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CHEM528: Protein Structure and Function

CHEM524 Tentative Course Schedule

Note:  The following schedule is tentative and may change as needed

Updated 4 January, 2012 

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

 

 

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