Hand-in task 1

Protein Physics SI2700 - Spring 2016 Hand-in task 1

Deadline: Feb 15. You will get feedback within a couple of days and from that date you receive feedback you have 1 week to correct and hand in the final version.

(Must be completed and passed before taking exam)

The point of this homework task is to look more into the thermodynamics of simple structure formation, and in particular to get a better feeling for enthalpy, entropy, and free energy in protein folding. You should describe your findings with about a page of text, and then you might want to add some figures (which might bring it to two pages in total) to illustrate. The most important step is to draw conclusions and show you understand how to use the equations rather than just citing numbers derived elsewhere. Most of this task relates to chapters 7-10 in the book, but you can also use online resources to find information.

1. Consider a peptide with a short stretch of an alpha helix. Compared to the coil structure, which term(s) favor the formation of the alpha helix and which term(s) disfavor it?

2. There are a couple of amino acids that are less common to observe in alpha helices. Two of these are Proline and Glycine. Using your knowledge, explain (preferably using equations) why this is the case for (i) Proline and (ii) Glycine?

3. Let’s assume your peptide can adapt two structures - either helix or a beta sheet - and when studied experimentally it has been observed to be a helix at low temperatures, but a sheet at slightly higher temperatures. What conclusions can you draw from that temperature dependence?

4. Show how you can derive reasonable numerical values for energy and entropy terms if you make some rough assumptions about the number of residues in an average helix, and how this can be used to estimate folding time numerically following the book.

Good luck! Magnus