CHEM-645 Protein Structure and FunctionFall 2009, Wednesday 6-9 pm, 221 Brown LabProf. Brian Bahnson, 312 Drake Hall, phone: 831-0786, bahnson@udel.edu Course web page: http://www.udel.edu/chem/bahnson/chem645/ Office hours: by appointment Textbooks and reference materials Class schedule - updated regularly Modeling -part II- coming soon Outline of course: The course will begin with an overview of structural biology, including how X-ray crystallography, NMR spectroscopy, homology modeling and other techniques are used to solve structures and develop models of macromolecules. Then representative classes of proteins will be discussed in terms of how the protein's structure relates to its function. This class is meant for both people directly interested in structural biology, as well as those that plan to collaborate with structural biologists. X-ray crystallography vs. NMR spectroscopy - Each method has advantages and disadvantages. Also each technique supplies different information. Topics that will be covered include: crystal growth and sample preparation, data collection and instrumentation, methods to obtain phases or obtain NMR distance restraints, model building and model refinement. Next we'll go through a homology modeling assignment. Your in class presentations and final projects will bring other related topics into our discussion. Examples of information about structure and dynamics from other methods include: CD, UV/VIS, raman, FT-IR, mass spec, fluorescence, genomics, structure prediction, protein folding, can structure be predicted ab initio? Modeling the dynamics of protein motion - molecular dynamics, potential energy functions, energy minimization, functional role of proteins in biological systems- enzymes, transporters, ion channels, energy transducers, signal transduction, molecular motors, structural scaffolds, gene expression, etc... "Crystallography Made Crystal Clear, A Guide for User's of Macromolecular Models" by Gale Rhodes, Third Edition, Academic Press (2006) ISBN 0-12-587073-6 You should have and refer to a decent biochemistry textbook. Review articles and primary literature will be used extensively.
Other useful texts - available to borrow short term from my office. "Introduction to Protein Structure" by Branden & Tooze, Second Edition (1999). "Protein Structure and Function" by Gregory A. Petsko and Dagmar Ringe, Sinauer Associates, Inc. (2003) "Nuclear Magnetic Resonance" by P. J. Hore (Oxford Chemistry Primers, 32) (1995). "Crystallization of Biological Macromolecules" by Alexander McPherson, Cold Spring Harbor Laboratory Press (1999) "Practical Protein Crystallography", by Dunan E. McRee, AcademicPress (1993) "Protein NMR Spectroscopy: Principles and Practice", by John Cavanagh, Academic Press (1996) "X-Ray Structure Determination: A Practical Guide", 2nd Edition by George H. Stout, Lyle H. Jensen, John Wiley & Sons (1989) and others... Midterm exam - 25% - take home. Homology modeling assignment(s) - 30% - will be problem set based and will utilize the primary literature, the world wide web, and classroom linux computers. You will be encouraged to load much of the software (freeware) on your own computers. Research Paper Discussions - 20% - our last ~4 weeks of class will be devoted to in depth discussion of primary litterature on selected topics. You will each be assigned a portion of the topic to lead the discussion on. Class participation - 25%.
http://www.udel.edu/chem/bahnson/chem645/ updated 11/9/09 |
