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Thread: How do Proteins move?

  1. #1 How do Proteins move? 
    Forum Junior AndresKiani's Avatar
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    What is the driving force behind calculated dynamics of protein function and folding. Where is the calculation occurring? This has really astonished me for years. Proteins are by far the most dynamic molecules in the universe.


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  3. #2  
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    Not quite sure what you are asking but protein folding and the actual physical shapes of organic molecules have to do with hydrogen bonds and other 'weak" forces of attraction and repulsion.


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    Forum Professor jrmonroe's Avatar
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    For protein folding, you can google protein folding and the results will provide plenty of articles. Wikipedia usually provides excellent information in response to questions like yours; however, I would actually begin with Wikipedia's Protein structure article, perhaps with side visits to its more detailed articles on amino acids and on each level of structure. Then, having learning this foundational material, move onto its Protein folding article.
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    Forum Junior AndresKiani's Avatar
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    Quote Originally Posted by Sealeaf View Post
    Not quite sure what you are asking but protein folding and the actual physical shapes of organic molecules have to do with hydrogen bonds and other 'weak" forces of attraction and repulsion.
    Yeah ofcourse, protein folding itself is based on which organelle the protein is targeted to, whether its part of the secretory pathway or cytosolic pathway, which is based on the first 70 amino acids not the amino acid configuration itself but the charges of the amino acid and polarity of the aa's. And of course the hydrogen bonds and the chemical properties (charges on the aa residues of the polypeptide chains).

    But my question is not that simple...

    Where does the protein calculation originate? Soluble proteins bind to Actin another protein, but its seems as though cellular proteomics or biochemistry or biophysics has not answered yet, how does the protein know where to go? How does it know what to do? How is Actin dynamics calculated?

    Its so dynamic that I can't imagine that it is all chemical substrate upon active site. There has to be more behind it, protein folding is interesting too, even if the hydrogen bonds and the amino acids fold up correctly, a protein my not be fully folded there for a Chaperone protein comes along and completes the folding which is very interesting how does the Chaperone protein know how to structure the denatured protein. Again is it chemical substrate upon active site or is there another explanation for Protein dynamics?
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    It is just physical chemistry. What other explanation could there be?
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    Forum Junior AndresKiani's Avatar
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    Quote Originally Posted by Strange View Post
    It is just physical chemistry. What other explanation could there be?
    I'm actually studying physical chemistry right now. But, I've heard all the arguments for the generic "substrate upon active site", chemistry to define cellular processes including protein dynamics. Though, I don't think this is the full answer, there is some very interesting protein dynamics that I just don't think can be explained by "substrate upon active site" chemistry.

    Maybe its define by other laws of physics that we just can explain yet... This is an inter disciplinary concept that's why I didn't know whether to ask it here in the Physics subform, or Chemistry subform or Biology subform.

    I had heard from Biophysicists that protein dynamics maybe explained by quantum theories, some sort of cellular consciousness.

    Many single cellular organisms for example have taxis with no neural system. This has always fascinated me on how such protozoans could possible have any sort of controllable taxis or another one would be binary fission of a protozoan, how does this protozoa know when to fission off into two separate organisms? No brain, no neural system? There is something about the dynamics of these systems that we don't fully understand.
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    Brassica oleracea Strange's Avatar
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    Clearly, we don't have all the answers to cell function, even for single-celled animals never mind the complexities of multi-cellular organisms. But I haven't seen anything suggesting we need "new physics". It is complex and hard to investigate - finding methods to analyse all the chemical reactions happening throughout a cell is difficult. But, for example, simulations of complete cells, as people are now working on, will probably tell us more.

    I had heard from Biophysicists that protein dynamics maybe explained by quantum theories
    Obviously, chemistry can ultimately be analysed and simulated in terms of quantum theory. And there has been recent work showing that quantum effects are significant in the efficiency of photosynthesis.

    But ...

    some sort of cellular consciousness.
    a) I don't what that has to do with quantum theory
    b) It sounds like it crosses the line to pseudoscientific woo.
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  9. #8  
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    Quote Originally Posted by Strange View Post
    Clearly, we don't have all the answers to cell function, even for single-celled animals never mind the complexities of multi-cellular organisms. But I haven't seen anything suggesting we need "new physics". It is complex and hard to investigate - finding methods to analyse all the chemical reactions happening throughout a cell is difficult. But, for example, simulations of complete cells, as people are now working on, will probably tell us more.

    I had heard from Biophysicists that protein dynamics maybe explained by quantum theories
    Obviously, chemistry can ultimately be analysed and simulated in terms of quantum theory. And there has been recent work showing that quantum effects are significant in the efficiency of photosynthesis.

    But ...

    some sort of cellular consciousness.
    a) I don't what that has to do with quantum theory
    b) It sounds like it crosses the line to pseudoscientific woo.

    Lol, that's exactly were I was trying to go to, without being too obvious about it. Yes, pseudoscience, pertaining to specifically to Planck Time Physics.
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  10. #9  
    Forum Professor jrmonroe's Avatar
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    Quote Originally Posted by AndresKiani View Post
    But my question is not that simple...

    Where does the protein calculation originate? Soluble proteins bind to Actin another protein, but its seems as though cellular proteomics or biochemistry or biophysics has not answered yet, how does the protein know where to go? How does it know what to do? How is Actin dynamics calculated?

    Its so dynamic that I can't imagine that it is all chemical substrate upon active site. There has to be more behind it, protein folding is interesting too, even if the hydrogen bonds and the amino acids fold up correctly, a protein my not be fully folded there for a Chaperone protein comes along and completes the folding which is very interesting how does the Chaperone protein know how to structure the denatured protein. Again is it chemical substrate upon active site or is there another explanation for Protein dynamics?
    I haven't seen these words used to describe molecules or proteins. Proteins do not calculate or know, per se. I suppose that knowledge (ie, stored data) could be used to describe a protein's primary structure and the characteristics of amino acids (side chains, stiffness, etc) and how they react to each other and to water (bonds, hydrophobia, etc).

    Brownian movement could be defined as a catalytic-like process that promotes all sorts of interactions between molecules.

    Evolution advances/preserves successful molecular interactions. The fact that failures/mistakes usually don't survive tend to obscure this fact.
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    Forum Junior AndresKiani's Avatar
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    In Neuroscience, some scientists will use the words calculation and how it knows. I've seen these words used before by people in my field.

    Cellular transduction pathways, and biochemical pathways at the surface seem to dictate most of the cellular dynamics (protein dynamics). Though in detail there is so much that can't be explained by textbook biochemical interactions. Protein dynamics, in proteomics seem to have a driving force other than biochemical signaling that we cannot explain. You will here from biophysicists all the time, we don't exactly know why a protein folds the way it does or why does it do that in that event. A lot of times its not as simple as antibody to antigen or active site to active site mechanics.

    I'm an undergrad so I have minimum understanding of a lot of things, though I've heard many Neuroscientists, Cell Biologists, Biophysicists talk about a "Plank Time" related level of consciousness that could possible explain the full behavior of protein dynamics.
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  12. #11  
    Forum Professor jrmonroe's Avatar
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    Quote Originally Posted by AndresKiani View Post
    In Neuroscience, some scientists will use the words calculation and how it knows. I've seen these words used before by people in my field.
    Thanks, this is new to me. What are the concepts surrounding calculation and knowing? What''s being calculated, and what needs to be known?
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  13. #12  
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    Quote Originally Posted by jrmonroe View Post
    Quote Originally Posted by AndresKiani View Post
    In Neuroscience, some scientists will use the words calculation and how it knows. I've seen these words used before by people in my field.
    Thanks, this is new to me. What are the concepts surrounding calculation and knowing? What''s being calculated, and what needs to be known?
    Its called protein, or cellular computation.

    For example how does a cell know when to divide. Well there are several reasons, including whether or not there is enough cellular food (Ex. Glucose) or EGF outside the cell. The cell will decide whether or not its enough for it to divide. It does this by sending out proteins that will turn on (phosphorylate or dephosphorylate) these kinases which will bind and turn on protein transcription factors that will turn on genes for cell proliferation.

    Now the interesting thing that some how these proteins will change shape and form without any interaction with any other molecule. They will conform to their substrates to phosphorylate a transcription factor or another kinase or even itself. Therefore these proteins do not follow the conventional "active site to substrate" biochemical approach, pathway upon pathway. Also these proteins my have dual or multi specificity, meaning they can phosphorylate many different sites of its substrate. Where does the calculation take place, "where does it say", ok in this situation I will phosphorylate the serine residues of this protein, or will phosphorylate the thymine residues now.

    These proteins are highly dynamic, GEF proteins have the potential to exchange GTP with a variety of different proteins at a single time.
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    Most Biochemists will say that its just physical chemistry. But some Biophysicists and some Neuroscientists will use the word calculation to describe protein and cellular processes.

    In Neuroscience, we see now that brain cells can proliferate, grow new connections, increase their firing frequency, and change their circuitry depending on how we think and which areas of our brains we use excessively.

    New research shows that neurons and the neural network of our brain is very much like circuitry system and it does not store information. A lot of people in my field are now talking about plank time approach to answering protein and cellular calculations, memory and consciousness. Supposedly that calculations of the cell occur within the microtubules of the neurons, within the cellular skeleton, like actin, and intermediate filaments. There is evidence now showing when we use anesthetics on patients their microtubules in their brain cells, their actin cellular skeleton will depolymerize. Therefore no cellular calculation theoretically can take place. Once the anesthetics wear of these structural protein will re-polymerize in the cell and start driving cellular processes, cell vesicles, cell transduction, protein interaction. ect.
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    Quote Originally Posted by AndresKiani View Post
    A lot of people in my field are now talking about plank time approach to answering protein and cellular calculations, memory and consciousness.
    I don't know what "plank time approach" is supposed to mean. I don't see how invoking things that might be happening at immeasurably small periods of time can relate to the functioning of proteins. It sounds like people have been taken in by "quantum consciousness" woo (just to be clear, quantum theory says nothing about consciousness).
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    I guess they may be thinking of something like this: Discovery of quantum vibrations in 'microtubules' inside brain neurons supports controversial theory of consciousness -- ScienceDaily

    But, apart from the fact that this is still pretty speculative, I don't see how it really solves the problem of consciousness. There still seems to be the "and then magic happens" step to get from quantum effects in neurons to consciousness. Which is no better than a classical description of how neurons work.

    And it doesn't seem to have anything to do with protein folding and behaviours (which are pretty well understood, but computationally intensive).
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    Forum Junior AndresKiani's Avatar
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    I mean this is just stuff that I hear from the professors, Neuroscience lectures online, debates, and recent research I look up online. I'm still an undergrad and I got 4 more semesters left till I get my BS in Neuroscience (like I said I was an engineering major before this year I took a lot of Computer Science and Programming Courses). I'm just astonished that I know so little physics even after taking two semesters of introductory physics. SMH, I only learned formulas, a little bit of classical physics, basic kinetics and basic dynamics. Never learned anything about Plank Time, Time as fundamental dimension of the universe, Space-Time, Relativity, much about Gravity, and Quantum Physics.
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  18. #17  
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    It's a big world out there!
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  19. #18  
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    Quote Originally Posted by AndresKiani View Post
    I mean this is just stuff that I hear from the professors, Neuroscience lectures online, debates, and recent research I look up online. I'm still an undergrad and I got 4 more semesters left till I get my BS in Neuroscience (like I said I was an engineering major before this year I took a lot of Computer Science and Programming Courses). I'm just astonished that I know so little physics even after taking two semesters of introductory physics. SMH, I only learned formulas, a little bit of classical physics, basic kinetics and basic dynamics. Never learned anything about Plank Time, Time as fundamental dimension of the universe, Space-Time, Relativity, much about Gravity, and Quantum Physics.

    I recognize your astonishment.
    I did not receive much physics in my first two semesters either and the subjects that were covered, did not include the stuff members in the Physics sub-forum are talking about. Of course, given that I want to obtain a B.Sc. in Biochemistry, I do not need a thorough understanding of General Relativity or QED (and as such they were not on the curriculum); yet, it is often frustrating to see that my ignorance does not enable me to take part in some of the discussions that are going on.
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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  20. #19  
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    BS in Biochemistry, do you know what specifically you want to go into? I really wanted to work on the Tau protein in Alzheimer's so I was thinking of doing Biochemistry, I've taken a lot of Chem courses.
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  21. #20  
    Moderator Moderator Cogito Ergo Sum's Avatar
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    Quote Originally Posted by AndresKiani View Post
    BS in Biochemistry, do you know what specifically you want to go into? I really wanted to work on the Tau protein in Alzheimer's so I was thinking of doing Biochemistry, I've taken a lot of Chem courses.

    I am still open to all the possibilities they offer, but I would like to study microbiology to identify and characterize bacteria and investigate their effects on human health. Next, I have not yet heard of the Tau protein. What kind of protein is it (as the PDB gives too much entries to distinguish the proper one)?
    "The only safe rule is to dispute only with those of your acquaintance of whom you know that they possess sufficient intelligence and self-respect not to advance absurdities; to appeal to reason and not to authority, and to listen to reason and yield to it; and, finally, to be willing to accept reason even from an opponent, and to be just enough to bear being proved to be in the wrong."

    ~ Arthur Schopenhauer, The Art of Being Right: 38 Ways to Win an Argument (1831), Stratagem XXXVIII.
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  22. #21  
    Forum Professor jrmonroe's Avatar
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    Quote Originally Posted by AndresKiani View Post
    Its called protein, or cellular computation.

    For example how does a cell know when to divide.
    This reminds me of quorum sensing in bacteria.

    However, to say that proteins "calculate" is a bit of a stretch of the word for me.
    Grief is the price we pay for love. (CM Parkes) Our postillion has been struck by lightning. (Unknown) War is always the choice of the chosen who will not have to fight. (Bono) The years tell much what the days never knew. (RW Emerson) Reality is not always probable, or likely. (JL Borges)
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