BIOL 6312
Proteins: Structure, Function, and Design
Spring 2007
Instructor: Steven Vik (214) 768-4228
Class: M 1:00-4:00 130 DLS
email: svik@smu.edu
WWW: http://svik.life.smu.edu or faculty.smu.edu/svik
Tentative Schedule
| Date |
Topics
|
Lab/HW | Readings: Petsko&Ringe |
| Jan 15 | Holiday | ||
| Jan 22 | Interactions in proteins, Secondary Structure | HW#1, Jan 31 |
Ch 1-0----1-7 |
| Jan 29 | Properties of Amino Acids, Helix Capping | HW#2, Feb 14 |
Ch 1-8, Handout |
| Feb 5 | Protein Folding, Tertiary Structure, | Jmol lab | Ch 1-9, 10, 13, 14 |
| Feb 12 | Structural Motifs, all alpha folds, coiled coils | Jmol lab 2 | Ch 1-14---1-17, 1-19 |
| Feb 19 | All beta, alpha/beta, alpha+beta, irregular | HW#3 | Ch 1-17---1-18 |
| Feb 26 | Quaternary Structure | Jmol lab 3 |
Ch 1-19---1-22 |
| Mar 5 | Protein purification, X-ray crystallography, HW#3 Presentations | Ch 5 | |
| Mar 12 | Spring Break | ||
| Mar 19 | Active Sites, Protein Flexibility, Ligand Binding, Catalysis | Jmol lab 4 |
Ch 2-0---2-12 |
| Mar 26 | Midterm Exam | ||
| Apr 2 | More Catalysis, Control of Protein Function, G proteins, | Jmol lab 5 | Ch 2-13---2-16 Ch 3-0---3-9 |
| Apr 9 | Motor proteins, Regulation, Sequence Analysis | HW#5 | Ch 3-10---3-17 Ch 4-1---4-3 |
| Apr 16 | Regulation, Protein Modifications, Prions, Serpins, Structure Predictions | HW#6 | Ch 3-18---3-20 Ch-4-14---4-15 Ch-4-6---4-7 |
| Apr 23 | Membrane proteins | Ch 1-11, Handouts | |
| Apr 30 | No Class | ||
| May 4 | Student Presentations |
The text for the course:
Protein Structure and Function (2004), available in the SMU Bookstore
Gregory A. Petsko and Dagmar Ringe
Publisher's Website: http://www.new-science-press.com/browse/protein
Other reading material will be provided.
In the computer lab we will learn how to use molecular visualization applications:
Jmol Version 11.0 is now available for downloading. This is free, open-source software. It is based on the Java programming language. It runs as a free-standing application, and it can be used to host interactive molecules on web pages.
Grading will be based on one exam, given at midterm, probably March 26 (1/3), several homework assignments, primarily involving analysis of proteins by computer (1/3), and a review paper with web tutorial including a Jmol applet describing recent studies of a protein, a group of related proteins or a new approach to the study of proteins, etc., due about May 4, Friday of Finals week, at 11:30 AM (1/3). The paper will be presented at a time to be determined later. The topic should be chosen in consultation with the instructor. Sample topics will be provided later.
Final Project Description-PDF file
Comments/questions: email me
Copyright 2007, Steven B. Vik, Southern Methodist University