If you have a simple organism, like an archaeal cell, here's how it goes: The DNA is all one giant circle. And it's not like there's just one conformation. 0. Log In Sign Up. TikTok wrap hack revived! I feel like I have seen a movie like Inception—-well coordinated plan of attack is executed. A ball on a hill will roll down hill until it settles into the lowest valley it can — the place where its potential energy is lowest. When you start to ask questions about how a protein moves over time, it becomes a much more complicated problem than predicting the overall conformation. An Australian woman first revealed a 'game changing' way to toast a wrap A mirror of Hacker News' best submissions. Hopefully this explains why there is a single shape that proteins are most attracted to when folding. Or imagine someone with less than 50% of the mining power trying to do a double-spend attack: normally this is discouraged by the fact that double-spend attacks are probabilistic, and the attacker has to pay the full cost for doing the attack regardless of whether it's successful. Otherwise, it's the other way around: the shape of the backbone is determined by the detailed interactions. New top story on Hacker News: New York City: The Most Expensive Mile of Subway Track on Earth. This is last year's entry from Deep Mind: I don't actually know. Couple other things that are crazy to me: Great video, but without any comments and the very few captions it's quite impossible to understand what's going on. I write all of the posts and host all of the podcast episodes you'll find on the Evolving SEO blog.iam jsut exploring my knowledge and help other people by writing article related Hacking and current ugrades. DNA is like the source code for protein. Create a sequence, fold it, see if it has the desired structure, tweak sequence until done. Menu; DUK News. The cell has chaperones that help proteins fold, and it has quality control mechanisms that try to remove misfolded proteins before they are released into the cell. So if you have, for example, cystic fibrosis, you have a defect in a cell channel called the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and its job is to handle traffic of specific molecules into and out of the cell. User account menu • What is protein folding? Proteins are large, complex molecules essential to all of life. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. I'm Akash kumar. I hope this comment is correct enough and clear enough for an ELI5 — though it might be more of an ELI15. What is protein folding? What does it mean when it says “Your DNA encodes these sequences”? Previous versions of the wrap have included chocolate, marshmallows, hot chips and deep-fried chicken. Especially in the plant world, sequencing advancements with nanopore sequencing only recently made it economical (and possible) to sequence a lot of the plant genomes that are many times larger than the human one. >When they start coming out with articles saying "This project has successfully predicted X and this is clinically useful in this way," I'm sure I will read it on the edge of my seat like a gripping thriller. Arc virus capsid-like protein used in the brain Oct 10, 2017. hRpe65 enzymatically produces the retinol required for human vision Sep 4, 2017. Maybe you even die and become an evolutionary dead end. More recently NMR has been used, which gives information about the environment that the various nuclei occupy, and what their neighbors are. Basically they alter the lowest energy to be a different arrangement. So they appear some ~4k in the genome, before each protein-coding gene. We can also imagine another scenario. The popular personal trainer, who has over a million followers on Instagram after a decade in the fitness industry adds zucchini, sweet potato and capsicum to her version of the wrap. Proteins may be small and unassuming, but these molecules are essential for a variety of biological functions in all living organisms, including digestion, immune response and even intracellular communication. I wish more complex concepts were explained with so much clarity and concision. Folding uses around 500MB of RAM so you'll be good with either a 1GB or 2GB model. I honestly have no idea what your point is. But, it doesn't explain why other shapes are somehow "invalid". 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. July 3, 2015 - The brain is like crumbled paper. Maybe I'm misunderstanding the purpose of the site, but this is silly. How on earth do we make sure that the ribosome starts at AUG? SaBE4-Gam converts specific C->T Jul 14, 2017. Discussion-worthy Proteins. hide. June 29, 2015 - Animal language vs. human language. 14 members in the fastvoted community. So your question is a little like asking "Why can't the cell just spit out random tools that randomly do different things?" According to the researchers, 10,000 measurements using an 81-qubit version of the experiment gave the correct answer just 13 times. Wow!!! rather than "what is the perfect way to do it? It's not uncommon -- it's essentially the norm. Scientists don’t yet fully understand the mechanics of protein folding. A mirror of Hacker News' best submissions. Proteins are not stagnant—they wiggle and fold and unfold to take on numerous shapes. Essentially all of it. Stanford's Folding@home project has simulated Src … [NOT LAUNCHED YET - ALPHA TESTING] A Hacker News mirror biased in favor of thoughtful discussion … Press J to jump to the feed. I think at least some of this can be solved for or inferred from the final shape once it is known. We know how certain residues affect tertiary structure, and we know the measurements of secondary structures with a surprising degree of accuracy, but for a protein with potentially hundreds of residues, there are simply too many degrees of freedom to simply tack on amino acids and come up with a structure (although this is essentially the approach that markov chain, monte carlo solutions use). Nearly every function that our body performs - contracting muscles, sensing light, or turning food into energy - relies on proteins, and how they move and change. Protein chemists have always wanted to follow kinetics in the mid-infra-red region (mid-IR) in order to better understand protein folding and to obtain information about secondary structure changes involved in the folding process. Additionally, proof-of-work systems used by a decentralized cryptocurrency can't rely on a centrally-produced dataset. But now as you come to rely on lactose, that protein will wind up back under purifying selection and become "fixed". (this is simplified but you get the idea). 2018; 559(7715):643-645 (ISSN: 1476-4687). Maybe the flagging system is too slow, or we need downvoting, there should be a better way to make sure that HN front page articles are informational. DeepMind's entry, AlphaFold 2, blew the field away. Like the parts of a mechanical machine, the protein's shape is part of what defines how the protein works, what it can "do", and how it fits together with other pieces of the cellular machine. Someone will probably need to correct me, but here's how I understand it. I enjoyed The Gene by Siddhartha Mukherjee. This is the TLDR from the article of the answer to the question "What is protein folding? Apologies if I spam this stuff too much but I'm so intrigued by the dynamic complexity of this whole thing. More News & opinions Deep Learning Aces Protein Folding Don Monroe Commissioned by CACM Staff The Non-Psychopath's Guide to Managing an Open Source Project George V. Neville-Neil The World's Most Magnificent Historical Calculating Machines Herbert Bruderer Here we aim to help as many people as possible suceed in the world of Technology. Really good explanation. Some studies suggest that Cystic Fibrosis is a predominantly Caucasian disorder because having one copy of the gene is protective against certain disease that were sweeping through Europe at one time. Thank you so much, so I can look at them like … A misfolded protein is at best useless, and as you can see with prions can also be actively harmful. Comment I replied to initially only said My point is that's a long way off. Nature. 50.8k members in the hackernews community. I genuinely thought it was helpful, too! Then, our protein would be totally different, and would look like this: So organisms also transcribe, at the beginning of the gene, a "ribosome binding site", or "Shine Dalgarna/Kozak" sequence. I unusual describe it as, someone gives you all Lego pieces in a Lego box. We need to study not only one shape of the viral spike protein, but all the ways the protein wiggles and folds into alternative shapes in order to best understand how it interacts with the ACE2 receptor, so that an antibody can be designed - From Folding@Home Takes up the fight against COVID-19 http://blogs.nature.com/news/2012/08/d-wave-quantum-computer... https://www.youtube.com/watch?v=B9PL__gVxLI. Which means if you want to access that data in the DNA, you need to go through an intermediate, which, when it leaves the restricted area, is ok if it gets destroyed, because that original copy is still intact. To be fair, "solves protein folding problem" is a, I guess the bigger question is: what can we. My impression as a non-expert from reading the last thread is: Great result, in sore need of external validation (just like every other piece of research). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3070458/, "Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation", https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456219/. Furthermore most proteins were measured in crystallized (i.e. April 29, 2018 - Painters & Hackers. Also I have read that it is believed that half or more of all human pregnancies probably end in the first two weeks and result in a heavier-than-normal period without the woman even realizing she was ever pregnant in most cases because those fetuses are simply not viable. The whole thing is really like a wiggly, jiggly, metastable mass, and the introduction of a slight perturbation is enough to send the blob spiraling into a new metastable state. to call a function, the cells look for the following DNA sequences (they all vary a little depending on what organism): The BRE: CCCTCC. It's going to take quite some time until this gets accepted at the same level of experimental data, if ever. Specific triplets of bases along the chain correspond to specific amino acids, so a DNA strand ultimately results in production of a specific protein molecule. not their natural) form, so the resulting static structure is likely not representative (even less if parts of the protein are "moving" to perform their function). So, RNA is basically DNA that's been read to memory, and can now be messed with. Any portions of these operations that require chemical energy to be input not only need to have the structural features required to support the reaction, they also need to have the structures required to allow ATP to power that reaction. The first triplet is usually AUG, which codes for the amino acid Methionine. Because of its rock-like stability, the protein has become a test bed for cryo-EM: a structure of the protein with a resolution of 1.54 ångströms was the previous record 3. It can do it a little bit, but it's not great. You should have selected a title that's more in line with the article. A specific protein called TATA-binding protein will bind this. A mirror of Hacker News' best submissions. E.g. I genuinely thought this was helpful! So that's how you get just the RNA for your gene. https://moalquraishi.wordpress.com/2018/12/09/alphafold-casp... https://en.wikipedia.org/wiki/Levinthal's_paradox, https://news.ycombinator.com/item?id=25253488. 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