BCH 2333 Lecture 10: Lecture 10 - Separation techniques

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viridianox481

2 Mar 2017

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Protein folding occurs on a complex energy surface. Just tries them all until it gets to the native folded state. On the right, the protein does not sample all the conformations that are available for a polypeptide. Like taking the nicest rout to going to the lowest state. Lots of cooperativity, lots of pathways as well. This is all in the context of cooperativity. Folded proteins do not always have the lowest energy. Oligomers and amyloid fibrils form is stuff goes wrong. Alzheimer"s is an example of the formation of amyloid fibrils, or amyloid plaques. Because the giant gap in between the energy levels between native folded state and aggregated amyloid fibrils. Native folding driven by cooperativity and molecular interactions. Chaperones will fix some proteins that are folded wrong using atp. Need to purify protein out of a sample. Native proteins have a wide range of purity. Red blood cells are essentially sacs full of hemoglobin 90% of mass.

Related Questions

Part 1: Amino acid properties.

Run the 2D protein simulation found at: https://learn.concord.org/resources/787/protein-folding, then answer the following questions.

Q1: Assuming the solvent is water, what rough shape will a protein entirely composed of hydrophobic residues be? How about a protein entirely of hydrophilic residues?

Q2: Given that proteins have to adopt a very specific 3D shape to be functional, would you expect the amino acid composition of a functioning protein to be mostly hydrophobic, mostly hydrophilic, or a mix? Why?

Part 2: This assumes you have already read chapter 4

Download and install the 3D protein folding game foldit, create an account, and play through at least the first 10 levels of the introductory puzzles. If you get frustrated, don't worry, you don't actually have to beat all the levels to complete the assignment.

https://fold.it/portal/

Q3: An important part of this "game" is packing amino acids to fill the flashing purple voids on the inside of the protein. Why is having voids bad? Think about what important class of molecules is notably missing from this simulation when you formulate your answer (hint, think about chapter 2).

Q4: In this game, the more realistic the protein shape, the better the "energy score" the player gets. In real life, proteins shuffle around different possible conformations without outside guidance until they find their native state, and this happens spontaneously. If you had X-ray vision and could see this happen, would you expect to see some trend between each conformation's "energy score" and the likelihood that the protein actually tries this conformation?

BCH 2333 Lecture 10: Lecture 10 - Separation techniques

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