Week 4 HW: Protein Design Part I
Week 4 — Protein Design Part I
This week focuses on how sequence, structure, and energetics can be modeled and manipulated to create or optimize proteins with specified functions.
Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip)
How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons)
Meat contains at around 26g of protein per 100g of meat, so, in 500g of meat, this would be 26 g x 5 = 130g of protein
Average aminoacid would be ~100 g per mol, so 130g / (100g/mol) = 1.3 mol of aminoacids
Mole = 6.02 x 1023, so 1.3 x Mole = 7.8x1023
So, 7.8x10^23
Why do humans eat beef but do not become a cow, eat fish but do not become fish?
Because there is no horizontal gene transfer, or at least an effective one
Why are there only 20 natural amino acids?
I’d like to think that it is because that is as optimal life gets
Can you make other non-natural amino acids? Design some new amino acids.
Where did amino acids come from before enzymes that make them, and before life started?
The primordial soup!
If you make an α-helix using D-amino acids, what handedness (right or left) would you expect?
Left-handedness
Can you discover additional helices in proteins?
Yes
Why are most molecular helices right-handed?
Almost all aminoacids are L-aminoacids, which means they’re gonna be right-handed helices as that is as optimal as it gets for energy.
Why do β-sheets tend to aggregate?
What is the driving force for β-sheet aggregation?
Because of their hydrogen bonds, their structure sets them up for said hydrogen bombs. I believe this happens in Alzheimer’s?
Why do many amyloid diseases form β-sheets?
Can you use amyloid β-sheets as materials?
Proteins that aren’t folded properly tend be these β-sheets, and so aggregation happens, and amyloid-β peptides instead of doing their functino, they aggregate.
Design a β-sheet motif that forms a well-ordered structure.