Summary
- Protein is structured by connection with Amino acids.
- Amino acid connection is called peptide bonds.
- Peptide bonds is bond between Amino group(NH2) and Carboxyl group(COOH).
- The reaction that these two group connection are “NH2 + COOH —> H2o + CONH”
- The Protein(Polypeptide) amino acid sequence is called Polypeptide Chain and this structure is called Primary structure.
- Then, Protein’s structure is not just as a line and each chain’s N-H & C=O are connected as hydrogen bond. These cased are called Secondary structure and there are two type of structure which are αhelix and βsheet structure.
- The α helix structure is helix structure same as name and it is like as ribbon. βsheet(Pleated sheet) structure is structured after connect neighbor chains by hydrogen bond and it is like a sheet. There are two type of βsheet structures which are parallel βsheet structure and anti-parallel βsheet structure. parallel βsheet structure has two same direction (N terminal residue —> C terminal residue) backbone and anti-parallel is vice versa.Simple difference between these two structures(αhelix and βsheet) is whether backbone is liner or not. If liner, it is whether The criteria of forming these two structures is spend in side chain.
- There are the section which connect αhelix structures and βsheet structures. It is called random coil. This is making 3D structure of protein and called tertiary structure. This random coils are making 3D structure as molecule. These molecules are structured with stable because of Hydrophobic bond, ionic bond, hydrogen bond, Van der Waals force etc.And PDB is providing variety of protein structures.
- Additionally,we call the polymer which is the group of two or more protein molecules quaternary structure. This is called Oligomer structure too because it is structured by several monomers. Protein molecules which structures quaternary structure are called subunit.
Assignment
1.Looking at protein structures using a viewer (PyMol or Chimera or Rasmol)
- I downloaded PyMol considering UX and visuality.
2.You’ll pick one of the five test cases in the homework folder and run structure prediction calculations.
3.To the run program, type the following command inside your specific test case folder.
- I started to run the program and it took almost overnight. (Ref.1)
4.Plot the score (or energy) vs rms plot.
- I opened the file by excel and plot it. (Ref.2)
According to this result, S_00000067 is the lowest energy and S_00000018 is the lowest rms. both are red dot in Ref.2.
| Ref.1 |
Ref.2 |
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5.Pick the lowest energy model and structurally compare it to the native. How close is it to the native? If its different, what parts did the computer program get wrong?
- Bule color model is natural model and purple color is the lowest energy model.
- 3D structure appearance : It seem totally different.
- α helix : native model has 2 α helix and the lowest energy model has 2 α helix.
- β sheet : native model has 5 β sheets while lowest energy model has 4 β sheet.
- Random coil : The lowest energy model has longer random coil than Native model.
| Native |
Lowest Energy |
Comparison |
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6.Pick the lowest rms model and structurally compare it to the native. How close is it to the native? If its different, how is it different?
- Blue color model is natural model and green color is the lowest rms model.
- 3D structure appearance : It seem similar.
- α helix : native model has 2 α helix and the lowest rms has 2 α helix. Direction and place and distance of each α helix is almost same.
- β sheet : native model has 5 β sheets while lowest rms model has 4 β sheet too. And direction is different.
- Random coil : Not so similar.
| Lowest RMS |
Comparison 1 |
Comparison 2 |
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Weekly Reflection:
Do your activities this week raise new ethics and/or safety considerations you had not considered in week 1? Describe what activities have raised these considerations and any changes you have implemented in response.
- It is not related for safety, but I exited Nature's excellence.Because I learned that proteins are structured with the most efficient styles automatically which is organized by nature not algorythum. It is great things and re-recognized that nature is great.