Rasmol image of porin complex

BIOLOGY 303 Structure and Function of Proteins

Requirements (Spring 2011)

• Two take-home closed-book quizzes (20% each)
  • The first quiz will cover the first four lectures on “Protein structure”.
    The second quiz will cover the next four lectures on “Advanced protein topics”.
• Presentations and abstracts(15%) (ABSTRACT INSTRUCTIONS) (PRESENTATION INSTRUCTIONS)
  • You will choose a protein whose structure has been solved, ideally with a ligand bound.  Your goal is to study the binding site and redesign the site to accommodate a different, but presumably related, ligand.  My recommendation is that you read the primary literature describing your structure so that you have a good understanding of what is known.  You may wish to use a program such as Pymol to review the structure and to prepare graphics for your presentation.  Your presentation will be in the style of a defense with members of the class acting as a review panel led by a two-person chair and providing critical feedback.  As a consequence, you will need to provide an abstract of your presentation to the panel chairs on the class before your presentation so that they can have some idea of what you are presenting.  The abstract should include your reference list.  More information about the style of the presentation will be provided later.
• Specific requirements for presentations (link will be added later).
• Pre-review of abstracts (10%)
  • Panel chairs are responsible for reviewing the abstracts of the presentations prior to the presentation date.  A meeting with me prior to the date of the presentation will be required to review your questions and to help you in organizing class discussion.
• Panel chair responsibilities and panel summary (15%)
  • Panel chairs will be graded on: (1) quality of critical feedback; (2) engagement of class in discussion; and (3) quality of panel summary.  Panel summaries will need to be completed within 24 hours and provided to presenters, with copies to me as well, so that presenters may incorporate comments.
• Written proposals (20%)(PROPOSAL INSTRUCTIONS)
  • The written proposal will include your abstract, the basic elements from your presentation, the panel summary, a point-by-point description of your response to the panel summary, and a reference list.  More information on the style of your written proposal will be provided later.

Required textbooks and reading assignments:

• Introduction to Protein Structure 2^nd edition, Branden & Tooze, Garland Publishing.
• Select readings from Proteins: Structure and Molecular Properties, Creighton, W.H. Freeman & Co. At least one copy is on reserve in White Science Library (Harris South 3).
• Select articles from the journals (see syllabus).