Monday, October 15 2007

Tuesday, October 16 2007

Wednesday, October 17 2007

WEB-PAGE LINKS FOR THE PROTEIN SECTION:

1. ANIMATED MODELS OF HEMOGLOBIN STRUCTURE * 10/18/07
http://www.umass.edu/molvis/tutorials/hemoglobin/heme.htm

2. PROTEIN MASS SPECTROMETRY 10/17/07

1. Protein Info from the Mass Of Tryptic Peptides: http://au.expasy.org/uniprot/P08588
   
   Click on SEQUENCE above “Entry Information”. You may need the table of single letter amino acid abbreviations from the first powerpoint slide of 10/16. There are other tools at the bottom. Explore as you wish, or choose from Sequence analysis tools> PeptideMass. Fill in the accession number if it isn’t there. Under this box choose: [M+H]+, monoisotonic, select Trypsin as the enzyme, 0 missed cleavages, display the peptides with mass > 0, sort by peptide masses, post-translational modification. Go back near the box at the top and click PERFORM the cleavage. You should be given the sequence of the protein and the tryptic peptides as well as their  mass numbers.
    
   Let’s do a thought experiment in proteomics. Imagine doing the above in reverse. Suppose you had a 2D SDS-Page gel of many proteins from a given cell (see for example. You elute one spot for the gel and wish to identify it and know its amino acid sequence. Using tandem mass spectrometry of a trypsin digest of the eluted protein to get precise mass numbers for the fragments in your digest. Then upload these into a data base (like this one) and it can compare your trypsin fragments to the mass of known fragments, often identifying the protein or if it an unknown protein providing  sequence information. Such an exercise is what the next link is about. Also see the type of information now available online from 2D SDS electrophoresis of whole cell extracts in 3. below.

2. Protein Fingerprinting and Identification:
   http://www.ionsource.com/tutorial/protID/fingerprint.htm
    
   This is a single page with information about an online database exercise with Aldente. Give it a try.  At least click on the link in the Short Exercise text on this site that show the screens of their input and of their results. You may find it helpful to have a list of one letter amino acid symbols for reference. You can find one on this MBM site by accessing the first powerpoint presentation for Proteins on 10/16.  The Aldente web site is http://us.expasy.org/tools/aldente/

3. Clinical: Newborn Screening
   http://www.acmg.net/resources/policies/pol-029.pdf
   This is old but suggests additional uses for mass spectrometry in clinical screening.

4. The Basis of Protein Identification by Mass Spectometry  (more than you want to know, but just in case you do.)
   http://www.astbury.leeds.ac.uk/facil/MStut/mstutorial.htm

3. PROTEIN STRUCTURE DATABASES 10/17/07

Info and tools to visualize and manipulate proteins: http://au.expasy.org/.

Click on Swiss-2D PAGE (gel electrophorisis). Click the button that says ”by clicking on a spot”.  Scroll down and click on a gel that you care to choose. Say ECOLI or DLD1_Human. When the next picture appears of the marked-up gel, put the cursor on a spot marked in red, maybe a star. Notice the window that identifies the pI  and MW of the protein. Write down the accession number of one protein you’d like to identify, but move the cursor around from spot to spot and get an idea of the range of MW anf pI values of the proteins in this source. Then double-click on a spot and wait. The protein will be identified. Use the accession number if you would like to  try other features of the site.

Other sites: http://www.ncbi.nlm.nih.gov

Thursday, October 18 2007

Animated Models Of Hemoglobin Structure:

http://www.umass.edu/molvis/tutorials/hemoglobin/heme.htm

Monday, October 22 2007

Tusday, October 23 2007

Wednesday, October 24 2007

Animated Model of DNA Structure:

http://www.umass.edu/molvis/tutorials/dna/dnapairs.htm

http://www.umass.edu/molvis/tutorials/dna/dnacode.htm

Thursday, October 25 2007

Monday, October 29 2007

Tuesday, October 30 2007

Wednesday, October 31 2007

Thursday, November 1 2007

Monday, November 5 2007

Tuesday, November 6 2007

Wednesday, November 7 2007

Thursday, November 8 2007

Friday, November 9 2007

Monday, November 12 2007

Tuesday, November 13 2007

Wednesday, November 14 2007

Thursday, November 15 2007 was Wednesday, December 5

Monday, November 19 2007

Tuesday, November 20 2007

Wednesday, November 21 2007

Thursday , November 22 2007

Monday, November 26 2007

Tuesday, November 27 2007