PROTEINS

There are many resources available that will help in your understanding of conformational space occupied by proteins. Most of these can be found on the Internet/You-tube, but here they are in one place for you.

[Also, I found a link that should have been given out the first week. The Chemistry Department at the University of Illinois-Urbana-Champagne has a link to a page of 30 tutorials on different General Chemistry Topics. Go half way down the page and find "Gen Chem Tutorials" with a "Visit online tutorials" button. Here you can review chemical equilibria, acids and bases, orbital hybridization, naming organic molecules, Henderson-Hasselbalch equation, and more.]

Overall protein structure videos and interactive exercises: Most of these were attained from the Protein Database (link). This includes exercises on amino acids, peptide bonds, secondary structure, and evolution of proteins and protein families.

1) Overall Protein-structure hierarchy(link):
2) What is a protein(link):
3) Edman Degradation(link):
4) Methods for Determination of Atomic structures(link):
5) Protein structure prediction(link):

Edman degradation video explaining the mechanism (link)

A lecture on MS and its use in molecular biology by Professor Nevan Krogan, titled Mass Spectrometry and its Application to Molecular Biology (on the ibiology.org site) (link). This is a 30-min lecture that discusses many of the uses of MS. At time 17:50 is where a detailed discussion starts discussing the fragmentation of peptides for sequence determination, including the use of database searching to identify and complete the sequence. At 21:40, the lecture starts a discussion of using MS to identify protein-protein interactions. So, between 17:50-21:40 (4 min) is the part of the lecture that is exactly pertinent to our discussion in this course. Of course, the take home lesson from this lecture is the appreciation of the power of MS for many applications in biochemistry and molecular biology.

Videos on determination of tertiary structure using X-ray crystallography:
(1) a link for a video showing the overall process of making protein crystals and getting a diffraction pattern.
(2) a link for a video showing how diffraction of a crystal results in a density map of the map.

(3) a link for a video showing another treatment of the overall process, but with a different voice.
(4) a link for a video showing another treatment of the overall process, but for "Dummies."

Problem on protein structure and Jmol tutorial, including quaternary structure problem (link)