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Given the DNA code for one of the "machines" that run cells, we can generate an atomic model of that machine. This means we can "compile" (one part of) the DNA
by candiodari 6y ago
Given the DNA code for one of the "machines" that run cells, we can generate an atomic model of that machine. This means we can "compile" (one part of) the DNA code. It was already possible, but so slow that entire datacenters would spend months calculating this for a single protein and even then we can't use them on the really complex ones at all, necessitating things like neutron spectroscopy which are totally insane, and only work on like 1% of proteins.
This is useful because for example chemical simulation tools don't run on DNA code, but on atomic models. And also to produce "images" of the molecules (images between quotes because most proteins are too small to interact with reasonable photons, and no interaction with photons means you can't see them in any way)
DNA has other parts that are really important but we don't understand at all yet, where this doesn't help at all. This applies to sections of DNA sent to ribosomes, to produce actual molecules. Besides that, there are pieces of DNA that "index" the DNA, pointers (from one gene to another), triggers (that for instance start production of an enzyme based on some external influence, like detection of a marker molecule) and export markers (that tell you what to do once the protein is produced, for example, mark a protein to be removed from the cell, incorporated into the cell membrane, or for instance used inside the cell nucleus, and there's also one that essentially says "at this point stop producing a protein and instead couple the rest of the DNA code to the end of the protein you just made").
- Rochus 6y agoThis is about proteins, not DNA.
- shawnz 6y agoProteins which are coded by DNA.
- Rochus 6y agoSo what? The DNA only codes for the RNA and amino acid sequence. Structure determination is yet another topic. When we determine the protein structure we already know the sequence. Neither DeepMind has to look at the DNA to train their DNN.
- shawnz 6y agoThey are two topics which are both relevant to the discussion. Structure determination is what allows you to see the purpose/effect of the sequence that the DNA encoded.
- Rochus 6y agoHave you read the article? It's about protein structure determination. The DNA only determines the RNA and amino acid sequence. But who cares. I will get a bit less work and citations because http://cara.nmr.ch/doku.php http://cara.nmr.ch/doku.php will be less used in future.
- candiodari 6y agoThe full chain is DNA -> mRNA -> Ribosome -> tRNA combinations -> amino acid chain -> protein. It's true that in nature there are many steps between DNA and proteins (this list doesn't even include the steps that mediate the translation, ie. start it, stop it, slow it down, ...), but the structure of a protein is fully determined by the DNA code. Protein folding is about you start from the DNA code that is fed into the ribosome ignoring all the meta information, and come up with an atomic model (VERY long list like "H atom at 3.27,2.17,12.18, C atom at 2.87, 2.19, 12.33, ..."). Now there's a million niceties we've discovered to make this problem simpler and nicer looking, but that's what it boils down to.
- Rochus 6y agoThank you very much; almost forgot I did a Phd on the subject ;-) But anyway your answer does not contradict my statement. What you say belongs to the basics of molecular biology, but does not justify that DNA should be considered when determining the structure of proteins. In practice, the amino acid sequence is always already present.
- Rochus 6y agoFor the sceptics: if you read the referenced article, you will see that it is about protein structure determination by means of deep neural networks. It's not about gene expression, which is a different topic. What benefit does it have to respond to the question "What are the immediate real-world applications of this" (see above) by reciting some molecular biology dogmas from text books mixed with misconceptions, instead of responding to the real question?
- shawnz 6y agoNobody is suggesting that this research has anything to do with gene expression or anything like that. Their point was simply that we now have better tools to actually see the meaning/effect of a given DNA sequence. Also, there is no need to passive-agressively highlight your credentials. I already researched them before replying.