Ubiquitin and Parkinson's Disease (2021) by Etsuko Uno wehi.tv

[@wafikiri_]

What makes your animation look real is the brownian movement of intra-cellular fluid's particles, constantly affecting the position and shape of the animated proteins. Also, one can almost see the electric polarity of aminoacids therein causing linkages every now and then. Not even the artificial colouring of protein parts detracts from the sensation that actual proteins have been filmed in the act. Fascinating animation!

[@y2kenh]

anybody happen to know what timescale one frame of this video represents? a femtosecond?

[@vblaas246]

@@y2kenh Protein (re)folding takes place in microseconds range. The vibrations and catalysis, reactions themselves take place in the pico and femtosecond range. This is particularly challenging for CPMD, qm-mm simulations (how to pick your dt usefully, time step). You can look up the real time transcription machinery video if you are interested.

[@y2kenh]

@@vblaas246 so... like from 5:40 to 6:10, is that just vibrations and catalysis reactions?

[@vblaas246]

@@y2kenh It's an animation, but that is more protein refolding and (brownian, random walk) protein motion. The phosphorylation reaction and linkage reactions themselves are femtosecond events 'clicks' I believe. The playback in video could be near real time in the video. Sorry if that confuses you. I don't know how best to explain. Remember it is very, very crowded in the cell. You see 1 only unit, while there are 10s of thousands proteins doing the same thing on 1 membrane. You wouldn't see a thing if all proteins would be rendered. With (FRET) color tagging you CAN actually observe how different proteins come together, real time. It is what informes creating these type of animations.

[@vblaas246]

I ment atomic bonds flexing and rotating btw with vibrations of 0,3 - 430 per second. You can see them too. They can be observed with infrared spectroscopy in pure (1 type of molecule) samples. (forget the IR glucose monitoring on wrist watches, that is not likely in my opinion, too messy a mixture, except for heart rate detection of course)

[@longboardfella5306]

Absolutely wonderful animation - it's a complex topic and this animation helps - thank you!

[@benincyprus]

I love your chaotically animated and perfectly informative videos. I know very little about biochemistry but your videos make me understand a lot.

[@Brazil-loves-you]

Best Channel from all youtube

[@arielholtz]

So f ing cool. These videos are mind blowing. Love the detail and sounds. To see at the molecule level is just crazyness! Big props to the scientists in the world.

[@dudewaldo4]

How can we learn more about the computer tools you have used to create these videos? Their faithful detail is so compelling compared to a textbook’s cartoons

[@problematic6523]

Incredible work. Wonderful animation and consistent explanations. Cheers.

[@poobertop]

The animations make me think deep about things small and large.

[@shipswithoutsails]

Excellent VoiceOver! Excellent animation! Excellent sound design! Excellent work!

[@numericalcode]

These are always amazing

[@sameerwani536]

Wow ,such an amazing animation. Thanks

[@JamesNewton]

So... When the old cell is NOT removed; that's what causes the disease?

[@vblaas246]

Same thought, not the cell though, but the old powerhouse's of the cell. The mitochondria can reproduce themselves. Still surprised me. Though tremors might be thought of burning excess of energy available? So too many mitochondria? Open questions for me.

[@pedroalvarez9146]

Actually when abnormal proteins are not degraded by ubiquitin-proteasome system, which will cause protein aggregation, obstruction of intracellular molecular traffic, and cell destruction.

[@b-chri]

I ask here because I can't seem to find really what I am searching for. There exists different ubiquitin linkages, and every one of them serves a purpose: for example, one is used for sorting (K63), and another is used for degradation (K48)...but how is the ubiquitin chain chosen? I mean, what is the mechanism that tells the various ubiquitin proteins to attach in a certain manner? Thank you for each one of you that will reply (if any)!

[@008diamond]

Fascinating!

[@namonef]

I've been thinking what if we develop parkin-antagonist. Will it cure parkinsonism?

[@bionic_yt9911]

Lipolysis next pls😢

[@medicalbiochemistry_]

Really amazing

[@sakubashiba3610]

question....What is the brown stuff in the sequence ??? is it all random everytime or is it like named differently or is it not discovered yet ???

[@regulate.artificer_g23.mdctlsk]

The entire ubiquitin protein is fully sequenced; you can check the many different sequences in the Protein Data Bank. The brown stuff are the various other amino acids that serve a structural purpose.

[@shobhitashree9294]

your videos help a lot in high school studies.. please upload some course related videos like gastrulation etc.. these are very very helpful 😊😊😊

[@paulvarn4712]

kzbin.infovideos

[@CookieAdept]

2:22 They call me cellular Pete! I'm the king of the protein beat.

[@otototeatr6293]

I'm 35y old, for 8 y I have pd, still in good condition, right hand and soft right leg to be controlled. Take care people

[@ulasdanacioglu]

What drugs do you use, we are the same age. and I haven't seen any benefit since the day I started taking the drugs. there is stiffness in the left arm.

[@shivamchatterjee2714]

So hypothetically Lys11 and Lys48 hijacking can be used as an Antimicrobial Agent? Let's say post translational selective toxicity inducing agents inserted in commensal bacteria undergoing virulence can be used as a bactricide by hindering metabolic functions?

[@regulate.artificer_g23.mdctlsk]

Bacteria don't have a ubiquitin system AFAIK

[@AK88.]

These animations need to come with drug side effect warnings holy cow that must be what acid/lsd trips are like, incredible!

[@Galbex21]

But how do scientist figur all this out? Its so tiny to see with a microscope right?

[@margueriteoreilly2168]

Brilliant Belfast Ireland 🇮🇪😎

[@spectris6306]

I still have extremely hard time understanding how the Ubiquitin gets to decide which proteins to attach to and in what form

[@shinchannohara5934]

Keep spreading knowledge bro by the way i dont know who u r since using robot ladies voice keep doing such drewberry animation they are easy to understand

[@snacktime66]

I swear to God I fucking love this.

[@kuutti256]

Wow, I never knew chicken legs could send out signals!

[@btudrus]

What is missing here is that high insulin (caused by eating sugar) is what is disrupting this process.

[@MeeMee-gz5vp]

The graphics are surreal.

Excellent! Cells work following logic processes because are controlled by biosignaly. Biochemistry has elegant metabolic pathways, complete energy production cycles and metabolic regulation and integration.

[@NewStarConstellation]

God did an extremely impressing job; it's amazing how he made this complex machinery functioning so elegantly and without disruptions.

[@tares07]

İngilizce bilmeden de bir yere kadar anlayabiliyormuş insan, bu videoda patladım işte sksjaka. Mekanizmasını tam olarak anlayamadım😢

[@6B26asyGKDo]

Amazing

[@alishanamakula]

I love proteins

[@ivankool7723]

imagine it turns to a game

[@nathanvieira5768]

Eu amo vcs pra caralho 😭

[@MercifulArchitect]

why does it all do all that stuff? I don't understand how it works, they're like nanobots. I get that they read genetic code instructions and use them to perform these tasks but I still don't get it, they're just nothing but molecules, chemicals, elements, etc... why do they behave in such a structured and almost predetermined manner. how do they even know how to move and where to go. is there consciousness on a microscopic level or are they being remotely controlled via quantum mechanics? I'm so confused, these animations are incredible at capturing and visualizing the biomolecular mechanisms... but I'm still so confused 😭😭😭

[@bili4591]

No, at these scale, molecules that have a speed of … 500 meters per second ( on average ) travel like 1 billion times or many more their size, so at these scales the molecules collides like hundred million times per second and travel in all the cell, this is called ( diffusion ). But if these proteins grab each other perfectly this is because of the specific matching form ( like a 3D puzzle ) and specific chemical property of some bits of the puzzle form that match for both protein. they need to have the good form otherwise they can’t grab. this is like that with all hormones and their receptor ( insulin, glucagon, adrenaline, angiotensin 2, etc )

[@sunisaseasan2417]

Interferon

[@Jelly-rj8fz]

this is SO intricate it beggars belief that so many still think this is accidental, not design. it is indeed beautiful and planned design.

[@riftinterloper]

Why would god create such an intricate system instead of just "creating" us without the need of complexity?

[@VariantAEC]

You understand that these things are attracted by electrostatic forces and move about the cell in a soup of other molecules based on those interactions with some randomness thrown in, right?

[@z0nx]

@@VariantAEC Yea, why do people feel the need to reach for a designer if all we know is just that the basic rules of the universe are being followed?

[@Jelly-rj8fz]

@@riftinterloper Would love to see you survive without complexity

[@Jelly-rj8fz]

@@VariantAEC this just makes me laugh it's so absurd --soup!! God does much better than that...

[@MyMy-tv7fd]

the genetic code and now the ubiquitin signalling code, it is almost like a genius designer created all these information systems inside the cell

[@VariantAEC]

Ah yes, all that random jerky movement looks absolutely... devine! Or maybe it's just how stuff moves when it's inside a fluid that contains other electrostatic forces which these amino acid chains are navigating through. Most of the fluid is made 100% transparent so it is able to be viewed by you. In reality water and other water soluble molecules are filling the "empty space" you see in these animations. So the actual functions are the result of natural forces, not intelligent design.

[@RavenWoodsDE]

@@VariantAEC Which still begs the question as to how these mechanisms came to be. There's gotta be a point to it, as complex as it is.

[@Poof57]

@@RavenWoodsDE These stuff also move like that because of their thermal energy, molecules are moving at insane speed inside a cell

[@vblaas246]

@@RavenWoodsDE Evolution to robustness in a messy environment. Competition for space within the cell. Timed clean up is essential for good signaling.

[@regulate.artificer_g23.mdctlsk]

You know, these "codes" can be - and can work in - a different combination in an alternate lineage of life, right? What you see here isn't the absolute and only possible "design" for life, it's one outcome of over 100 or 1000 million years of accumulated changes - or, as we know it as: evolution.

[@Danuxsy]

and people think they have free will? LOL

[@sunisaseasan2417]

Vaccine

[@bradhilton2283]

Is this just me or does the narrators voice sound like Angela White.