BIOL 6312
Proteins: Structure, Function, and Design
Spring 2005
Instructor: Steven Vik (214) 768-4228
Class: M 1:00-4:00 132DLS
email: svik@smu.edu
WWW: http://svik.life.smu.edu or faculty.smu.edu/svik
Tentative Schedule
| Date |
Topics
|
Readings:Petsko&Ringe | |
| Jan 14 | Introduction to the Class | Tentatively | |
| Jan 17 | Holiday | ||
| Jan 24 | Interactions in proteins, Secondary Structure | HW#1, Jan 31 | Ch 1-0----1-7 |
| Jan 31 | Properties of Amino Acids, Helix Capping | HW#2 (pdf) | |
| Feb 7 | Protein Folding, Tertiary Structure, | RasMol | Ch 1-9, 10, 13, 14 |
| Feb 14 | Structural Motifs, all alpha folds, coiled coils | RasMol 2 | Ch 1-14---1-17, 1-19 |
| Feb 21 | All beta, alpha/beta, alpha+beta, irregular | HW#3 | Ch 1-17---1-18 |
| Feb 28 | Quaternary Structure | Lab RasMol images |
Ch 1-19---1-22 |
| Mar 7 | Protein purification, X-ray crystallography, Presentations | Ch 5 | |
| Mar 14 | Spring Break | ||
| Mar 21 | Active Sites,Protein Flexibility, Ligand Binding, | Jmol lab template |
Ch 2-0---2-5 |
| Mar 28 | Catalysis, , | Jmol lab | Ch 2-6---2-16 |
| Apr 4 | Midterm Exam | ||
| Apr 11 | G proteins, motor proteins, Sequence Analysis | HW#5 | Ch 3-0, 3-1, 3-4---3-10 |
| Apr 18 | Regulation, Protein Modifications, Structure Predictions | HW#6 | Ch 3-11---3-17 |
| Apr 25 | Prions, Serpins, Membrane proteins | Ch 1-11, 3-18---3-20, 4-15 | |
| May 5 | Presentations, Paper due |
The text for the course:
Protein Structure and Function (2004), available in the SMUBookstore
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 two molecular visualization applications:
Jmol Version 10.0 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 moleculaes on web pages.
RasMol Version 2.7.2.2 is also free, open-source software. It is a stand-alone application that can be used for making images of molecules, or can be used in conjunction with Jmol. Download
Grading will be based on one exam, given at midterm, probably April 4 (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 May 5, Thursday of Finals week, at 11:30 AM (1/3). The paper will be presented in class during the scheduled Final exam. 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 2005, Steven B. Vik, Southern Methodist University