Simulation of millisecond protein folding: NTL9 (from Folding@home)
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- Опубликовано: 8 сен 2024
- Simulating protein folding on the millisecond timescale has been a major challenge for many years. In a recent paper (pubs.acs.org/do..., Folding@home researchers Vincent Voelz, Greg Bowman, Kyle Beauchamp, and Vijay Pande have broken this barrier. This is a movie of one of the trajectories that folded (i.e. started unfolded and ended up in the folded state). From simulations like these, we have found some new surprises in how proteins fold. Please see the paper (url above) for more details.
Biocem prof. played this in class and people were howling at the instant replay. That C terminus... damn. Gotta love it.
The music though 😂🤣
😂
Mesmerizing. It's quite unbelievable that structures and processes incredibly complex and precise simultaneously, such as those featured in the video, all arose naturally in biological systems, propelled by the laws of probability alone. Biological molecules never cease to amaze me, with their virtually unlimited capabilities originating from their seemingly disordered structures. It's as if order randomly arose from the disorder of randomness, and is creating more order by means of it. Perhaps that should be the true definition of life. And in that sense, not only complex biological systems, but also every one of these proteins and other organic polymers composing them should be considered "alive".
It is, isn't it. You wouldn't even think this stuff exists, and yet it does, and even if you knew mostly everything about the basic atoms... The things they build when combined with other atoms.... Magic occurs.
All of this magic, created itself by probability alone. And there could maybe be an infinite amount of such proteins.
@@tiffanyfrank3654 . . . to each his own comfort zone . . .
It's a nice sentiment -- but if that's your definition I think anything that has crystallized also would count and that doesn't make sense to call it 'alive' imo.
Suppose the end fold of every arranged set of molecules possible along with time necessary could be predicted in a millisecond on a microprocessor. And suppose you had a supercomputer with as many such microprocessors and memory as there are proteins on earth. And suppose you had just one generic protein fold pattern in mind. Using either random molecule generation, or a genetic (mutation) algorithm, or some other genetic algorithm or even the fastest algorithm anyone has yet come up with, could your computing apparatus find the protein that most optimally folds into that shape? I'm presupposing you let your apparatus run for 3.8 billion years non stop? NO. Therefore, how did evolution do it and redo it for thousands of different protein shapes?
what makes them alive is the electro static charge, electrical fluid, china calles yin yang primordial qi, vapor,gas, americans say electrons or positrons, electro static fluid, all matter is inert,or passive, what makes them move,or alive, is the electric fluid you should seriously read chinese or indian metaphysics, because all matter moves only from that
Haha I love the choice of music!
too dramatic?
better to have a voice explaining what heck is going 0n?
man the body can do this by itself while we need thousands of pcs from around the world to simulate this in like 500 years, insane
Great simulation and music.
I would love to see the folded protein from a covid - 19 virus molecule! I hear its quite interesting!
*molecular structure 🤓
@@ahtzee9078 errmm, its actually called a polymolecular structure, or polymer, but i understand your confusion. happy to help though!
How do you make this! From primary to final protein structure please reply me
How long did this simulation take folders to complete? Days...for 1 millisecond? Worth it :) Hope we all reach the personal supercomputer age soon.
if you have a few xp titans thats probably faster than the hardware being used lol.
Beautiful.
Love it!
LOL @ instant replay!
very good
If you would make such computers available for our simulations guys, I think they will worship you as their new god.
In reality many research institutions have to go with normal clusters crowded by many people with different objectives, making it usually only possible to simulate small proteins for nanoseconds (and then maybe no explicit solvent, and other simplifications of the system)
i'm hyped
this is oscar-worthy
that protein is meant for great things!
I'm sorry for my unacademic comment but,
SCIENCE BITCH!
IT'S F-ING AWESOME
This is nature not science.
GeorgeGR8 uhh you don't get crystal structure of proteins without a scientific approach my silly combative friend!
@fucker999 no, of course not. the video is timescaled to about 10000x slower speed.
Could we simulate water molecules and protein inside it bumping into water molecules to have 100% accurate prediction of folding?
Yup if you can simulate the electric field gradiant you can predict what goes where once you know the starting point. I can run simulations like this rather quickly and one surprizing one was substituting a few molecules of ethonol in the sequence. This would cause misfolding of the original c19 spike as one part is tightly wound. It was put to the test in feb of 2020. A few shots of hard liqor as hot toddies gave relief in less than 12 hours. Go figure. 🤔
@@christopherleubner6633 thats actually a common misconception, since the electric field gradient is actually 3d, youd need really complex vector calculations thatll cause your hardware to shit the bed. so although its technically possible, its highly unlikely you could do it yourself on your little home pc.
mindblowing
Every molecule looks blind but alive, searching its partner blindly, CREATING STABLE AND ORDERED STRUCTURE. But this blind effort is based on systematic principles of maths, chemistry, physics....
👏👏👏👏👏👏👏👏
The suspense is KILLING ME!
So what takes our biology 1 millisecond took this long to simulate??...that's a lot of figuring out power needed for the computer to even come close...
Can somebody dumb it down and tell me if this is how a protein would look like under a powerful microscope? I know this is just a model (hence the yellow arrows), but I get so confused by all these colorful spirals and those balls that are folding on my computer. What exactly am I doing with F@H?
I know this comment is 7 years old, but I don't think you could see see proteins on this scale very well with current microscopes. Not 100% on that, but these are very tiny. Check out info on secondary, tertiary, and 4tionary folding, you'll see about things like beta-barrels, alpha helixes, and other stuff that you can see up in this video.!
Estácio University send regards.
Don't these chains get all tangled up? I mean you should see the ungodly pile of spaghetti behind my TV! (and that's a much simpler system) :/
Dramatic😂
I just want a crown hat! lol...
hi john
You can see how jittery the molecule is. That's why xanax works in humans. #science
hi lucas, lovely weather, eh?
Do I need a background in bioinformatics to work on the software side? I would like to create a protein folding simulator.
astrophysx do reasearch and use anim8te Windows
I got ur c-terminus all right....... Hangin
Ok! and what did this just prove, for the guy that has no idea what hes watching?
protein go foldy
When the C-Terminus slid into place Life became possible
So where are the cures? With PentaFLOPS of computing power you'd expect major breakthroughs in so many years.
i don't think you understand how science works. try again.
daMN UR HARSH AS FAQ >.
prevention is key to the cure?
as long as there is $$$ in medicine the cure is not in near future? illness is a huge industrial machine which many holding power want to keep it that way(iNdirectly).
penta, hexa, hepta, octa, nona, deca floppity floppity flops. Someone does not know neither science nor greek
so dramatic
boring...
hi john
hi john