8 - Monday, September 13, 2010 Lecture 8 Announcements: 1....

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Monday, September 13, 2010 Lecture 8 Announcements: 1. Do LG problems 10 - 17 for this week. PyMOL Assignment #3, Protein Folds. 2. Any student who has just added this class: Meet Prof right after lecture to discuss how to catch up. 3. Want your quiz re-graded? Just staple a written request/explanation, and place both in the purple re-grade folder that will be at the front of the lecture hall. No oral argumentation!!!! The procedure is to submit a written request that is attached to your quiz. 4. For questions regarding course administration, e.g. re your quiz scores, or adding this class, or dropping this class: do not ask the TA who runs the VOH. Contact the prof. 5. CU Undergraduate Health Cooperative info session Monday 9/13 at 6:00PM in 253 Malott Hall. Friday’s Lecture: Turns, β -structure, collagen structure folds, superfamilies, families Today's lecture: Multifold proteins Repeated folds Quaternary structure (IV) Protein stability Page 61: The concept of a protein "Fold" is simple enough, but the rest of the protein classification scheme shown on LG p. 60 is confusing! We need to consider a specific example for some clarification. An example to clarify the meaning of "Superfamily" and "Family" is the human Kinase Superfamily , aka the "Human Kinome". Because the entire human genome has been sequenced, researchers now believe that they have identified every kinase protein, all 518 of them. They all catalyze the same chemical reaction: addition of a phosphate to a protein, with ATP or GTP as the source of the phosphate. Most have related AA sequences and 3D structures. They are further grouped into Families , e.g. members of the TK (Tyrosine Kinase) family all catalyze addition of a phosphate to a tyrosine residue; the AGC family includes protein kinase A, protein kinase G, and protein kinase C molecules. The proteins within a Family are more closely related to each other, by evolution, and usually by sequence and protein function, than are proteins within a typical Superfamily. Page 62 of the LG shows two proteins. On the left is one polypeptide chain of HIV reverse transcriptase. This one chain contains 4 different protein folds !
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On the right, the protein pyruvate kinase, again a single polypeptide chain, consists of 3 different protein folds. But now for something a little different: Starting from the N- terminus, AA 1-115 start to fold as the protein is being synthesized on a ribosome, but before this structural unit is complete, the polypeptide chain “loops out” at residues AA 116-223, forming an anti-parallel 6-strand beta barrel as a distinct structural unit (a distinct fold). Then the chain rejoins the first fold, and AA 224-387 complete the alpha/beta barrel fold. Finally, the last fold is formed from AA 388-530, an alpha/beta barrel. From this example you see that a protein can be formed from several folds, and that these are not necessarily continuous runs of the polypeptide. In fact, ~ 30% of all folds are not continuous runs of polypeptide. Essentially all the folds that have been discovered are found in the proteins of all the life
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8 - Monday, September 13, 2010 Lecture 8 Announcements: 1....

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