Protein Folding with Rosetta

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