This week is all about proteins! The homework is divided into two parts. Part A is focused in protein analysis and protein informatics. Part B, is about coumputational protein folding.
Assuming that the average molecular weight of each amino acid (M) is 100 Daltons or g/mol and mass (m) is 1g, leads to n = m/M = 0.01 mol of amino acids. Taking Avogadro’s constant 1 mol = ~6.022𝐸23 mol(-1) then, X = 0.01 mol * 6.022𝐸23 mol(-1) = 6.022𝐸21 amino acids. Considering that 100 g serving of red meat provides around 28g of protein, this approximates to 3.011E26 amino acid molecules.
The choice of why only 20 still remains a mistery. Francis Crick proposed in the 60s, that the choice of amino acids was arbitrary, suggesting that a different group of 20 would be just as good. Recent studies suggest that the 20 amino acid properties, such as hydrophobic vs polar, size, charge, etc. are evenly distributed through the chemical space. Other theories suggest that other amino acid structures could have been used. Another interesting question is how the amino acids are encoded in the nucleotide code. The smallest combination of four bases that could encode all 20 amino acids would be a triplet code. However, a triplet code produces 64 (43 = 64) possible combinations, or codons. Thus, a triplet code introduces the problem of being more than three times the number of codons than amino acids. There are few cordons that encode just one amino acid, such as the codon for tryptophan. In addition, some cordons encode start and stop information. So, one hypothesis could be that nature often resorts to redundancy for encoding information. More Info.
The protein I picked is the Crystal and molecular structure of the serine proteinase inhibitor CI-2 from barley seeds (2CI2). I picked this protein because of the interesting ring-like structural shape. More info on the protein here.
2CI2 Cartoon Visualization
2CI2 Lines Visualization
2CI2 Ribbon Visualization
2CI2 Mesh Visualization
2CI2 Licorice Visualization
2CI2 Ball and Stick Visualization
In addition to the standard modes, I exported the protein as a 3D model and rendered it for cool visuals.
Red areas correspond to hydrophobic areas.
Yes, the protein has a hole and multiple pockets.
Check out the Jupyter Notebook here.
Short description of next week's assignment.