rahma zakaria
how to grow almost anything
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protein design
part A: protein analysis
  1. Why are there only left-handed amino acids? One hypothesis suggests that our side of the galaxy experienced polarized light which destroyed right-handed amino acids and then amplified left-handed amino acids.
  2. Azurocidin 3D structure
    • Azurocidin is a monocyte- and fibroblast-specific chemotactic glycoprotein with antibacterial activity: it is cytotoxic to many species of Gram-negative bacteria, such as P. aeruginosa.
    • Amino acid sequence
      • It is 251 amino acids long, and its most common amino acid is glycine.
        • A pBLAST search gave 100 sequences with homology to azurocidin, with the sequences of highest homology being azurocidin in the chimpanzee, Sumatran orangutan, and macaque.
      • It belongs to the trypsin-like serine protease family.
    • Protein structure
      • The structure was deposited into the RCSB database in 1998, and has a 1.2 Angstrom resolution.
      • The structure includes some small molecule ligands, including chlorine and ethanol.
      • One protein, a heparin binding protein, was found with a similar structure to azurocidin, with more than 40% sequence identity to chain 4l8H.A.
    • There are two beta sheets and a few alpha helices.


part B: how to (almost) fold (almost) anything

 Unfortunately I couldn't get PyRosetta to work! I did all the steps I could, from installing Bash on Ubuntu on Windows to extracting and installing Python to the environment, facing a bunch of errors along the way. But in the last step, trying to verify the installation, I got an error indicating that I had glibC 2.23 instead of the required 2.27. Acquiring 2.27 was possible but it would involve either updating Ubuntu completely or acquiring a whole new library and several other sources and softwares required, and take quite some time and storage. In the end I didn't follow through, but here are the steps I followed and resources I tried to use.