Tuesday, March 27, 2007
Last year's exam posted
There is a link to last year's exam over on the right-hand side. It's all about the PLP. Well, mostly, anyway.
Thursday, March 22, 2007
Protein Modeling Exercise
Instructions for accessing material for the Chem 355 Modeling Project
1. Go to http://dcchem.wikispaces.com/Protein+possibilities and choose a protein from the available list. Edit the page by adding your name; save the page.
2. On the PDB website for your protein, click the "Structure" tab and choose "Download Files." Click "PDB file" to download the file to your computer. Also search for "1HEW" and download the pdb file, as that is the file that will be used in the tutorial.
3. Download the Swiss Viewer (http://www.expasy.ch/spdbv/text/download.htm). The instructions are written for version 3.7 using Mac OS 9 (Classic). There are PC versions and also a beta version of a Mac OS X program. Last year, students used the PC version and the Mac OS 9 version successfully. The tutorial author recommends against using the Mac OS X version. Do not use a beta version!
4. Go to the tutorial/assignment site (http://www.usm.maine.edu/~rhodes/SPVTut/index.html) There is a menu to the left; you will do the first six lessons and then do assignment 1 for your protein.
Opening the file can present a problem -- the default application is generally Graphic Converter on a Mac. I do it this way: hold down the control key, click and hold on the icon for your pdb file. A menu appears. Navigate to "Open With..." and choose "other." Find the Swiss Viewer on the computer and choose it.
1. Go to http://dcchem.wikispaces.com/Protein+possibilities and choose a protein from the available list. Edit the page by adding your name; save the page.
2. On the PDB website for your protein, click the "Structure" tab and choose "Download Files." Click "PDB file" to download the file to your computer. Also search for "1HEW" and download the pdb file, as that is the file that will be used in the tutorial.
3. Download the Swiss Viewer (http://www.expasy.ch/spdbv/text/download.htm). The instructions are written for version 3.7 using Mac OS 9 (Classic). There are PC versions and also a beta version of a Mac OS X program. Last year, students used the PC version and the Mac OS 9 version successfully. The tutorial author recommends against using the Mac OS X version. Do not use a beta version!
4. Go to the tutorial/assignment site (http://www.usm.maine.edu/~rhodes/SPVTut/index.html) There is a menu to the left; you will do the first six lessons and then do assignment 1 for your protein.
Opening the file can present a problem -- the default application is generally Graphic Converter on a Mac. I do it this way: hold down the control key, click and hold on the icon for your pdb file. A menu appears. Navigate to "Open With..." and choose "other." Find the Swiss Viewer on the computer and choose it.
Continuing Chapter 5
OK, so I've fallen a bit behind with the postings. We are still covering Chapter 5 material; right now we are part way through the catabolism of tryptophan. Your task for tomorrow is to see if you can figure out how PLP can help with the elimination of alanine from the molecule that we had at the end of the lecture.
The picture is a photomicrograph of alanine.
Monday, March 05, 2007
PLP, an outstanding molecule
Today we started to look at the transformations of amino acids. The first step was to begin an analysis of the chemistry of PLP, a co-enzyme used in a large number of the reactions. The key concept here is that PLP is essentially an electron sink and can generate two different imines. These imines will give different C=O compounds upon hydrolysis. If we are clever about manipulating the PLP adducts we can force the amino acids to undergo a wide variety of changes.
Friday, March 02, 2007
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