If biological synthesis of proteins and cell-free DNA expression are not flexible enough for you or you consider them inhumane then you have to resort to stepwise chemical peptide synthesis. Since proteins and peptides are an important area of modern research, many efforts have been made to make them accessible by synthesis. In current methods the peptide chain is bound to a solid resin. This makes purification easier. Excess reagents can be washed away without losing product. Even with modern techniques of solid phase peptide synthesis combined with chemical ligation it is difficult to get far beyond 100 amino acid residues.
Last summer I had an internship about protein synthesis. By it I was inspired to play around a little bit with PyMOL, a nice graphics program. If you use it, check out the sculpting function.
The image shows a peptide chain bound to a solid resin (green). The main chain is shown in red, side chains in orange. Side chain functional groups are protected by light blue protecting groups. The amino acid Lysine is in place for the next coupling step. Its α-amino group is protected by t-Boc. The carbonyl is activated by an active ester to Hydroxyazobenzotriazole (purple). The picture is drawn according to literature .
A different perspective:
This is what the protein looks like with just sticks.
 Miranda, L. P. et al. 2001. Total chemical synthesis and chemotactic activity of human S100A12. FEBS Letters 488 85-90
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