|
Date
|
Topic
|
Assigned
Reading Due
|
|
1/9
|
Course Introduction
|
Molecular Machinery
Structural Biology of HIV
|
|
1/11
|
Protein Structure and Function: Overview
|
Chapter 1 - Crystallography Made Crystal Clear.pdf
|
|
1/13
|
Databases: Entrez
|
|
|
1/16
|
Martin
Luther King, Jr. Holiday, No Class
|
|
1/18
|
Sequence Analysis: BLAST and Multiple Alignments (Clustal)
|
Chapter 4: 4-0 to 4-3
The BLAST
Sequence Analysis Tool.pdf
|
|
1/20
|
Tools: Jalview
|
|
| 1/23 |
Amino acids and Basics of Protein Structure |
Chapter 1: 1-1 to 1-7
|
| 1/25 |
Introduction to Protein Folding |
Chapter 1: 1-8 to 1-22 |
| 1/27 |
Structural Domains |
Structural
Patterns in Globular Proteins.pdf
The Protein Chart
|
| 1/30 |
Tools 3: Introduction to the PDB |
|
|
2/1
|
Tools 4: UCSF Chimera
|
http://www.cgl.ucsf.edu/Outreach/Tutorials/GettingStarted.html
http://www.cgl.ucsf.edu/chimera/tutorials/semliki/semliki.html
|
| 2/3 |
Structural Basis of Protein Function |
Chapter 2: 2-1 to 2-6
Chapter 2: 2-7 to 2-16
|
| 2/6 |
|
|
| 2/8 |
Mechansims of Protein Regulation |
Chapter 3: 3-1 to 3-11
|
|
2/10
|
|
Chapter 3: 3-11 to 3-20
|
|
2/13
|
Review
|
|
2/15
|
Student Presentations |
|
2/17
|
Test 1 |
|
2/20
|
Small Molecule Docking
|
Small Molecule Docking.pdf
|
|
2/22
|
Tools: Autodock Vina
|
Autodock
Vina.pdf
Vina_tutorial.doc
|
|
2/24
|
Spectrophotometry: CD and Fluorescent Methods |
|
|
2/27
|
Calorimetric Methods: ITC and DSC |
|
|
2/29
|
Protein Interaction Analysis: SPR and Biacore |
|
|
3/2
|
Determination of Protein Structure: NMR methods
|
Chapter 5: 5-0 to 5-2
Wuthrich Nobel Lecture.pdf
Wuthrich_Protein Structure Determination in
Solution by NMR Spectroscopy.pdf
|
|
3/5
|
|
|
|
3/7
|
Protein Crystallization |
Chayen, N. E., and Saridakis,
E. (2008) Protein crystallization: from purified protein to
diffraction-quality
crystals. Nat. Methods 5:147-153.
Wlodawer, A., Minor, W., Dauter,
Z. and Jaskolski, M. (2008) Protein crystallography
for noncrystallographers,
or how to get the best
(but not more) from published macromolecular structures. FEBS J. 275(1):1-21. |
|
3/9
|
X-ray Diffraction Analysis of Protein Crystals |
|
|
3/12
|
Spring
Break
|
|
3/14
|
|
3/16
|
|
3/20
|
Phasing of Crystallographic Data |
|
|
3/22
|
Introduction to Model Building and Validation |
|
|
3/24
|
Tools: Coot
|
(17)
Coot_Tutorial.pdf
|
|
3/27
|
Protein Evolution
|
(19) Evolution of
Function in Protein Superfamilies from a structural
persp.pdf
(20) Evolution of
Enzyme Superfamilies.pdf
(21) Structural classification.pdf
|
|
3/29
|
|
|
|
4/2
|
Enzymes: Transferases
|
|
|
4/4
|
Enzymes: Hydrolases
|
|
|
4/6
|
Enzymes: Lyases
|
|
|
4/8
|
Enzymes: Isomerases
|
|
|
4/11
|
Enzymes: Ligases
|
|
|
4/13
|
Review |
|
4/15
|
Test
2
|
4/18
|
Final Presentations |
|
4/20
|
|
4/22
|
