Part 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)

• Why are there only 20 natural amino acids? There are hundreds of naturally occurring amino acids. One theory - genetic code can not grow beyond 20amino acids because the incorporation of new tRNA identities compromises tRNA-ARS recognition [ ]

• Why most molecular helices are right handed?

• Where did amino acids come from before enzymes that make them, and before life started? From the environment. Which came first ? DNA/RNA/Proteins. Most common theory seems to be the RNA world theory. In 1953, Miller and Urey attempted to re-create the conditions of primordial Earth. In a flask, they combined ammonia, hydrogen, methane, and water vapor plus electrical sparks (Miller 1953). They found that new molecules were formed, and they identified these molecules as eleven standard amino acids

• What do digital databases and nucleosomes have in common?

  Reading/Writing. Efficiency of storage.

Part 2

• Briefly describe the protein you selected and why you selected it.

  I chose Top7 (1QYS on PDB) because it is protein not found in nature and has a unique fold. One of the first examples of a protein made from scratch. The crystal structure of this protein shows up in rosetta's logo.

• Identity the amino acid sequence of your protein.

  • How long is it? What is the most frequent amino acid?

    It has 93 Residues.

    DIQVQVNIDDNGKNFDYTYTVTTESELQKVLNELMDYIKKQGAKRVRISITARTKKEAEKFAAILIKVFAELGYNDINVTFDGDTVTVEGQL
    

  • How many protein sequence homologs are there for your protein?

    Since this is an aritificial designed protein with an unique fold - I didn't expect much from the BLAST

    

  • Does your protein belong to any protein family? No. See above ^

• Identify the structure page of your protein in RCSB

  • When was the structure solved? Is it a good quality structure?
    • Method: X-RAY DIFFRACTION
    • Resolution: 2.5 Å
  • Are there any other molecules in the solved structure apart from protein? No
  • Does your protein belong to any structure classification family? No

• 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? Selector: selection "hydrophilics" defined with 369 atoms.

  

   Hydrophobics
  

  Both

• Visualize the surface of the protein. Does it have any "holes" (aka binding pockets)?

  

Part 3 - Folding this protein in rosetta using Ab initio Modeling - I didn't use Thras's notebooks