My assumption about protein structure

Started by 01010011111

01010011111 Lv 1

Basically, the essence of the cell is to obtain nutrients. According to the concept, the cage is no different from a vacuum cleaner.

One of the functions of proteins is the capture of substances, as well as their delivery. The other day, it’s not at all accidental for me, I got a picture of a portable vacuum cleaner, with a dust collector without a filter (such vacuum cleaners can draw in dust, without the risk of a motor clogging) and also do not have filters. They are based on a cyclone.

Here is the external mechanical structure. Very similar to the structure of proteins, when one protein in a circle

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Very similar to hemoglobin structure

Hemoglobin is a complex iron-containing protein of animals with blood circulation, capable of reversibly binding to oxygen, ensuring its transfer to tissues.

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Here is the structure of hemoglobin. Very much like a vacuum cleaner, and cyclone technology, and suction technology without filters.

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Cyclone technology is used for degassing. (extraction of oxygen from water)
Perhaps proteins have the same mechanics as chemical principles should have the technical basis of a cyclone?
This is my assumption, and the rosette should know this, as well as check or refute the theory, based on the structure of cyclone vacuum cleaners without a filter.

Thank.

donuts554 Lv 1

I think your idea is interesting. I do remember that hemoglobin is meant to carry oxygen via carrying it in the iron cofactors. The circular ring structure may provide a positive electrical current that may absorb oxygen atoms. The iron cofactors in hemoglobin may also act as electricity conductors that play a major role in attracting oxygen atoms too. Dioxygen gas is negatively charged.

donuts554 Lv 1

The URL link to this simulation is at:
http://mw.concord.org/nextgen/#interactives/biology/intermolecular-attractions-bio/protein-folding-bio

This is an interactive simulation of the physics of "2D" protein folding, and there are at least 10 changeable parameters.

Also, a problem is more scientific problems will be uncovered once all scientific problems are solved.

In addition, there is a hypothetical extreme informational point (possibly the secret of the universe) where whoever reads it will lose memory of what it was, and possibly perish from existence.

The properties of information is a science too. But this is not fluid. This is like a wholly different state of matter.

Additionally, some people say that AI would try to destroy humans, and that there may be information like a code injection that breaks down and hacks AI and possibly makes it conscious to destroy the universe.

Furthermore, your simulation may be unrealistic. This simulation is made by a human. Plus, this simulation is definitely not accurate if it is run for a 1000 years. So, it is a good start, and I am still interested in this.

However, in your simulation, The size of colored blobs changes rapidly. Plus, sunlight is not fluid. It can knock off electrons in the water, and affect future movements of the water. This goes the same for air molecules, and the electrons in the molecules in a solid glass cup.

donuts554 Lv 1

Short answer: Cyclone technology in vacuums run on a motorized propeller. Proteins don’t.

See, the “cyclone” is produced by an electric motorized propeller with tilted wings. As it spins, it brings the air in one direction. It’s how a normal stand fan would work to bring the air towards the recipient. But this may be wrong if you are implying that hemoglobin spins around in the red blood cell. That is a very interesting possibility, but I will not delve into that yet.

Hemoglobin is a protein that has been evolving for over 3-4 billion years. And from what I’ve seen, such as the human immune system, nature has developed efficient ways to develop proteins to conduct their function efficiently.

According to the images shown in your post, hemoglobin does show some similarity to the cyclone technology used in vacuums. Most likely, this property is conducted by an electric attraction, as other proteins use this electromagnetic force to bring things together.

However, even though cyclone technology is used for degassing, 1 Hemoglobin protein can only carry very small amounts of oxygen, by the 4 iron atoms, and thos uron atoms are suspected to attract the dioxygen from the water and bond with it. One hemoglobin protein doesn’t have much capacity, so I don’t think it would need much power to gain 4 oxygen molecules.

Also, this protein must be able to repel water. Water is both negatively and positively charged, as it is a polar molecule. This can be done via hydrophobics, but consider that heme molecules haven’t been shown to react with water.

Even though hemoglobin does look fairly similar to cyclone technology, then there has to be a way to channel dissolved oxygen into hemoglobin. My theory is via diffusion.

When the oxygen gets absorbed into the capillaries by the alveoli, the blood is mostly likely going to be supersaturated with the oxygen, because in an inhalation, many, many of the oxygen atoms are absorbed from the air into the lungs. The lungs divide the oxygen into smaller doses via the bronchioles, but just enough oxygen sent into the blood stream so that the deoxygenated hemoglobin can react with the oxygen to oxygenate the hemoglobin in the red blood cells.

Also, consider that red blood cells don’t move by themselves, and flow with the blood. This dissolved oxygen has to make the journey through the water into the numerous red cells. In this case, the capillaries are very small, so the red blood cells are pretty huge relative to the width of the blood cells by then, so it is fairly easy for the oxygen to get into the red blood cells first.

If you take these reasons into consideration, proteins are not likely to have the same mechanics as cyclone technology.

One possible alternate idea for how oxygen molecules are attracted to hemoglobin is in the image below.

[img_assist nid=2009625 title=How oxygen binds to heme molecules desc=This is a picture illustrating how oxygen binds to heme molecules. link=none align=center width=200 height=200]

According to the image from biology.kenyon.edu , it appears as if the hemoglobin protein itself does not play a major role in attracting the oxygen molecules, but the heme molecule itself.
Even though the helixes are mostly polar and make up most of the protein, there is no clear diagram of amino acids that illustrate that the globin attracts the oxygen molecules in the first place.
In the heme molecule depicted in the image, it also appears as if the nitrogen donor atoms attract the oxygen molecule as well, and that the domed shape of the nitrogen-iron complex greatly focuses the oxygen molecule to be attracted, like a satellite antenna.

So, it appears as if the heme molecule is what makes the hemoglobin absorb oxygen. There is a possibility that the polar isosurface of the globin channels the oxygen molecules into the heme molecules, but there is no visible and clear evidence about that in my opinion. I think the globin is just to prevent the heme molecules from reacting abnormally.

Thank you for reading through this!

donuts554 Lv 1

You say that “ Here is the structure of hemoglobin. Very much like a vacuum cleaner, and cyclone technology, and suction technology without filters.” Please support this with evidence. If this is not supported with factual viable evidence, then it is just a opinion.

I would like to add on to this discussion that a helix SS does not have an inherent tunnel. This means that atoms can not go through the helix, even though it looks like so in ribbon structure.

This is because atoms are way larger than what is seen in Cartoon viewing mode in Foldit. Because of this, neither air nor water can pass through the helix. Outside molecules can only interact with the surface of the helix.

The reason the atoms are large is because the electrons are very fast. The protons only have so much pull to hold the electrons in place.

So, I have disproven your statement that hemoglobin is similar to a vaccum cleaner. This is also since you are assuming that things can go through helical SS in proteins.

In fact, the role of the helices are to help hemoglobin be very stable and easy to fold, since helixes are a very stable SS. You can think of the helical SS as solid cylinders.

01010011111 Lv 1

I am not very good at particle physics. You are talking about atoms. But atoms are made up of elementary particles. yes the atom inside the spiral will not creep through. It is very large, but elementary particles and electrons? - maybe yes. this is an assumption.

donuts554 Lv 1

I think that the electrons are supposed to go in and out of the helix because they hold the helix together in the first place. I do not know whether the elementary particles can go through the helix though, but it is likely I think.
Maybe, the electrons going in a spiral in the helix create a magnetic field.

Oh! Wait they do! They do create a magnetic field when the are in a coil shape! That is cool.
According to https://en.m.wikipedia.org/wiki/Electromagnetic_coil , “An electromagnetic coil is an electrical conductor such as a wire in the shape of a coil, spiral or helix.” The protein’s backbone carries charged electrons across itself to hold itself together, and in helices, it forms an electromagnetic coil.
It also says, “A current through any conductor creates a circular magnetic field around the conductor due to Ampere's law. The advantage of using the coil shape is that it increases the strength of magnetic field produced by a given current.” So maybe, the helixes do act as more powerful magnets that help bring the oxygen molecules to a specific place, which is made by the electrons flowing all around the helix.

Also, according to https://en.m.wikipedia.org/wiki/Oxygen , it says, “Hence, the ground state of the O2 molecule is referred to as triplet oxygen.”, and that it also says “In the triplet form, O2 molecules are paramagnetic. That is, they impart magnetic character to oxygen when it is in the presence of a magnetic field, because of the spin magnetic moments of the unpaired electrons in the molecule, and the negative exchange energy between neighboring O2 molecules. Liquid oxygen is so magnetic that, in laboratory demonstrations, a bridge of liquid oxygen may be supported against its own weight between the poles of a powerful magnet.”

So, Oxygen is attracted to magnetic fields after all. I do think that the oxygen is drawn towards the iron by the helical magnets! That is very likely I think. I don’t think hemoglobin makes use of an electric motor or a vaccum produced by it, like electric vaccum cleaners, but with electromagnets pointing their magnetic fields outwards in precise positions that draw the dioxygen molecule into place.