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In several animations of biological processes (eg protein synthesis (go to frame 1.20mins), DNA replication, etc), molecules such as amino acids are shown heading straight to the replicating protein as if drawn by a magnet. As far as I know they move randomly. But still, translation occurs at a rate of about 15 amino acids/second and 75 ATP/second, so the rate of gobbling shown in the video clip is not off the mark.

I can think of two explanations:

1) The microscopic world is counter-intuitive. It is so frenetic that normal diffusion is enough to supply the hungry protein. The video simply doesn't show all the input molecules in order not to clutter the picture but essentially it is correct. However, amino acids are not small, and they are attached to the much larger tRNA, so they must be moving relatively slowly by Brownian motion.

2) There are additional helper proteins that concentrate or channel amino acids and ATPs in the vicinity of the ribosome or replicator. Never heard of these.

What is the real explanation?

Edit: To clarify, the question is not about the simulation side of things as such, such as how hard it is to actually make a true simulation. Most simulations, including weather prediction, involve a certain degree of approximations and simplifications. But in this case, there is something definitely untrue in the video clip, namely the molecules being attracted to the ribosome. As explained by a moderator, this means that it is not a true simulation but a "cartoon". So the question is: what would an ideal "non-cartoon" true simulation look like? Would the tRNA be diffusing in at a very fast rate, or are there helper proteins that, for example, tether tRNA in the vicinity of the ribosome? The moderators seem to indicate that diffusion is enough, but I would like to see a reasoned out answer with numbers that show this is the case.

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  • $\begingroup$ You are not talking about computer simulations, you are talking about video cartoons. But it is not clear what your problem is. You have provided no calculations that suggest that the concentration of amino acids and ATP and GTP in the cell are insufficient to support the reactions of protein synthesis in which they are involved. Until you do so, there is no question to answer. $\endgroup$ – David Sep 9 '18 at 18:45
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    $\begingroup$ @David I think the argument on computer simulations vs cartoons is missing the mark here. The OP has a pretty clear question that isn't related to the simulation/cartoon issue: is diffusion at the scale of protein synthesis fast enough to explain the rate of synthesis, are there helper proteins such that there is locally a higher concentration of amino acids than in the rest of the cytosol, or is there something else going on. $\endgroup$ – Bryan Krause Sep 10 '18 at 21:45
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    $\begingroup$ @David I understand your criticism, but I don't think the OP has that problem. They are having a hard time imagining conceptually how complex molecular reactions like protein synthesis occur; they show pretty clearly that they know it's not exactly like what they saw in an animation because they realize that the amino acids aren't just magically flying in. Just because you know one of their hypotheses is wrong doesn't mean you need to ridicule it - in fact, they already show some uncertainty about that idea because it doesn't quite seem feasible to them. $\endgroup$ – Bryan Krause Sep 10 '18 at 22:00
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    $\begingroup$ @David I think their comment about an established research group came as a reaction to your comment that they provide calculations that show there isn't enough ATP around - I found that somewhat rude. They just seem to be trying to defend why they have a question: the rate at which things proceed seems inconceivable to them in part because we don't have daily experiences at a molecular level. They are asking if diffusion is enough or if there is something else. I don't see why a calculation is necessary to have that question. Their title could be improved but that's it. $\endgroup$ – Bryan Krause Sep 10 '18 at 22:07
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    $\begingroup$ And my comment about ridicule was about your comment that you deleted. Thank you for revising it. $\endgroup$ – Bryan Krause Sep 10 '18 at 22:10
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tldr:

  1. Making these things accurate representations is really hard
  2. Accurate representations can be hard to look at anyway, so aren't always good to convey understanding

Molecular dynamics simulations that span long periods can be really expensive because of how computationally demanding they are, and they rely on accurate structural information about all of the molecules involved which isn't always available. The animation you linked might not be an actual simulation for that reason, but you'd have to check for yourself. Really fine grained accuracy probably isn't a priority for making a cool teaching tool like this one, you just want people to understand the just of it and the Brownian motion there might be a stylistic choice. Again, you'd have to chase it up for this specific example, I just want to give you something generalizable to other animations.

To make macromolecules like this actually interpretable by humans it's important to simplify them. One of these simplifications is normally called a 'cartoon', I don't think they guy in your comments was taking a dig at credibility of the video. It's also important to hide all the water molecules because they get in the way of you and seeing what's going on, so that's another way in which it's been simplified.

If you haven't already, have a look at some proteins in the PDB on the structure viewers and switch the mode from the cartoon/ribbons to other models like ball and stick. Ribbons are a useful way to simplify the structure representation so that you can see what the backbone is doing.

Here's one that I like: https://www.rcsb.org/3d-view/4KEY/1

And you're right, at the systems level of something like protein synthesis, lots of stuff is involved and it's not practical to show all of it. For something like that it's easier to show these processes a a graph (term for connected nodes), check out the KEGG database for examples:

https://www.genome.jp/kegg/pathway.html#cellular

Hope this helps

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  • $\begingroup$ What I don't understand is, why exactly is it so hard to simulate accurately? Is it because there are many more tRNA molecules than can be shown clearly (they would clutter the visual), or is it because the molecules are moving much faster than in the video clip (you would hardly see the tRNA fly by)? $\endgroup$ – Chrystomath Sep 11 '18 at 8:16
  • $\begingroup$ It's more the number of time steps and the number of atoms in the simulation. So in that video we have a few different proteins, some DNA, tRNA etc and a lot of water molecules (which are hidden). That's a lot of atoms and for each one you need to calculate its new coordinates between each time point based on its local environment. So the demand on a computer is really huge. Also all the parameters are based on measurements taken from model systems like dialanine (maybe, out of my comfort zone a little bu here), which might not be perfect. If this doesn't help, could you restate the question? $\endgroup$ – JEngleback Sep 11 '18 at 12:55
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The good explanation is the second part of your question which you never heard of.

Actually for every movement in the cell, proteins play important role rather than nature of solvent (hydrophobicity, hydrophilicity or other forces) play any significant role. Brownian movement is also insignificant as you know AA (Amino Acids) can be more polar or less polar. Also they can't guide themselves to the desired location in the cell. Proteins which relocated them, cause their faster efficient and direction movement (may be due to formation of gradient or some sort of pulling pushing force due to interaction with other proteins.)

[UPDATE]

Exploring more into this, I came to know that the movement of anything is dependent on a gradient (May be concentration, electrochemical, pH etc...). So everything inside the cell is well planned and well documented inside the genome.

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  • $\begingroup$ Please cite peer-reviewed papers or reviews that provide evidence for your assertion that there are proteins that relocate amino acids in a cell. $\endgroup$ – David Sep 9 '18 at 18:42
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    $\begingroup$ Better I move to researchgate or some other place or I try to publish my review paper than arriving here. You are continuously engaged with my interaction. $\endgroup$ – Vishal Kumar Sahu Sep 10 '18 at 17:44
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    $\begingroup$ That is your decision, however it may be worth your while reminding yourself how SE works. It is a Q&A site in which answers are assessed, not only by the poster but also by other members of the site. If you make an assertion without providing evidence in support, the poster has no way of knowing whether or not you are right. Nor can other list members who may know something on the topic assess your answer properly. In this case I could have just said "this is wrong", but perhaps there is some recent work I have missed. So it was more appropriate to offer you the chance of providing evidence. $\endgroup$ – David Sep 10 '18 at 19:49

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