Apologies if I spam this stuff too much but I'm so intrigued by the dynamic complexity of this whole thing.<p>The following three videos describe the process of DNA Transcription (copying a single gene's worth of RNA from the DNA strand), Translation (subject of TFA, creation of the protein from that RNA), and Replication (the process of making a complete copy of DNA for purposes of cell division.<p>Keep in mind that the functional components you see in here are themselves (generally) proteins that are created (and have evolved) by a similar process.<p>Transcription - <a href="https://www.youtube.com/watch?v=SMtWvDbfHLo" rel="nofollow">https://www.youtube.com/watch?v=SMtWvDbfHLo</a><p>Translation - <a href="https://www.youtube.com/watch?v=TfYf_rPWUdY" rel="nofollow">https://www.youtube.com/watch?v=TfYf_rPWUdY</a><p>Replication - <a href="https://www.youtube.com/watch?v=I9ArIJWYZHI" rel="nofollow">https://www.youtube.com/watch?v=I9ArIJWYZHI</a>
Could someone ELI5 why proteins fold in a <i>unique</i> way? Why can't there be multiple "valid" ways for them to fold (ignoring mirror symmetries)?
> Proteins are long chains of amino acids. Your DNA encodes these sequences, and RNA helps manufacture proteins according to this genetic blueprint.<p>What does it mean when it says “Your DNA encodes these sequences”?
I worked besides my wife on some protein folding problems. People often want to know why it is so expensive.<p>I unusual describe it as, someone gives you all Lego pieces in a Lego box. The job of the folding algorithm is, to re-create what's on the picture of the package without looking.<p>I think it's easy to see, even if you only had 2 Lego bricks, that you have quite a lot of option to put the 2 bricks together. That grows quickly the more bricks you have.
The Playstation 3 used to have Folding@Home that users could opt-in to. I've always thought that the cycles that crypto currencies burn for mining could be much better used for something like performing protein folding calculations (or something else beneficial) and mine some coin in the process.
Quick question on Alphafold - is it a one time effort ? Like human genome sequencing.<p>Like if we 3d map all the 170 million sequences (using alphafold or whatever),we are done right ? We can just look up in the library.<p>New protein sequences don't continually get created ?
>> "DeepMind seems to be calling the protein folding problem solved, which strikes me as simplistic".<p>I have a couple of questions, which might be related<p>(1) Why did you call it out as "simplistic"?<p>(2) Will the DeepMind team have to throw the same amount of computer power at each structure they seek to solve?
Slightly tangential, but does anyone have recommendations for pop sci books on modern genetics / epigenetics? (Not specifically molecular cell biology/biochemistry).
One thing the article didn't mention is what else is untouched by AlphaFold in protein folding? I've read somewhere that dynamic folding is still unsolved?
This is the TLDR from the article of the answer to the question "What is protein folding?":<p><i>If a protein is essentially a self-assembling nanomachine, then the main purpose of the amino acid sequence is to produce the unique shape, charge distribution, etc. that determines the protein’s function.</i><p>The article goes on to talk about other things, like "What if, instead of measuring a protein’s structure, we could predict it?" and that's cool, but it's sort of outside of the scope of the question posed in the title.<p>I only kind of skimmed that section because it's about this project that is trying to figure out how to predict what shapes proteins fold into. Nifty tech, but not something I care a whole lot about.<p>(Edit: If that tech interests you, there's also this on HN today: <a href="https://news.ycombinator.com/item?id=25253488" rel="nofollow">https://news.ycombinator.com/item?id=25253488</a> and I imagine that's why this was even posted -- because some people are probably wondering "What's a 101 explanation of <i>protein folding</i>?")<p>Not covered by the article:<p>Misfolded proteins are the crux of the problem with most genetic disorders. Your body produces this string of protein sequences and it fails to fold up into the unique shape that makes it a useful tool that does a specific job.<p>(I always think of some old cartoon where two kids are playing with "gender neutral spiffy spiffy high minded description" toy from Switzerland -- think LEGOS only blocks you string together and bend as you see fit -- and their two mothers are talking and then one of the kids folds the bendable blocks into the shape of a gun and says "Bang" and one of the moms is all "Never mind.")<p>Chemical derangement of the cell can interfere with protein folding. You have these little factories inside the cell that produce protein strings and as they come out, if the climate is chemically deranged (usually pH balance or salt imbalance are the culprits), then it won't fold. It just lays there, a stringy useless mess of protein.<p>When you cook an egg, the egg white turns white and solidifies due to proteins being denatured. Denatured means they got unfolded.<p>Sometimes when a protein is denatured -- unfolded -- it's reversible. Sometimes -- like with egg whites -- it's not.<p>So in some cases if you could figure out why the protein is failing to fold properly, the body can potentially re-use denatured proteins and turn them back into working nanomachines.<p>And sometimes it can't and then it has to go to some kind of garbage chute in the cell and some serious genetic disorders involve a failed garbage chute, so misfolds can't be effectively removed from the cell, which is a really huge problem. The "garbage chute" is some thing that basically digests the proteins.