Graduate Protein Crystallography

Graduate Protein Crystallography & Proteiin Structure
Fall 2011

 Wed.   10:00 A.M. – 12:00 P.M.

Room: Biomed I Room 200

Course Director
K.I. Varughese




Slides and Readings are located HERE

 Class Schedule

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.