76-456/731 Biophysical Methods - Protein structure component

Modified November 1998

[Department of Chemistry and Biochemistry Home Page] [University of Guelph Home Page]

Lecture 1
Revised for Fall 2000
This is a web page with the notes of the first lecture: view and print this out from your browser.
The remaining notes should become available the morning of the day before lectures.
Tour of Protein Structure
This is a web page for you to view in your own time. There's a fair number of computer generated color images, so please be patient while the pages load. It can be printed, but is best viewed on screen because of the color.
Lecture 2
Revised for Fall 2000
Lecture 3
Revised for Fall 2000: there are many figures so please be patient with the load time for this page!
Revised for Fall 2000

Rasmol exercises

Rasmol is molecular visualization software that's specially adapted for viewing protein database files. It allows you to display structures in several different modes and color schemes, and to selectively edit portions of a protein or nucleic acid structure for viewing.

Rasmol 2.6.4 is more bug free, but Rasmol 2.7.1 has more features.

Click here to download RasMol software

Here's help on how to use RasMol.

Install Rasmol first, then go get some files to view:

The link shown at the end of this section will get you to the Protein Data Base (formerly the Brookhaven Protein Database). The initial screen appears as a search request form. There are basically two approaches:
1) If you already know the PDB accession number for the protein. Many papers showing protein structure now list the accession number. Fill in the appropriate space near the top of the form, 1AP9 for the Pebay-Peyroula bacteriorhodopsin X-ray diffraction structure, and click the Search button.

The next page has a variety of crystallographic data; Click the link to Download/display structure. On the Next page look for the Download table, and select "uncompressed" and "PDB format".

2) If you don't know the accession number or you wish to see what else is available, enter the protein name in the keyword space. Enter membrane protein porin and click the search button. You should now get a list of porin entries in the Protein Data Base. Scan the list for Porin (Crystal Form B), and click the Explore button. Then proceed as for case 1 to get the Rasmol file. Save it as 2POR.PDB. (That tells you what accession number you are after, but the objective here is to try out the search procedure.

Click here to go to the Protein Data Base Browser

More instructions on what to do with Rasmol will follow.

Another neat link for protein structure information:

Click here for the Principles of Protein Structure Course

Course-related comments can be sent to Dr. Keates  at keates@chembio.uoguelph.ca

Web-related comments can be sent to Uwe Oehler at DrIguana@chembio.uoguelph.ca