Jinzou Ningen – Artificial Human project

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Exploring possibilities

Protein Synthesis; Design Of Synthesis Unit

In the previous article on protein synthesis [1] we addressed the way biological (eukaryotic) cells synthesize the proteins which make up said cells and other structures in the body in addition to performing various other tasks. The basic summary of this process is transcription of DNA into messenger RNA (mRNA) which is then fitted into ribosomes which use transfer RNA (tRNA) as an intermediate form to translate codons of three nucleotides on the mRNA into one of about twenty possible alpha-amino acids [2]. The resulting string of amino acids then folds due to molecular forces into a 3D form, its final shape determining its function due to the active surfaces on the outside of the protein.

In artificial synthesis of proteins there are a few possible ways to approach this issue, which will be the focus of this article. The most basic approach is essentially the use of an artificial ribosome, whereby the transfer of mRNA through it is simulated and tRNA units with alpha-amino acids are present. The faster, superior, but possibly more complex approach is to directly attach the relevant amino-acid onto the protein string. We’ll examine both option.

The artificial ribosome option (AR approach) is attractive in that it stays close to the existing eukaryote setup, something which we’re all familiar with. We can use existing tRNA, and just keep adding the proper amino-acids to the fluid. The artificial ribosome would need to receive information and adapt the template on its surface based on it to protrude the relevant codons for the anti-codon of the matching tRNA unit to attach to and thus proceed with the formation of the protein string. This means a fairly light-weight setup, within reach of existing nano-technology. The synthesis of an AR unit would be quite involved, but not impossible. The communication protocol would be interesting, and may result in something very much akin to mRNA. In the end this may end up being a fairly complex imitation of the biological system.

On the other hand there’s the ‘2D printer’ setup of the Direct Attachment (DA) approach, which at first does seem more complex, but reduces protein synthesis to the very basics. There’s no more mRNA, ribosome, tRNA and free-floating resources and data in fluid. Instead there’s a single unit which has reservoirs containing the alpha-amino acids which could be drawn into the reservoirs or otherwise refilled, which opens or closes the relevant reservoirs when a particular amino acid is needed. Either the protein string could be moved along the reservoirs, or the reservoirs could be moving in a kind of head, or a pick-and-place approach could be used to transport the amino acid. Or maybe a simple transport system, such as the endoplasmic reticulum uses.

Frankly, given the choice I would go with the DA approach for the simple reason that it allows for many adaptations and much more control. The communication protocol is still an issue, but by dropping the complex addressing of mRNA to tRNA to protein string and using a simple direct addressing in theory this shouldn’t be too much of an issue. As remote control may be desirable the use of something reliable such as the electric signaling of a nerve cell could be used. One wouldn’t be limited to purely biological structures either, and use semi-conductor techniques, akin to those of lab-on-a-chip configurations.

The next article on protein synthesis should further work out the design of the DA approach. Please look forward to it 🙂

Maya

[1] https://jinzouningen.wordpress.com/2012/03/02/protein-synthesis-polymer-design/
[2] http://en.wikipedia.org/wiki/Amino_acid

Filed under: Polymers, Synthesis, , , , , , ,

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Maya Posch: professional software engineer and game developer. Graphics artist and all-around science junky.

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