BIOM 230, FALL
2008, SCHEDULE |
Dr. Tracy Handel
|
|
07/16/08 |
Course Directors
|
Text: Handouts and Assigned Reading By
Lecturers
|
Week |
Date |
Topic |
Reading |
Lecturer |
|
1 |
Th 9/25 |
Intro to Course Review Principles of
Protein Structure |
|
Handel |
|
Tu 9/26 |
NMR |
|
Handel |
|
|
2 |
Tu 9/30 |
X-ray Crystallography |
|
TBD |
|
Th 10/2 |
Electron Microscopy/CryoEM |
|
Dorit Hanein |
|
|
Fri 10/3 |
Visualization and Analysis
Tools I Web-based |
|
PeterRose/Andreas (Bourne) |
|
|
3 |
Tu 10/7 |
Protein Thermodynamics and
Stability I |
|
R. Abagyan |
|
Th 10/9 |
Protein Thermodynamics and
Stability II |
|
R. Abagyan |
|
|
Fri 10/10 |
Molecular Modeling/Molsoft
ICM Visualization and Analysis Tools II |
|
R. Abagyan |
|
|
4 |
Tu 10/14 |
Enzyme Kinetics I: Catalysis |
|
J. Adams |
|
Th 10/16 |
Enzyme Kinetics II: Catalysis |
|
J. Adams |
|
|
Fri 10/17 |
PreSteady State and Rapid
Kinetics |
|
Dmitri Davydov |
|
|
5 |
Tu 10/21 |
Protein-Protein
Interactions with Focus on Fluorescence/FRET |
|
Dmitri Davydov |
|
Th 10/23 |
Mathematical Methods of
Spectral Analysis |
|
Dmitri Davydov |
|
|
Fri 10/24 |
Receptor:Ligand Binding I |
|
Handel |
|
Week |
Date |
Topic |
Reading |
Lecturer |
|
6 |
Tu 10/28 |
Receptor:Ligand Binding II |
|
Handel |
|
Th 10/30 |
Mass Spectrometry I |
|
Pieter Dorrestein |
|
|
Fri 10/31 |
Mass Spectrometry II |
|
Pieter Dorrestein |
|
|
7 |
Tu 11/4 |
Structure selection
criteria and tools for selection and analysis |
|
PeterRose/Andreas (Bourne) |
|
Th 11/6 |
Off-target Binding |
|
Bourne |
|
|
Fri 11/7 |
TBD or No class |
|
|
|
|
8 |
Tu 11/11 |
Holiday |
|
|
|
Th 11/13 |
Docking Lab/Drug Receptor
Interactions (1-3pm) |
|
Michael/Bourne |
|
|
Fri 11/14 |
Small Angle X-ray
Scattering and Bioinformatic Analysis of Complexes |
|
Susan Taylor |
|
|
9 |
Tu 11/18 |
GPCRs Structure and
Activation Mechanisms |
|
Student Presentations |
|
Th 11/20 |
G proteins |
|
Student Presentations |
|
|
Fri 11/21 |
Protein Kinase Structure
and Activation |
|
Student Presentations |
|
|
10 |
Tu 11/25 |
Phosphatases |
|
Student Presentations |
|
Th 11/27 |
Holiday |
|
|
|
|
Fri 11/28 |
Holiday |
|
|
|
|
11 |
Tu 12/2 |
In Vivo Studies of
Signaling Complexes |
|
Student Presentations |
|
Th 12/4 |
Ligand Gated Ion Channels |
|
Student Presentations |
|
|
Fri 12/05 |
Voltage Gated Ion Channels |
|
Student Presentations |
Long versions
Biom230,
Structural and Quantitative Pharmacology:
The goal of this course is to give students a
foundation in more quantitative approaches to studying topics in pharmacology.
The first 2/3 of the course will be didactic and focused on topics related to
protein structure, thermodynamic stability, energetics and interactions. Lectures will fall into three general
classes: theoretical (structure,
forces that stabilize proteins, thermodynamic stability, receptor-ligand
binding theory, enzyme kinetics), methods (crystallography, NMR, mass
spectrometry, fluorescence), and practical approaches (tools for visualization
of structures, protein-ligand docking,
mathematical analysis of data). The last part of the course will be
student driven with presentations on various topics in pharmacology that
utilize quantitative concepts covered in the first part of the course, and
present the current state of knowledge as well as future directions and
questions. Examples include structure and activation mechanisms of GPCRs, G
proteins, and Ion Channels. Grades will be based on the presentation and a
short research proposal related to the presentation, as well as student
participation throughout the course.
40
Word Limit Version
This course is essentially biophysical
pharmacology. 2/3 will be didactic, covering: protein structure, thermodynamic
stability, receptor-ligand binding, enzyme kinetics, biophysical methods,
visualization of structures/docking, mathematical analysis of data. The last
section will involve student presentations of topics in biophysical
pharmacology.