This project takes a look at one of the scientific approaches that researchers use to study Bird Flu virus.
Flu is a common viral infection of lungs that affects millions of people annually and a leading cause of death in the United States. Research on the influenza virus will provide information to design strategies for early diagnosis, treatment and prevention of the disease as well as better design antiviral drugs and antibodies against the virus.
Flu virus enters the epithelial cells of lung via binding of the hemagglutinin(HA) protein on the surface of the virus particle. HA is also the main antigen that human immune system recognizes and responds to by making antibodies and mounting immune response.
We will take the protein sequence of Hemagglutinin gene from protein data bank, visualize it in a protein structure viewer, and then simulate the structural change of the protein using molecular dynamics packages NAMD and VMD.
ANIMATIONS
SI2008
SI2007
REFERENCES
Avian Flu:
http://www.cdc.gov/flu/avian/
http://en.wikipedia.org/wiki/H5N1
Concepts to learn:
the molecular structure, and life cycle of a flu virus
Molecular Biology:
Any introductory textbook in molecular biology
Concepts to learn:
structures of biological molecules (DNA, RNA, protein, lipid membrane) protein membraneinteraction
Using UNIX at OSC:
Introductory UNIX: http://www.osc.edu/supercomputing/training/bunix/
Batch processing: http://www.osc.edu/supercomputing/training/batch/
Molecular Dynamics:
http://www.ch.embnet.org/MD_tutorial/index.html
VMD and NAMD tutorials:
http://www.ks.uiuc.edu
Yuan Zhang is the group leader for the Molecular Structure of Flu Virus project. Her office is in 420-17, phone 614-292-7259.
For assistance, write si-contact@osc.edu or call 614-292-0890.
