Intelligent Design

Why Don’t Globular Proteins Knot UP?

Spread the love

Here’s an abstract from the Journal of Physics tackling the issue of “knottiness” in polymeric chains.

Notice that the authors were able to “design” sequences which either knotted up all the time or did not knot, using polymer lengths of 500. Now, I wonder what the odds of arriving at a sequence which does “not knot” randomly? (1 in 20^500) And, if you couldn’t get beyond the knotting up of a protein molecule, then how could life continue?

Everyday experience shows that strings easily knot. Preventing this requires careful folding or winding when stowing away. Molecular ropes, like polymer chains, can suffer the same fate, but that is not true for biopolymers like proteins and DNA; despite their complex folded conformations, they rarely get knotted. A new study by Thomas Wüst from the Swiss Federal Institute of Technology (ETH), Zurich, and colleagues suggests the differences in the interactions between different parts of the chain of a protein (due to the sequence of amino acids forming it) is what controls and prevents knotting.

Wüst et al. simulated simplified, coarse-grained proteins made of 500 monomers (“residues”), which were either hydrophobic or polar. The authors compared different types of sequences: homoresidue chains, randomly ordered ones, and chains designed with specific repetition patterns, calculating their various ground-state conformations and checking for knots. They found that the knottiness of the chain depended on the sequence, and they were able to design sequences that were either highly knotted or almost completely knot-free. Sequences that were free of knots typically produced neatly folded, locally ordered structures, with none of the extended loops seen in the knotted sequences.

The proteins and sequences investigated here are much simpler than real proteins, which are made of twenty amino acids, rather than two. However, the authors speculate that sequence could have been a controlling factor in the evolution of proteins, allowing them to evolve towards knot-free conformations that can reliably perform their functions.

You’ll notice that they tackled the much simpler case of using only TWO residues (hydrophobic and polar) in forming the 500 residue polymer. Note that for ‘actual’ proteins the difficulty of “designing” would be 10^500 more difficult.

Also notice that the last sentence of the abstract makes no sense whatsoever. How many “trials” would be necessary to find a protein that does not ‘knot’?

Another day, another bad day for Darwinism—this time from the field of physics.

31 Replies to “Why Don’t Globular Proteins Knot UP?

  1. 1
    Mung says:

    They should try this in a non-aqueous medium!

  2. 2
    Radioaction says:

    Hmm, interesting.
    It appears that the study found “just one additional degree of freedom per monomer facilitates evolution towards a protein universe in which knots are rare.” This was in part of the abstract you left out I guess.

  3. 3
    tjguy says:

    “….allowing them to evolve towards knot-free conformations that can reliably perform their functions.”

    Evolve TOWARDS knot-free conformations???

    Evolution does not evolve towards anything consciously or purposefully.

    Did it go from say 10 knots to 9 knots to 8 knots, etc. down to 0 knots? Is there really a difference between 10 knots and 9 knots? If it doesn’t work with 10 knots, what are the chances of it working with 9 knots?

    Aren’t knots fatal to the protein? If so, I don’t see how it can evolve towards “knot free conformations”.

    Wouldn’t it have had to be knot free FROM THE BEGINNING for it even to work?

    Another example of irreducible complexity perhaps?

  4. 4
    Me_Think says:

    There is no need for ‘above the UPB’ tactics. Allosteric motion derived from just the hydrophobic nature of monomers alone could account for the mystery of no knots. Paper here

  5. 5
    rvb8 says:

    Oh good, another quote mined study which leads to the ID conclusion; ‘see, we don’t know how this could possibly work, why are the evolutionists even trying, give up, throw away your curiosity, goddidit!’

    Thanks ID for another wonderful contribution to science.

    Yes tjguy, we all understand that you, “don’tsee how it can evolve towards ‘knot free conformations.” That’s why they’re (the scientists) studying the evolutionary pathways, to enlighten us and produce new knowledge. Your medieval way of being cowed by the majesty, and leaving it at that, was dropped long ago for the new approach of trying to understand the grand mechanism of life.

  6. 6
    tjguy says:

    rvb8:

    Oh good, another quote mined study which leads to the ID conclusion; ‘see, we don’t know how this could possibly work, why are the evolutionists even trying, give up, throw away your curiosity, goddidit!’

    rvb, this is simply another illustration/example of how Materialists’ faith in chance is at risk. At this point, it is not a win for either side. But there are many examples of issues like this for which there is no experimental evidence for the Materialistic story.

    It’s fine to believe in it anyway, but just don’t tell us it is fact or proven or undeniable or whatever other emphatic word you want to use. Don’t call your commitment to Materialism, “science” and our willingness to consider other options “religion”. We both have metaphysical beliefs that cannot be proven.

    At this point, neither our nor your beliefs in this and many other areas are not science/fact/settled. They remain beliefs/hypotheses/ideas.

    I’m not against research. Go for it. Try and solve it.
    Will you be able to? Who knows?

    How long will it take? Who knows?

    You can always hide behind that moniker and accuse us of faith, because it is impossible for anyone to prove a negative.

    Just like you cannot prove that God does not exist, neither can we prove that life could not evolve by totally natural unguided means.

    You can always say “Well, we just haven’t worked on the problem long enough.” or “We’re making progress. It’s a difficult problem. Just give it more time.” or the excuses can go on forever. No matter what, your faith that science will solve the riddle sometime remains strong. Great! But just remember, you too have a faith problem.

    Looking at the evidence, including what this study shows, it is NOT unreasonable to posit the idea that intelligence may have been involved in the origin of life. Since we just don’t know, there is no reason to say that it had to happen by totally natural forces, or that intelligence could not have been involved, unless of course, your worldview does not allow for it.

  7. 7
    PaV says:

    Radiation:

    I left nothing out of the abstract. I copied it and then pasted it.

    Here we have physicists who have been trained to believe in evolution employing this viewpoint in an attempt to explain their results.

    I don’t think they have a clue as to what they are saying.

    They “design” sequences, and then presume “evolution” will some how ‘find’ their design. They just suppose this. Is there any reason to believe this?

    If polymers ‘knot up,’ and DNA and RNA and proteins are bio-polymers, then how does life arise? If, in some miraculous way, life begins (which is, of course, Darwin’s starting place in the OOS) then how does a ‘new’ protein ‘evolve’? That is, you have to ‘blindly’ (you know…..random mutation) find a sequence that doesn’t ‘knot’. Well, there are 20^500 possibilities. How many of those do not ‘knot’? I’m sure it is a very, very small number. This means that the ‘evolution’ of a protein, from scrap, is virtually impossible.

  8. 8
    PaV says:

    rvb8:

    Oh good, another quote mined study which leads to the ID conclusion; ‘see, we don’t know how this could possibly work, why are the evolutionists even trying, give up, throw away your curiosity, goddidit!’

    Thanks ID for another wonderful contribution to science.

    First, what has been “quote-mined”? Could you point that out?

    Second, the “evolutionists [weren’t] even trying” before this experiment, which is more of a ‘simulation.’ No one had thought about it. These are physicists who are asking this question, not biologists. Biologists don’t ask it because they know they can’t even begin to answer it; so they just leave it to the one side.

    Third, that biologists leave these tough questions “to the one side,” as I just stated, is actually what you’re accusing IDists of doing–“throwing away [their] curiosity.”

    Their answer is: “Evolution did it!!”

    Maybe you ought to rethink some of this before you post the next time.

  9. 9
    Radioaction says:

    Are you kidding me PaV? You just made the same mistake twice. You’ve lost all credibility. You’re going to say that the researchers “have no clue what they’re saying” when you can’t even tell the difference between a press release and an abstract?

    I guess I shouldn’t be surprised, this is UD.

  10. 10
    Me_Think says:

    PaV @6
    Not all proteins are globular. A lot of types of protein do have knots. You can visualize protein knots here

  11. 11
    Hangonasec says:

    Why do proteins have to be 500 residues long as a minimum? A logical possibility is that they started smaller, hence less knot-prone. If knottiness were significantly detrimental, which parts of protein space would not be visited by evolution? If a short sequence does not knot, what process(es) could extend it in a way that also does not knot?

  12. 12
    Zachriel says:

    PaV: How many of those do not ‘knot’? I’m sure it is a very, very small number.

    Me_Think: Not all proteins are globular. A lot of types of protein do have knots.

    Heh. Then there’s whether they fold or not. That’s gotta be incredibly rare.

    Davidson & Sauer, Folded proteins occur frequently in libraries of random amino acid sequences, PNAS 1994

  13. 13
    PaV says:

    Radiation:

    You’ll notice that there is very little difference between the last sentence of the ‘abstract’and the last sentence of the summary which I included above.

    So, what is the big deal? Specifically, do you know what they mean by the “additional degree of freedom”?

    If you know what this is, then please point out to me how one goes from this notion to the idea the “evolution” is now in play?

  14. 14
    PaV says:

    Zachriel:

    If you want to pick nits, I’m sure there are very few sequence strings that have but one, or a few, knots. Again, the improbabilities are staggering. That’s the point here.

    If you want to hand-wave all of this away, fine. But I would suggest to you that this decision puts you a road that leads to nowhere.

    What you choose to do, or not do, well, that’s, of course, your choice.

    Everything here is rather straightforward. It’s a matter of interpretation.

  15. 15
    Radioaction says:

    PaV, despite your inability to differentiate between the abstract and the press release of this paper and against my better judgment, I will continue.

    You are partially correct. In both final sentences there is very little difference in the subject. But there is a huge difference in detail, and it is all in the details! This is why it is important to not rely on press releases over the primary source itself.

    In fact, if you had read the abstract, specifically the last sentence, you probably would not have even created this post.

    Allow me to explain:

    Homopolymers are known to be highly knotted. This study introduces an additional degree of freedom to the polymer, which they call “sequence.” They do this by generating polymers that are not just hydrophobic or just polar, but combinations; this is “sequence.” And this is why you were confused by the press release. When they say “sequence,” they are not talking about a specific sequence of residues, but instead just the fact that there is some combination of different types of residues.

    What they found was that introducing sequence to polymers favored the formation of more organized structures, which lowered the likelihood of knot formation.

    Evolution “is in play” because with just this single increase in the degrees of freedom, the polymers are already favoring the formation of proteins without knots.

    Now as you said, this was a very simple case only taking into account polarity of monomers and yet they still saw a significant decrease in knottedness in their random polymers. Now imagine if they were able to run these simulations using all 20 amino acids, with their actual structures.

    Another bad day?

    I think not.

  16. 16
    PaV says:

    Radioaction:

    Thank you for humoring me with your answer.

    Yes, as you explained, the ‘extra’ degree of freedom is the fact that they’re creating a polymer which combines monomers into ‘sequences.’ But this is nothing I, nor others, didn’t understand.

    There are two points here: (1) the immense complexity involved in ‘actual’ protein families, and (2) the conjecture that ‘evolution’ has a place to act in ‘sequence’ space.

    These are related to one another.

    You say: “Now imagine if they were able to run these simulations using all 20 amino acids, with their actual structures.”

    You’re simply falling on your face here. This is the whole point of the post. They CAN’T run these simulations. They’re too complex. They involve too many degrees of freedom. They don’t have the computer power to do this (did they say something along the lines that in the future they hope to do a simulation using actual amino acids? No.).

    When you get a number for these degrees of freedom–20^500–it is obvious that if cell replications are needed to provide mutations for probing these DOF, the actual number of cell divisions that have ever taken place on earth since life began is infinitesimal to this number. How, then, can “evolution” make use of this space?

    Another day; another bad day for Darwinism. (Another hurdle that sequence space must overcome for life to ‘begin’, let alone to ‘evolve.’)

  17. 17
    PaV says:

    BTW, Radiation, what I ‘blockquoted’ above is not the “press release.” You’ve now made that mistake twice.

  18. 18
    Hangonasec says:

    It is not necessary for evolution to probe every nook and cranny of 20^500 sequence space. Obviously, it can’t. But if evolution started with (say) 2 residues, one hydrophilic and one hydrophobic, it would be bizarre to insist that, as the library expanded, evolution would stall because it had too many degrees of freedom! The fact that modern proteins are long polymers of 20 acids does not mean that all proteins, ever, were.

    Take the alpha helix, which tends to resist knottiness. All one needs for a simple turn of an alpha helix is 4 residues. All one needs to get 2 turns is that sequence end-joined to itself. Now some amino acids destabilise alpha helices because they are too large, too small, or they are the eccentrically conformed Proline. But you can still make an alpha helix from a dozen or more different residues, provided the 4-residue repeat is consistent in its polarity sequence. The extra degrees of freedom coming from an expanded library add subtle variation of conformation; the massive space they generate does not contain just the one, or a few, target sequences, in a vast sea of nothingness.

  19. 19
    Daniel King says:

    Compare what PaV quoted in the OP with the ACTUAL ABSTRACT of the paper:

    Knots are abundant in globular homopolymers but rare in globular proteins. To shed new light on this long-standing conundrum, we study the influence of sequence on the formation of knots in proteins under native conditions within the framework of the hydrophobic-polar lattice protein model. By employing large-scale Wang-Landau simulations combined with suitable Monte Carlo trial moves we show that even though knots are still abundant on average, sequence introduces large variability in the degree of self-entanglements. Moreover, we are able to design sequences which are either almost always or almost never knotted. Our findings serve as proof of concept that the introduction of just one additional degree of freedom per monomer (in our case sequence) facilitates evolution towards a protein universe in which knots are rare.

  20. 20
    PaV says:

    Hangonasec:

    It is not necessary for evolution to probe every nook and cranny of 20^500 sequence space. Obviously, it can’t. But if evolution started with (say) 2 residues, one hydrophilic and one hydrophobic, it would be bizarre to insist that, as the library expanded, evolution would stall because it had too many degrees of freedom!

    Welcome to UD.

    The 20^500 figure comes from the simulation that was run, where a sequence 500 monomers long was used. If you’re dealing with just two monomers, the sequence space would be 2^2, or 4. The odds of finding that combination is but 1 in 4. So, yes, something like that could easily happen. The trick is to move on from there.

    The fact that modern proteins are long polymers of 20 acids does not mean that all proteins, ever, were.

    You’re asking us to consider something we don’t find in life forms today. How can/should I respond to a complete hypothetical? As far as I know, we’re ignorant of whether proto-proteins existed, so it’s tentative at best to base an argument on such a supposition.

    Take the alpha helix, which tends to resist knottiness. All one needs for a simple turn of an alpha helix is 4 residues. All one needs to get 2 turns is that sequence end-joined to itself. Now some amino acids destabilise alpha helices because they are too large, too small, or they are the eccentrically conformed Proline. But you can still make an alpha helix from a dozen or more different residues, provided the 4-residue repeat is consistent in its polarity sequence. The extra degrees of freedom coming from an expanded library add subtle variation of conformation; the massive space they generate does not contain just the one, or a few, target sequences, in a vast sea of nothingness.

    I can’t give you a technical reply; however, let me make a point or two using the conditions you’re laying out.

    First, if an alpha-helix can be made only out of a “dozen or more residues,” then, assuming for the sake of argument that 14 such residues will work, then this means that for each position—degree of freedom—there is a (1-6/20) chance of not working. So, for each degree of freedom, the chance that it won’t knot is 0.7, and the probability it will knot is 0.3. It seems to me that if we consider 500 such degrees of freedom, all interplaying and dependent on the sequence, then the chances of finding such a length, knot-free, is (0.3)^500. This is like 4^500 x 10^100/10^500 = 10^100 x 10^100/10^500 = 10^-300.

    Second, when you say that the “polarity” of the residues has to be correct, then, again, we’re dealing with some subset of ‘polar’ residues, which would result in a similar probability calculation as above.

    Combined, this means that a 500 a.a. sequence made up of only alpha-helices, would have a probability of happening by chance of much less than 1 in 10^300. Isn’t that a “vast sea of emptiness”?

    Of course, all this would change if you could ensure some environment where the only residues at hand would be those 14 residues that will form the alpha-helices. However, I can’t begin to imagine such an environment—except in an intelligently run biology lab.

  21. 21
    PaV says:

    Daniel King:

    What’s your point? If you can’t make one soon, I’ll be deleting your post.

  22. 22
    Radioaction says:

    And you choose to continue digging yourself deeper and deeper into that hole.

    Not only is it obvious that you didn’t know what they meant by “sequence,” but you also have a fundamental misunderstanding of how molecular biology works. On top of this you don’t seem to understand how “degrees of freedom” works.

    When we are talking about the degrees of freedom in residue composition of a protein, the highest number of degrees of freedom is 20. What you came up with (20^500) it the number of possible combinations in the 500 residue chain. There’s a big difference.

    This study showed that an increase in the degrees of freedom by just one, decreased knottedness. This is because having residues with different properties favors the formation of more ordered structures, which decreases the likelihood of knot formation. How many times do I have to repeat myself?

    Now, as Hangonasec has just told you, alpha-helices resist knottedness. This is because they are ordered structures. However, all 20 amino acids can exist in a helix, and do. Also, you cannot compute the likelihood of forming a knot from a single residue as you did. There is so much wrong with what you responded to hangonasec with, I’m not willing to dive any deeper. Maybe he will.

    In summary:

    A single degree of freedom increased order and decreased knottedness. Proteins secondary structure as we know it (with 20 degrees of freedom) increases order and decreases the likelihood of knots even further. And yet you still seem to want to argue that it should be difficult for proteins to have found sequences that don’t knot.

    And what would you call it, if not a “press release?”

  23. 23
    Daniel King says:

    PaV:

    What’s your point? If you can’t make one soon, I’ll be deleting your post.

    The point is that you misrepresented the research in your OP, as Radioaction pointed out. Repeatedly.

  24. 24
    Daniel King says:

    By the way, PaV, deleting a post that one doesn’t understand or finds challenging is a cowardly act.

  25. 25
    Hangonasec says:

    PaV – proteins substantially shorter than 500 residues are found in life today, so it’s not that much of a stretch. An evolutionary scenario would inevitably include the possibility that the predecessor is extinct, so the absence of a particular feature in modern forms is a neat, but unsatisfactory, method of denying all evolutionary possibilities.

    Granted there is in modern life a significant clustering towards the ‘longer’, but this could as easily mean ‘longer is better’ as ‘shorter is fatal’. Length is not essential for catalysis. The shortest catalytic peptide is actually also the shortest possible peptide: Seryl Histidine, a dipeptide. Ser-His is found at the active centre of many longer enzymes, with quite diverse functions, but it exhibits catalytic activity in isolation.

    Of course this does not prove a direct connection between such a general catalysis and the exquisite substrate-specificity and cofactor binding found in the modern enzyme, but it does demonstrate that primitive catalysis is available to much shorter strings.

    Your numerical analysis, I feel misses the point. There are in fact about 500 different amino acids, so you could beef up your probabilities still further – 500^500. But it’s not relevant. The point would be that a short stable motif can arise from a string of just 4 polar/nonpolar residues in a particular sequence. To get a hypothetical 500-residue protein consisting solely of alpha helix, one would not need to toss a coin for each residue. You can get HTTHHTTHHTTHHTTHHTTH (…) simply by taking one HTTH and end-joining repeats. The first operation generates HTTH, duplicate and splice you get HTTHHTTH, repeat and you get HTTHHTTHHTTHHTTH and so on. Proteins don’t lengthen in quite this simplistic way of course, but it’s closer to the evidence than the assumption of 500+ random picks for every protein.

  26. 26
    PaV says:

    Radioaction:

    When we are talking about the degrees of freedom in residue composition of a protein, the highest number of degrees of freedom is 20. What you came up with (20^500) it the number of possible combinations in the 500 residue chain. There’s a big difference.

    I knew exactly what I was calculating. And your view of 20 degrees of freedom simply means that there are, in life, 20 different a.a. to choose from. The “single” dof used in the experiment simply toggled between ‘hydrophobic’ and ‘polar’. Isn’t this simply straightforward?

    This study showed that an increase in the degrees of freedom by just one, decreased knottedness. This is because having residues with different properties favors the formation of more ordered structures, which decreases the likelihood of knot formation. How many times do I have to repeat myself?

    You would have been better off not stating the obvious in the first place. This isn’t the issue here.

    Now, as Hangonasec has just told you, alpha-helices resist knottedness. This is because they are ordered structures. However, all 20 amino acids can exist in a helix, and do. Also, you cannot compute the likelihood of forming a knot from a single residue as you did. There is so much wrong with what you responded to hangonasec with, I’m not willing to dive any deeper. Maybe he will.

    I should have used (7/!0)^500 as the probability. Nevertheless, the point is always the same—–are you paying attention?—-that is, having to ‘avoid’ knottiness represents an additional constraint into DNA sequences, and represents an obstacle to easily finding a pathway through the entirety of what sequence space represents.

    I don’t understand why you can’t see the obvious here? What, exactly, are you barking at?

    In summary:

    A single degree of freedom increased order and decreased knottedness. Proteins secondary structure as we know it (with 20 degrees of freedom) increases order and decreases the likelihood of knots even further. And yet you still seem to want to argue that it should be difficult for proteins to have found sequences that don’t knot.

    Your thinking here seems to backwards. It’s as if you’re saying that because ‘order’ avoids ‘knottiness’ this means, ipso facto, that this makes everything ‘easier’ for ‘evolution’; in fact, it makes it more difficult because it involves an added constraint on what is possible in the sequence space of living beings.

    And what would you call it, if not a “press release?”

    When something is found with a journal, how can you call such a thing a “press release”? It’s a “summary.”

  27. 27
    PaV says:

    Hangonasec,

    I fully know that shorter proteins exist; I was simply following the example the authors used for their simulation. And, certainly, for shorter strings, probabilities would be much more accessible, so that for the seryl histidine one could not infer any necessity of ‘design.’ So all of that is granted.

    However, here’s where I would see things differently:

    The point would be that a short stable motif can arise from a string of just 4 polar/nonpolar residues in a particular sequence. To get a hypothetical 500-residue protein consisting solely of alpha helix, one would not need to toss a coin for each residue. You can get HTTHHTTHHTTHHTTHHTTH (…) simply by taking one HTTH and end-joining repeats. The first operation generates HTTH, duplicate and splice you get HTTHHTTH, repeat and you get HTTHHTTHHTTHHTTH and so on.

    One thing that I think is so often forgotten is that a huge number of degrees of freedom are needed where uniqueness is needed. Dembski has point this out. When you choose a password, you’re asked to give one of a certain length, often a combination of numbers and letters, small case and capitals. Not only does this guarantee “uniqueness,” but it protects against ‘hacking,’ since the sample space created from such a combination becomes huge, making the finding of a password almost impossible using ‘random’ methods.

    So, yes, you could construct a protein in the simplified manner you describe; yet, this makes its “uniqueness” almost negligible. With hundreds of thousands of proteins swimming around in the cell, how does one substrate distinguish this particular protein? So, a huge number of degrees of freedom are needed. But the flip-side of this is that this huge number of degrees of freedom creates a sample space so infinitely big that it cannot be navigated randomly. This, then, is the problem Darwinian evolution must face.

    Your view here is analogous to Richard Dawkin’s view of “Mt. Improbable.” Instead of exponential growth in small probabilities, it sees things in an independent fashion, with the consequence being that small probabilities are ‘added’ instead of being ‘multiplied.’ Where this argument fails is that huge improbabilities are needed in order to sequester needed proteins within the sample space, of which the absence brings about a ‘blurring’ of identity (of whatever you’re considering in this way).

    Proteins don’t lengthen in quite this simplistic way of course, but it’s closer to the evidence than the assumption of 500+ random picks for every protein.

    I’m not sure what you mean by “closer to the evidence.”

  28. 28
    Radioaction says:

    PaV, this is going nowhere. You have no idea what you are talking about.

    The issue here is that you think finding a sequence that does not ‘knot’ is a problem.

    The paper shows that introducing a single degree of freedom decreases the knottedness.

    A sequence 1^500 is highly knotted.

    A sequence 2^500 (from this paper) significantly decreases knottedness by increasing order.

    Now do you think a sequence 20^500, that is known to promote highly ordered secondary structure, will have trouble finding unknotted folds?

    Hint: the answer is no.

    Avoiding knottedness is a simple task when using amino acids that tend to form ordered secondary structure.

    You argument that is adds another constraint onto sequence space is BS. As I have pointed out multiple times, it is not the sequence that limits knottedness, it simply is the fact that different amino acids are in the sequence.

    And what you copy/pasted is a press release, or “news release” if you must. It’s a dumbed-down explanation of the results by a science writer, in an attempt to make it easier for the layman to learn about the original published work. It’s meant for consumption by the general public and any news sources that may want to report on the findings if the work is high-profile.

    I simply cannot go on repeating myself any longer. Just about every sentence you utter demonstrates a fundamental misunderstanding of biology. Please feel free to continue misinterpreting scientific findings in your attempts to make a case against evolution, it’s quite amusing.

  29. 29
    Hangonasec says:

    I’m not sure what you mean by “closer to the evidence.”

    I mean that there is significantly more reason to conclude that protein motifs are related than that they each arose independently, and there is much more likelihood that ‘successful’ shorter motifs will be preserved and donate sequence to others than that a mechanism akin to coin-toss for the entire length of each protein was involved. That is: you, like Hoyle, are tilting at the wrong ‘Darwinian’ mechanism.

    Of course there is also a scrambling mechanism at work: further mutation. So the time period during which any 2 segments are detectably related on sequence is not indefinite. And the same goes for the parts of a single multi-turn helix. If (in my simplified scenario) there were gradual substitutions along the length, chemical constraints will limit the size, charge and polarity of viable substitute acids. Some positions may admit more substitutes than others. But after a period, it would appear that all the different elements of the helix were positionally essential. This becomes much more clear if you ascribe letters to acids by chemical property instead of unique molecular structure. The different hydrophilic acids, for example, act more like the letter A rendered in different fonts than a set of ‘true’ alphabetic variants, granted that they do introduce subtle conformational effects.

  30. 30
    PaV says:

    Radiation:

    I just happened onto this response today; so I’m responding.

    You wrote:

    You argument that is adds another constraint onto sequence space is BS. As I have pointed out multiple times, it is not the sequence that limits knottedness, it simply is the fact that different amino acids are in the sequence.

    Here’s what the “summary” from Physics had to say:

    They found that the knottiness of the chain depended on the sequence, and they were able to design sequences that were either highly knotted or almost completely knot-free. Sequences that were free of knots typically produced neatly folded, locally ordered structures, with none of the extended loops seen in the knotted sequences.

    The quote I included above completely contradicts the position you’ve stated. If you can’t see that, then you’re not looking hard enough.

    They had to “design” sequences so as to avoid “knottiness.” Your fundamental argument is that “sequence,” in, and of itself, overcomes the “knottiness” problem. No, there is a constraint.

    If you choose to reply, then watch your tone, or I will simply delete it.

    Finally, a “summary” contained in the very journal where the original paper is found, can hardly be called a “news release.” It is a “summary,” plain and simple. News releases will normally involve some kind of interview with the authors, and more background information. It’s a “summary,” thank you.

  31. 31
    PaV says:

    Hangonasec:

    Are you familiar with this paper by Axe and Gauger? It addresses your contention.

    I’m simply not convinced that simple random mutations, even involving “blocks,” will solve the problem. Axe and Gauger look simply for 7 mutations within a related protein family, and they calculate that 10^27 years would be needed to “find” those 7 mutations all happening within ‘one’ protein sequence.

Leave a Reply