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Advanced Topics in Biophysics
Structure Function and Dynamics of Biomolecular Systems

Spring 2007 Phys 498/598

Instructor: S. Banu Ozkan

Time: MWF 1:40-2:30

Room: PSF-462

You can access lecture notes through ASU-Blackboard

Course Description:

The genomic revolution is providing gene sequences. Converting the sequence information into functional information and understanding the sequence-structure-function relationship is the challenge for post-genomic biology. In this course we will explore the relationship between structure, function and dynamics in biomolecules by (i)an overview of the biomolecular databases (bioinformatics part) and (ii) application of computational methods to understand molecular interactions and networks including protein-protein, protein-DNA, protein-ligand interactions.

Course Materials:

Course notes and related published articles


Introduction to Protein Structure
Branden C & Tooze J, 2nd ed. 1999, Garland Publishing

Molecular Modelling:Principles and Applications
Andrew Leach 2nd ed 2001, Prentice Hall

Structure and Function in Protein Science: A Guide to Enzyme Catalysis and Protein Folding
Alan R. Fersht 3rd ed., 1999 W.H Freemand & Company


1. Review of Structural Biology
Proteins: Structure, Conformation and Function (Branden and Tooze)
Generalized coordinates, Phi,psi angles
Secondary and tertiary structures
DNA/RNA: structure and function

2. Structural and functional databases and their applications
(PDB, SCOP, CATH, Functional domain, gene ontology, CONSURF)
Secondary Structure Prediction Databases
Sequence-Alignment Databases (BLAST, CLUSTALW)

3. Relationship between sequence, structure and function,
Molecular Modelling using ab-initio techniques,
Homology modeling, threading

4. Relationship between function and dynamics
a. Confromational changes in proteins (structural changes due to ligation, hinge motions, allosteric changes in proteins and consecutive function change)
b. Analysis of conformational changes by normal mode analysis
c. Analysis of conformational dynamics by Monte Carlo Simulations
d. Analysis of conformational dynamic Molecular Dynamics

5. Protein-protein interaction Principles
Recognition, structural matching
Principles applied to model protein-protein interactions

6. Docking
Principles of Docking
Docking Scoring
Small Ligand Docking
Protein-Protein Docking
Protein-DNA Docking

Center for Biological Physics Arizona State University Bateman Physical Sciences Building F-Wing, Room 359 Tempe, AZ 85287-1504