refinement          Ellenberger
Dec 12  X-Ray V: Protein Crystallography in Practice                Ellenberger
Dec 19  Final Examination

Classes are held in the DBBS Classroom (521 Medical Library, 5th Floor).
Bio 5325 is required by the Graduate Programs in Biochemistry and in
Molecular Biophysics. Lectures coincide with the corresponding Medical
School course; 1st-year Medical and MSTP students may substitute Bio 5325
for credit.

There are no required textbooks. However, the following books may be useful
for parts of the course, and are available from online booksellers:

Introduction to Protein Structure, 2nd Ed., Branden and Tooze, 1999
Protein Structure and Function, Petsko and Ringe, 2004
Principles of Physical Biochemistry, 2nd Ed., van Holde, Johnson and Ho, 2005