Graduate Protein Crystallography
Graduate Protein Crystallography & Proteiin Structure
Wed. 10:00 A.M. – 12:00 P.M.
Room: Biomed I Room 200
IMPORTANT CLASS UPDATES
|1||Aug 24||Overview of Crystallography:||KIV|
|2||Aug 31||Crystal Symmetry ( Crystal lattice, point group, Space group)||KIV|
|3||Sep 7||Molecular modeling||CC|
|4||Sep 14||Theory of X-ray Diffraction||KIV|
|5||Sep 21||Fourier transforms, Patterson Function, Phase problem||KIV|
|6||Sep 28||Structure solution of a small molecule (Location of a heavy atom – heavy atom phased Fourier, refinement). Class room + Computer lab||KIV|
|7||Oct 5||Isomorphous Replacement , Anomalous dispersion Techniques and Molecular Replacement technique||KIV|
|8||Oct 12||Principles of protein folding (1 hour)||RC|
|Oct 12||Midterm exam||KIV, CC|
|9||Oct 19||Crystallization of proteins:||RC|
|10||Oct 26||Crystallization ( Lab)||RC/KIV|
|11||Nov 2||Data Collection data processing ( Lab): R-axis||KIV|
|12||Nov 9||Model Building, Structure Refinement and validation||KIV|
|13||Nov 16||Protein structure solution: (Molecular Replacement technique, model building and refinement). ( lab)||KIV|
|14||Nov 23||Protein Modeling||CC|
|15||Nov 30||Ligand Docking /drug design||CC|
|16||Dec 7||Final Exam||KIV, RC, CC|
PHYO 5012 Protein Crystallography and Protein Structure (I):
The goal of this course is to provide a basic knowledge for analyzing molecular structure using x-ray crystallographic techniques. The topics will include the general principles of x-ray diffraction, crystallization techniques and model building. The course is also intended to give the students an insight into structure-function relationships of biological molecules.
An outline of the course: Crystallography is the most powerful tool to elucidate 3-dimensional structures of molecules or molecular assemblies. X-ray diffraction of single crystals is being used to solve structures of small organic/inorganic molecules and also very large assemblies like viruses or ribosome.
The course will comprise mostly of lectures, but there will be a few labs where students will have a hands-on experience. Lab work will include the following aspects: crystallization, data collection and computation of Patterson maps and electron density maps and using them to build models of molecules.
Certain proteins are good targets for structure based drug design. Therefore 3 weeks are devoted to in-silico techniques which include model building docking and drug design.
B.S. degree in Science. (Open to all graduate students).
Evaluation: The evaluation will be carried out on the basis of examinations and assignments:
1. The midterm exam will count for 25% of the grades
2. The final exam will account for 35% of the grades and
3. The assignments will account for the remaining 40%.
Teacher evaluation: An anonymous student evaluation will be conducted at the end of the semester.
None, but the following books will be used as reference books.
1. Principles of x-ray diffraction: Jan Drenth: Springer-Verlag: ISBN 0 387 98587 5.
2. Modern X-ray analysis on single crystals: Peter Luger: de Gruyter: ISBN: 3-11-006830-3
3. Crystallization of Biological Macromolecules: Alex McPherson: Cold Spring Laboratory Press: ISBN-0-87969-527-7.