Week 4 HW: Protein Design Part I

Contents

Part A: Conceptual Questions

Need to answer 9/11 questions; I skipped

  1. 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)
    $$ 500g * \frac{1 mol AA}{100g} = 5 mol AA $$ $$ 5 mol * \frac{6.02*10^{23} molecules}{1 mol} = 3.01 E24 molecules $$
  2. Why do humans eat beef but do not become a cow, eat fish but do not become fish?
    We break down the proteins during digestion to the constituent amino acids. These amino acids are then used in our cells to build human proteins.
  3. Why are there only 20 natural amino acids?
    It’s been hypothesized that the 20 naturally occurring amino acids fairly effectively cover the “chemical space”, which would indicate that more complex or diverse amino acids are not needed for increasing function. This includes variation in chemical properties like molecular size, hydrophobicity, and charge, but also rotational conformations. These twenty sufficiently cover the space for effective function while also being relatively low in energy (easy to synthesize). Another paper hypothesizes that all twenty natural amino acids predate the RNA world, and in fact were naturally synthesized prebiotically with mineral catalysts - thus suggesting that the development of the three-base 64-codon alphabet actually was because a two-base 16-codon alphabet would restrict to sixteen instead of the existing 20 amino acids.
  4. Can you make other non-natural amino acids? Design some new amino acids.
    There are a new non-cannonical amino acids that people have designed and used, by changing the residue for an unnatural one.
  5. Where did amino acids come from before enzymes that make them, and before life started? In 2018, Bywater suggested that amino acids were synthesized prebiotically, with the simpler structures occurring through aqueous reactions, and more complex structures requiring mineral catalysts. Many amino acids have been identified on meteorites, suggesting that amino acids could have originated in outer space, but more likely that the conditions to synthesize the “simpler” amino acids exist in multiple places. Other researchers have suggested that the “complex” amino acids must have been biosynthesized by early proteins made up of “simple” amino acids, and in particular, that histidine, phenylalanine, cysteine, methionine, tryptophan and tyrosine had to come after molecular oxygen because they have redox functionality.
  6. If you make an α-helix using D-amino acids, what handedness (right or left) would you expect?
    I would expect D-amino acids would form a left-handed helix because L-amino acids form right-handed helices.
  7. Can you discover additional helices in proteins?
  8. Why are most molecular helices right-handed?
    In general, naturally occuring amino acids are L-enantiomers, which leads to right-handed helices because of steric hindrance requiring the side chains to point outwards.
  9. Why do β-sheets tend to aggregate? What is the driving force for β-sheet aggregation?
    Because beta sheets are flat, they can stack, and the large surface area means that the side-chains can have interactions (especially hydrophobic side-chains) between the sheets.
  10. Why do many amyloid diseases form β-sheets? Can you use amyloid β-sheets as materials?
  11. Design a β-sheet motif that forms a well-ordered structure.

Part B: Protein Analysis and Visualization

  1. Briefly describe the protein you selected and why you selected it.
  2. Identify the amino acid sequence of your protein.
    • How long is it? What is the most frequent amino acid?
    • How many protein sequence homologs are there for your protein?
    • Does your protein belong to any protein family?
  3. Identify the structure page of your protein in RCSB
    • When was the structure solved? Is it a good quality structure?
    • Are there any other molecules in the solved structure apart from protein?
    • Does your protein belong to any structure classification family?
  4. Open the structure of your protein in any 3D molecule visualization software:
    • Visualize the protein as “cartoon”, “ribbon” and “ball and stick”.
    • Color the protein by secondary structure. Does it have more helices or sheets?
    • Color the protein by residue type. What can you tell about the distribution of hydrophobic vs hydrophilic residues?
    • Visualize the surface of the protein. Does it have any “holes” (aka binding pockets)?

Part C: Using ML-based Protein Design Tools

Part D: Group Brainstorm on Bacteriophage Engineering