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@Ascintony3 ай бұрын
Hey I have a question. If the hydrophobic regions of the proteins are on the inside, then how do membrane proteins have a hydrophobic outer region enabling them to be inserted in the lipid bilayer?
@Tark0r20 күн бұрын
I have something can build nanobots its on my blueprint :)
@enestaylan1183 ай бұрын
This is just a correction for sickle cell disease: the mutation is on the 6th amino acid of the beta chain of hemoglobin, which causes glutamic acid to be replaced by valine, not lysine.
@differentone_p3 ай бұрын
🤓☝️
@kiuk_kiks3 ай бұрын
Great correction on a disease that evolved in (west) Africa and spread to the rest of Africa and a few places in Asia through black migrations there.
@yayforfood1003 ай бұрын
@@differentone_pur the one commenting on a video about protein folding, 🤓
@romainbourqueАй бұрын
yup, or a charging cable that can last more than 2 months
@natsora64662 ай бұрын
<a href="#" class="seekto" data-time="156">2:36</a> Wish you spent more time talking about the funnel shaped energy landscape, which is the true MVP in protein folding. Cyrus Levinthal once estimated that a protein has 10^300 different conformations, and that it would take MANY times longer than the AGE OF THE UNIVERSE to fold into the native state... but this ONLY holds true if we assume a FLAT energy landscape (such as for intrinsically disordered proteins). A funnel shaped landscape ensures that regardless of the starting conformation, unfolded proteins (almost) always fold into the correct conformation in a timely manner, just like how a ball rolls down a hill. The other things you mentioned (ribosome, chaperones, ubiquitin proteasome system) are indeed important, but the energy landscape comes first
@Clockworkbio3 ай бұрын
Such a sick setup for an AlphaFold video! Really excited to see what you’re building towards!
@danielnoon40322 ай бұрын
yoo clockwork! I'm only on this video because your plant series kick-started an interest in molecular biochemistry. thank you for your efforts and I'm so excited for the rest of season 2!
@Clockworkbio2 ай бұрын
@@danielnoon4032 really glad my videos catalyzed you enough to get to the big leagues in here! Nano is KILLER at helping folks understand the big math concepts in bio. MASTER THE CALC. RUB IT IN NEWTON'S FACE.
@amelieschreiber65023 ай бұрын
At about <a href="#" class="seekto" data-time="165">2:45</a> you mention that there is only one correct conformation for any given protein. There are about 1%-4% of proteins with multiple metastable conformations. These are called metamorphic proteins, or sometimes "fold-switchers". This is why AI models like Distributional Graphormer exist, to sample the Boltzmann distribution.
@ShauryaAlapati3 ай бұрын
ive been waiting for these to come out
@tcaDNAp3 ай бұрын
Prof. Thibault Mayor has the coolest vibe and great production in this video 🙌
@mrjesuschrist2u3 ай бұрын
10^30 possibility only takes millions of years? If you tried a new fold every second for 10^30 tries.....The protein folding problem is very interesting when it comes to origins of life on earth, time is a huge hurdle. For every 1 properly folded protein there are 10^77 non-functional(axe, 2010). Without DNA/RNA the possibility of folding into a functional protein is even worse. The math is not friendly if you appreciate the magnitude of the numbers.
@shannontaylor18493 ай бұрын
This has been explained ad nauseum. These substances have no goal, but they do have a filtered funnel to select for advantages. It's like hitting from the tee every stroke until one finally goes in vs hitting the 2nd shot from where the first shot landed, etc.
@Akazon3 ай бұрын
Yeah but it even gets crazier that proteins somehow fold together in a specific way and RIGHT time to function What would be the odds?? I cant even wrap my mind around that
@shannontaylor18493 ай бұрын
@@Akazon The odds are 1 in 1. This has already been explained.
@mrjesuschrist2u3 ай бұрын
@@shannontaylor1849 lmao where did you learn statistics? You tried to sound smart "explained ad nauseum" . Not only don't you understand the stats/maths but you don't understand the chem/bio complexity. Flipping a coins, rolling dice or shuffling a deck of cards, it doesn't have a goal and even if you got partially correct outcomes the products aren't stable so you don't get to keep the parts of the product you like and build off it. The protein problem and cellular development in general suffer from this irreducible complexity. You hit from the tee in new random direction Everytime. You role the 20 sided dice Everytime. You flip all 150 coins at once Everytime. That's just to make 1 protein and you need multiple proteins at once. The conditions on early earth were hostile, the swing, flip, or roll may be your only shot. Imagine golfing while drunk and blind folded. You can have as many swings as you want once you get out of the gold cart. You put a lot of faith in this "filtered funnel" lol
@mrjesuschrist2u3 ай бұрын
@@shannontaylor1849 1 in 1 is 100% .... You meant 1 to 1 (or 1:1) which is 50/50 lol. That's if you did one factor at a time and they only had 2 possibly outcomes, neither of which is accurate or useful in this scenario.
@br3nto3 ай бұрын
Wow. It really does seem like a 3D version of a Turing machine at multiple scales. First at the DNA scale, then at the protein chain scale with the alphabet being the different forces. That’s pretty cool. Then at the level of the completed proteins, etc etc etc.
@johnnuaxon33 ай бұрын
Holographic principle tells that information is encoded in 2d and 3d is a hologram
@IsaacMorton2 ай бұрын
Makes me wonder why we aren't trying to harness it for computation
@br3nto2 ай бұрын
@@IsaacMorton I agree. I suspect no one who gets taught biology has made the connection. Or maybe they have but they can’t do anything useful with it. I doubt many biologists or geneticists would have also studied computer science and computational mathematics.
@Witcheridoo3 ай бұрын
Your visuals always amaze me
@ramanShariati3 ай бұрын
quality is LEGENDARY
@kacemtoubal35803 ай бұрын
Hello everyone, It's been a long time since I've been on NanoRooms, I hope you are doing well, and I really hope to reveal the mystery of my question: How do our cells know that a specific protein has mutated? I appreciate your effort and time in making those videos, it is magnificent work. Thanks for everything!
@coldmossonarock77433 ай бұрын
If an aminoacid is replaced by an incorrect one during translation, even if on the catalytic site. The cell doesnt usually cares, for it makes hundreds of proteins per hour. It is always on the DNA level where it is always looking for and correcting missmatches and various types of mutations (even having different enzymes for different mutations types). As for how does the cell does that, it really depends on what caused the mutation and what effect it had on the DNA.
@ch1pnd4132 ай бұрын
The proteins that do the cell’s protein production has a double-check mechanism ensuring the code found in the dna matches up to the proper amino acid. In DNA, a set of 3 base pairs in the DNA codes for a specific amino acid or a start or a stop “codon” or encoding region.
@alsund18663 ай бұрын
I always thought that proteins each had only one way to fold but now hearing that they can accidently fold in so many other ways is really eye opening
@jpphoton3 ай бұрын
Excellent presentation and synopsis - clear and no fluff. Tanks
@charadremur3333 ай бұрын
Finely another video! 25 minutes ago nonetheless. I would love a video on how some of these misfolded proteins cause others to misfold.
@AlanZucconi3 ай бұрын
Thank you for making this, I really enjoyed it! 🧬 Can I ask which software did you use to render and animate the proteins?
@peterwhite84243 ай бұрын
Lego bricks arranged themselves more or less random and somehow our consciousness pops out in it
@fnnnn59863 ай бұрын
Thank you DNA polymerase for keeping us alive
@johnnyaxon_3 ай бұрын
Sarcasm
@grygoriyzolotarov32283 ай бұрын
I love your channel
@jIMwILLIAMS-im7kk16 күн бұрын
Imagine all these protiens foliding into the correct parameters then attaching to their corresponding protien one sfter another while being in the exact same spot all at once. (In order to swirll first life into functionality). Where did the information come from to coordinate all the individual parts of a cell ?
@OzGoober3 ай бұрын
Great work!
@Dmadiroe3 ай бұрын
Great video, thank you.
@zachreyhelmberger894Ай бұрын
Wow! great Stuff!
@SlavTiger3 ай бұрын
can you make a video talking about prp and dopple?
@jorgearango61083 ай бұрын
Extraordinary
@gleb71863 ай бұрын
Do we know why some misfolded proteins causing other proteins to do the same (like in mad cow disease)? At least a theory?
@cjdabes3 ай бұрын
An example of this, as you mentioned with Mad Cow, are prions. Some misfolded proteins induce misfolding in other normally folded proteins because many proteins in cells homomultimerize to some extent - this refers to when multiple copies of the same protein interact with one another to form a multi-unit complex. An example of this would be the Spike on the surface of SARS-CoV-2, which is a homotrimer (3 copies of the Spike protein bound together). Proteins multimerize like this because certain amino acids on an interface of the protein are compatible with amino acids on the surface of other copies, enabling them to interact. In the case of the human prion protein (PrP), the normal fold has a series of alpha-helices formed by the amino acid series; however, when misfolded into a prion form, many of these helices become beta-strands that form a sort of solenoid structure. Both ends of this solenoid structure likely serve as points at which more proteins can be induced to misfold, ultimately leading to polymerization of proteins at these ends that form cytotoxic fibrils in neurons. Here is a short article about prion structures from Virology Blog, if you'd like to read more. virology.ws/2016/09/15/structure-of-an-infectious-prion/ As to the exact mechanistic underpinnings of how the prion induces misfolding of normally folded proteins, I'm not sure that's been uncovered in detail yet. Hope that helps.
@NeidlichesSchwert2 ай бұрын
New narrator now!
@Valgween3 ай бұрын
<a href="#" class="seekto" data-time="168">2:48</a> laughs in intrinsically disordered proteins.
@ultrasoft55553 ай бұрын
Would be worth to mention intrinsically disordered proteins
@LPesi-eh3qi3 ай бұрын
Great video! I really would want to know what kind of study you did to gain this knowlodge, im a software development student, i hope to hear from you
@diabmourani96013 ай бұрын
that's so great i cannot wait until humanity will be able to defeat disease for ever
@Ascintony3 ай бұрын
Hey I have a question. If the hydrophobic regions of the proteins are on the inside, then how do membrane proteins have a hydrophobic outer region enabling then to be inserted in the lipid bilayer?
@SlavTiger3 ай бұрын
pretty sure the hydrophilic side is faced out and the hydrophobic side is faced inside the bilayer, making the two hydrophobic sides point at each other.
@Ascintony3 ай бұрын
@@SlavTiger the membrane channel transport polar substances like ions and water because of it's inner hydrophilic parts. They are also inserted in the hydrophobic lipid bilayer due to it's outer hydrophobic parts. It's the opposite of the proteins inside the cell, whish has a hydrophilic outside and hydrophobic inside. My only confusion is how the membrane proteins are made.
@SlavTiger3 ай бұрын
@@Ascintony ohhhh i was confused on that bit, i wonder if the channel substances are attracted more strongly to the membrane than they are the water by some means, or if it's more mechanically fit in like an eyelet
@Ascintony3 ай бұрын
@@SlavTiger I'm not really sure which is more attractive but the transport substances(ions and polar molecules) eventually move into the cell which is made up of water and are used for metabolic reactions
@Ascintony3 ай бұрын
@@SlavTiger are you studying a course related to biology or something
@evgenigenev59582 ай бұрын
What program do you use to make these animations
@cozumel56083 ай бұрын
oh thanks
@bradhilton22833 ай бұрын
That is some very interesting stuff.
@AmruMagdy3 ай бұрын
ارتبط صوت اللواء فايز الدويري بنصر السابع من أكتوبر ربنا لا يحرمنا من صوتك
@Ousmanedembele811Tbos3 ай бұрын
This information makes me feel fragile. 😂
@noelbreitenbach86733 ай бұрын
This channel is very awesome 😎
@Jia-9443 ай бұрын
just out of curiosity , type of protein (intrinsic disoriented proteins) does not have a specific shape, is it possible to predict its structure😢
@No2AI3 ай бұрын
Advanced Chemistry machines …. That is all we are .
@vincentcleaver19253 ай бұрын
Statistics! Or, as chemistry students used to joke, sadistics!
@Jia-9443 ай бұрын
Hi,I just want to say that your videos are soooooo amazing! ❤❤❤I am a high school student from china, I have long been wondering if using fundamental formulas like physic!! I really hope more people could know about this amazing topic therefore I am wondering if i could get your permission to share your videos on a Chinese video platform Bilibili, so more people would be able to access this amazing topic!!!😊❤
@Khashayarissi-ob4yj3 ай бұрын
With luck and more power of you.
@pyropulseIXXI3 ай бұрын
My major was physics but I took many major level biology courses because I was interested in it. It seems to me that protein folding and all this stuff is just a model that happens to explain things satisfactorily to a human mind. We have a disease that we say is caused by misfolded proteins. We have a drug that ‘treats’ this disease, so we say that the drug is helping the proteins to fold correctly. But how do we actually know all this? We don’t (since we cannot observe it, only pseudo-observe it); it is just a model we use, but this model may not have any relation to the actual truth of what is actually going on. Beyond that, it is likely not even possible to know for sure what is going on, so a model that gives sufficient explanatory power is all that we can hope for. But there are infinite models that could work on doing this job, so why did we pick the one we are correctly using? It is because that is the path humans happened to go down, and we build off prior work, so we keep building an ever increasingly complicated edifice. It is like this in physics, too, but many don’t like to admit it. They claim we are discovering actual truths rather than just constructing a model that happens to work, a model that is just one of many. But we cannot probe those other models because it takes the effort of thousands upon thousands of humans all building off each others work. For instance, we claim the higgs bosom was ‘discovered,’ but what was actually seen? Just a small blip/deviation on a graph that has nothing to do with any actual observations of particles (because such observations are impossible). With a complicated mathematical framework and statistics, we can say the model that uses higgs bosons ‘predicated’ such a blip would occur, therefore the higgs boson exists. But there are an infinite number of mathematical models that can generate such a blip, thereby ‘predicting’ whatever we want via the injection of an explanation that is attached to the predictive model. Science claims to be empirical, but it isn’t entirely (and isn’t mostly). It is far more in the depths of rationalism, using 1% of ‘observations’ to claim stuff exists we never observed, just because our rationalism-generated model has a blip, and we observe a blip, therefore this thing we never saw, but attached to the blip via our model, exists. It is like this in molecular biology. I can observe the projectile motion of a baseball; I cannot observe anything on a molecular scale. It is all just rationalism, where 99% of stuff we believe in isn’t ever observed. But we observe something that our model attaches to the thing we cannot observe, and then we claim the thing we cannot observe has been observed (via the model) and that it therefore exists. Same with these proteins and protein folding, and drug interactions. We cannot observe how drugs actually work, so it is just a story we tell ourselves of how it works. If we could actually observe such interactions, we’d know how all drugs work, just as easily as observing someone throwing a ball, or how a mechanical watch works (actually observe it, not pseudo-observe it). But since we can’t, we don’t know how anesthesia works…. until we create a model that explains it, then we claim to know how it works (when we don’t; we just know how the model works). The model is not reality, so don’t confuse the model for reality.
@98danielray3 ай бұрын
good job rediscovering philosophy of science
@bataalexander97033 ай бұрын
If a protein is prone to misfolding, then perhaps its primary structure is not optimal, there has to be a better one.
@vinniepeterss3 ай бұрын
top notch
@jinanren20263 ай бұрын
nanomachines son.
@kaba19963 ай бұрын
Let's goo!
@franciscomendoza7543 ай бұрын
This is so cool, and so soooo interesting, but is too much for my little mind :c
@sssssnake2223 ай бұрын
Atomic dimensional life designed us.
@empmachine3 ай бұрын
Hydrophobic VDWs eh? Sure you aren't buzzwording a bit?? ;p Great video!
@hamzacasdasdasd3 ай бұрын
neture is the only think cleverly designed not by humans
The information for a human being or other multicellular animal is not only stored in the DNA. The DNA is one long term memory system within a cell but not the only one. One major point of this is that scientifically we know beyond a reasonable doubt that there is a swarm intelligence going on inside cells and between cells, but we only have a partial understanding of how this works and there are a number of aspects to it we completely do not know. On the other hand, we know enough to be able to see that it will be only a matter of time before we do fully understand this, whether it takes 10 years, 100 years, or a 1,000 years to gain such full understanding.
@anon5897316 күн бұрын
Wrong
@MusingsFromTheJohn0016 күн бұрын
@@anon58973 sorry you are unaware of what is going on in science and technology. Fortunately science and technology continues to advance regardless of what you believe or what you want.
@jdkingsley65433 ай бұрын
It blows my mind that we can study something like this but cant solve some of humanities other issues. Like poverty- just amazing b
@vinniepeterss3 ай бұрын
❤❤❤
@htopherollem6493 ай бұрын
better vid title suggestion "biological protein folding and what can go wrong " because of the prevalence of "clickbait titling " I nearly disregarded your video about a subject that I would love to know more about.
@Valgween3 ай бұрын
there is a browser extension called DeArrow. which is a browser extension that removes clickbait by replacing it with a user sourced thumbnail and title.
@Alpha_GameDev-wq5cc3 ай бұрын
What’s the clickbait? These are literally nanobots
@htopherollem6493 ай бұрын
@Alpha_GameDev-wq5cc I didn't label it clickbait, I nearly mistook the title for clickbait. the title doesn't give much of a hint as to the subject matter and if clearer may garner more views.
@earthbndmsfit3 ай бұрын
Bioweapon
@SB-nd4yv3 ай бұрын
suberb!
@양익서-g8j3 ай бұрын
Westworld
@IB4UUB4ME3 ай бұрын
I’m sure that there won’t be any argue I g here over who is right and who is not, right people? 😂 😂🤦♂️🤦♂️ Unfortunately they were perfect at one time, and will be again.
@hamzaabu-zaid25963 ай бұрын
AAAAAAAAAAAAAAAAAAAAAAAAAUG
@gianpaulgraziosi61713 ай бұрын
It’s called the immune system.
@peopleofearth62503 ай бұрын
Protein folding is foundational to the immune system, not the other way around.
@tom-hy1kn3 ай бұрын
But who made our cells?
@johnnuaxon33 ай бұрын
George
@123ghassan1233 ай бұрын
Science is the 20th century Gods Last Messenger.
@Duggleftforthemilk3 ай бұрын
This is proof of the Lord's Design.
@ILoveTinfoilHats3 ай бұрын
Ok buddy
@Philalethes1013 ай бұрын
@@ILoveTinfoilHats Let me guess, it just evolves?🤣
@johnnuaxon33 ай бұрын
Nuclear weapons is the proof
@Alpha_GameDev-wq5cc3 ай бұрын
@@Philalethes101 Yes you illiterate
@Alpha_GameDev-wq5cc3 ай бұрын
Literally the opposite… get out
@differentone_p3 ай бұрын
good morning I hope you had a great day today love you too baby girl I love you too baby girl I love you too baby girl I love you too baby girl
@Alpha_GameDev-wq5cc3 ай бұрын
<a href="#" class="seekto" data-time="508">8:28</a> Oh My God get this professor out of the video… he can’t F-ing use a marker without constantly creating that unbearable squeaky noise. Literally unwatchable, I had a physically painful experience… Jesus christ
@tausifnazim50482 ай бұрын
Thanks to Darwin. He made such evolution possible.