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What plagiarism even means in context of proteins? That one protein steals a fold of another protein without giving proper credit to it?

by jeejay1 4mo ago

gilleain 4mo ago
I understood it as metaphor - just that evolutionarily distant sequences can adopt the same (or very similar) folds because there are only a limited number of stable, accessible folds that are possible.
- hirenj 4mo ago
  Yes, that is exactly what I meant! Here’s an experiment to try: Frances Arnold got a nobel prize for work related to directed evolution. However, we know evolution is limited by the tools available to it as you mention. If we add random chaperones and co-factors to bacteria that we know other organisms use, can we push evolution outside of the known fold space? Is the limited fold space an absolute limit or the “accessible” limit?
  - gilleain 4mo ago
    I see. I meant 'energetically accessible', but you mean more like 'affordably accessible' (in the sense that the molecular toolkit of a cell is what can 'afford' certain structures, due to chaperones available and so on). Who knows what might be possible if you designed a cell from scratch - perhaps you could rework all the machinery to access other parts of fold space. After all, there are some weird and wonderful machines out there like the 'Vault' (https://en.wikipedia.org/wiki/Vault_(organelle) https://en.wikipedia.org/wiki/Vault_(organelle)) that can fit whole proteins inside them. Possibly a different cage-like structure could help fold designed proteins into as-before unseen structures.
    - pfdietz 4mo ago
      It could also mean "evolutionarily accessible". The basin of attraction in sequence space has to be sufficiently large that evolution could stumble across it.
- jeejay1 4mo ago
  Do you have an example of such sequences in mind? Because I can’t recall any example.
  - gilleain 4mo ago
    A very reasonable question, that I don't have an immediate concrete answer to! Apparently I upvoted this question in the past (found it by searching for an answer - no AI, like the good old days) https://biology.stackexchange.com/questions/2507/are-there-any-examples-of-proteins-with-no-or-minimal-sequence-identity-but-hig https://biology.stackexchange.com/questions/2507/are-there-a... One answer mentions actin and hexokinase. I'm not familiar with the actin fold, but looks like a bab sandwich of some kind. Another commenter on this page mentioned the 'Rossman fold', another classic, and TIM barrels also occur to me. One caution is that some of these I would consider higher-level patterns - the 'Topology' level of CATH hierarchy. Naturally, the more high-level (abstract) the fold pattern, the larger the sequence space it covers. It is less interesting to say that a helical bundle (for example) covers a lot of diverse sequences.

What plagiarism even means in context of proteins? That one protein steals a fold of another protein without giving proper credit to it?

by jeejay1 4mo ago

What plagiarism even means in context of proteins? That one protein steals a fold of another protein without giving proper credit to it?

gilleain 4mo ago

I understood it as metaphor - just that evolutionarily distant sequences can adopt the same (or very similar) folds because there are only a limited number of stable, accessible folds that are possible.

hirenj 4mo ago
Yes, that is exactly what I meant! Here’s an experiment to try: Frances Arnold got a nobel prize for work related to directed evolution. However, we know evolution is limited by the tools available to it as you mention. If we add random chaperones and co-factors to bacteria that we know other organisms use, can we push evolution outside of the known fold space? Is the limited fold space an absolute limit or the “accessible” limit?
- gilleain 4mo ago
  I see. I meant 'energetically accessible', but you mean more like 'affordably accessible' (in the sense that the molecular toolkit of a cell is what can 'afford' certain structures, due to chaperones available and so on). Who knows what might be possible if you designed a cell from scratch - perhaps you could rework all the machinery to access other parts of fold space. After all, there are some weird and wonderful machines out there like the 'Vault' (https://en.wikipedia.org/wiki/Vault_(organelle) https://en.wikipedia.org/wiki/Vault_(organelle)) that can fit whole proteins inside them. Possibly a different cage-like structure could help fold designed proteins into as-before unseen structures.
  - pfdietz 4mo ago
    It could also mean "evolutionarily accessible". The basin of attraction in sequence space has to be sufficiently large that evolution could stumble across it.
jeejay1 4mo ago
Do you have an example of such sequences in mind? Because I can’t recall any example.
- gilleain 4mo ago
  A very reasonable question, that I don't have an immediate concrete answer to! Apparently I upvoted this question in the past (found it by searching for an answer - no AI, like the good old days) https://biology.stackexchange.com/questions/2507/are-there-any-examples-of-proteins-with-no-or-minimal-sequence-identity-but-hig https://biology.stackexchange.com/questions/2507/are-there-a... One answer mentions actin and hexokinase. I'm not familiar with the actin fold, but looks like a bab sandwich of some kind. Another commenter on this page mentioned the 'Rossman fold', another classic, and TIM barrels also occur to me. One caution is that some of these I would consider higher-level patterns - the 'Topology' level of CATH hierarchy. Naturally, the more high-level (abstract) the fold pattern, the larger the sequence space it covers. It is less interesting to say that a helical bundle (for example) covers a lot of diverse sequences.