BIOL 363

ExPASy Molecular Biology Server
Goals: Learn use of Swiss-Prot, Prosite and Swiss 2-D PAGE
to obtain protein information.

Select the Swiss-Prot protein database.
Search: src; opsin; fibronectin 1.
Try searching both with and without "human."
Use the "feature table viewer" (square graphic).
What protein domains are found?
Where in fibronectin do we find disulfide bridges?
What is special about fibronectin residues 528 and 542?
Compare tutorial.

Use Prosite to find more information about the domains.
What is the detailed structur of the fibronectin domains?
For opsin, what 3D structure is shown by the PDB files?
(bottom of page)

Swiss 2-D PAGE maps
Select acid (pI range) plasma map.
Find paraoxonase.
Check out what is is in Human Map Viewer.
Find protein in Swiss-Prot.
Get protein sequence in FASTA format.

Question: Is paraoxonase in expected position on 2-D gel?
To find molecular weight and isoelectric point (pI):
Swiss 2-D Database
Use "by description."
Compute theoretical pI/Mw.
How do these compare with actual protein spots?  Check map.
What other tissues show paraoxonase?

Try: albumin; carcinoma; globin;
as well as the other proteins above.
Does this database seem as "complete" as the others?
Why or why not?  What questions are answered by 2-D gels?
Try other plasma proteins such as microglobulin; hemopexin.