Ambrx technology may make drugs more effective

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me@rescam.org

Fascinating topic!!!! Apparently, Ambryx technology allows researchers to modify a protein's sequence in a way that nature cannot. tRNA naturally has the ability to incorporate any 20 of the natural amino acids in the respective sequence coded for in the mRNA to form a protein. Basically, mRNA is the "book" with the instructions on how to make certain proteins. tRNA "reads the book" and assembles the individual amino acids to form the protein. Up until this point, tRNA could only incorporate the "naturally occuring" 20 amino acids. I am not exactly sure how, but they somehow either manipulate the way tRNA "reads" mRNA or actually modify the properties of tRNA so that in incorporates "unnatural" or synthetically produced amino acids. This can all be done inside the human body (in vivo). The ability to do this is advantageous because the technology gives us a larger "book" and we can create improved proteins that nature itself could not have created. Feel free to correct me if my interpretation is incorrect!

@Roseetta Scientists AND/OR anyone one that can answer these questions: Does the software that you use to determine the shape of proteins have the ability to read synthetically produced amino acids and determine the structure of them? Is there a such thing as "native structure" when a protein has an unnatural or synthetically produced amino acid incorporated into it? Is it possible these types of proteins can be included in the next CASP?

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Fascinating topic!!!! Apparently, Ambryx technology allows researchers to modify a protein's sequence in a way that nature cannot. tRNA naturally has the ability to incorporate any 20 of the natural amino acids in the respective sequence coded for in the mRNA to form a protein. Basically, mRNA is the "book" with the instructions on how to make certain proteins. tRNA "reads the book" and assembles the individual amino acids to form the protein. Up until this point, tRNA could only incorporate the "naturally occuring" 20 amino acids. I am not exactly sure how, but they somehow either manipulate the way tRNA "reads" mRNA or actually modify the properties of tRNA so that in incorporates "unnatural" or synthetically produced amino acids. This can all be done inside the human body (in vivo). The ability to do this is advantageous because the technology gives us a larger "book" and we can create improved proteins that nature itself could not have created. Feel free to correct me if my interpretation is incorrect!

@Roseetta Scientists AND/OR anyone one that can answer these questions: Does the software that you use to determine the shape of proteins have the ability to read synthetically produced amino acids and determine the structure of them? Is there a such thing as "native structure" when a protein has an unnatural or synthetically produced amino acid incorporated into it? Is it possible these types of proteins can be included in the next CASP?

I don't know anything about Ambryx, but your interpretation is correct. In fact, Rosetta is now being refactored to make it very easy to introduce new amino acid types during protein design calculations. (some of this has been done already, but is a bit awkward under the current framework). The problem with using unnatural amino acids is that it is much more expensive to produce the proteins, so fewer designs can be tested.
A small number of native proteins do contain more than the 20 standard amino acids. We model these when we are doing modeling that starts with the known structure (for predicting or reengineering binding interactions for example). They are rare enough though that for general protein structure prediction (like next CASP) we probably wouldn't consider them.

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A small number of native proteins do contain more than the 20 standard amino acids.
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how?

What I mean is how does the body produce these proteins when all the code groups are already assigned to the standard ones?

Of course, it is relatively easy for the body to produce the non-standard amino acid itself, that is no harder than producing any non-protein organic molecule, generate a suitable enzyme (out of the standard 20) and hey presto that catalyses the formation of the non-standard amino acid.

But the how does the DNA / RNA code to put the non standard amino acid into the sequence of normal amino acids? Do we yet know how this occurs in naturally produced proteins that incorporate non-standard amino acids?

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how?

What I mean is how does the body produce these proteins when all the code groups are already assigned to the standard ones?

Hi River~~,

the genetic code is not uniform over all life forms on earth, it is not even uniform in your own body. E.g. the mitochondria (the little power plants in our cells) code different than the cells themselves. The differences are normally pretty small.

Then there are special sequences in the m-RNA of your cells that can tell the ribosomes that e.g. UGA will now stand for Selenocysteine instead of being one of the "stop" codons. The same accounts for the stop codon UAG that can instead also code Pyrrolysine.

As you see the stop codons are used instead of exchanging any of the standard codons. Why does the cell do that? It is very logical if you look at it closer.

The m-RNA codes the amino acids that will be used in a protein. Then there are the t-RNAs that carry these amino acids to the ribosomes. The m-RMA carries the codons and the t-RNAs carry just the opposite three nucleotides that will bond to the m-RNA. What now happens it this: The m-RNA is kind of driven through the ribosome. Only one codon at a time can be accessed by the t-RNAs. One t-RNA after the other will thus dock at the respective codons and the animo acid attached to each t-RNA is attached to the end of the currently synthesized protein. This will continue until a stop sign appears.

In other words: there are t-RNAs with the respective rare amino acids attached to them waiting to bring them into synthesis. Normally these t-RNAs are waiting but are not used, as UAG and UGA code a stop sign. Only if special sequences appear in the m-RNA, the t-RNAs equipped with the rare amino acids are used.

This has the advantage that those rare amino acids will not be introduced into a protein by mistake. The sequence that tells the cell it has to alter its normal program will either be recognized and an unusual amino acid will be inserted next; or the stop codon is taken for what it is: a stop sign. No protein with wrong sequence is produced this way, as the synthesis is simply stopped.

Using standard codons for that would mean that you would have to have t-RNAs with the same docking sequence carrying different amino acids, which is not sensible. The ribosome can only tell what amino acid is attached to a t-RNA by its docking sequence. So using "punctuation marks" for the purpose is the best alternative.

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"I know that you believe you understand what you think I said, but I'm not sure you realize that what you heard is not what I meant." R.M. Nixon

Good explanation. I did not know that the ribosomes could do that. Thanks Christoph!

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