Hi, computational protein engineer and person who-thinks-biology-can-do-amazing-stuff here.
Just wanted to report that while “Proteins are like Folded Spaghetti Held Together By Static Cling” is obviously incorrect as a matter of fact, I immediately thought it was a pretty good analogy for capturing some critical and often under-appreciated aspects of the functionally important character of proteins. When I read the sentences you’ve quoted him saying about proteins held together by covalent bonds, I (think) I understood what he was pointing at with this and roughly agree. I absolutely did not think he was saying proteins did not contain covalent bonds, but rather that you could imagine an alternative protein-like molecular structure which had all of its key structural and functional characteristics determined by covalent bonds. I believe such a “protein” would, among other things, be predicted to function at a much wider range of temperatures than extant proteins, maintain its structure and function in many different solvents (and probably gas phase?) etc etc.
This analogy is also definitely failing to capture other important characteristics of proteins, some of which the OP mentioned and I agree with.
By the way, if I was forced to say one thing which “held together” proteins (in the sense of “is most responsible for determining the functional characteristics of a polypeptide chain) it would be tough but I might pick something I don’t think anyone has mentioned: hydrophobicity/ hydrophilicity.
I’m not sure what’s a truer analogy than static cling for hydrophobia as a force holding things together which the general audience has any experience with. Macroscopic experience of hydrophobia is, like, oil collecting on the surface of water, which isn’t experienced as a binding force the way that static cling is.
Yea, idk. I was thinking of the quotes where you explicitly mentioned Van der Waals forces. Tbc, my preference would be to not be forced to pick a single force
Hey, thanks for replying! I explained my issues with the wording he used in a different comment. I would rather know more about what you think about the subject.
but rather that you could imagine an alternative protein-like molecular structure which had all of its key structural and functional characteristics determined by covalent bonds. I believe such a “protein” would, among other things, be predicted to function at a much wider range of temperatures than extant proteins, maintain its structure and function in many different solvents (and probably gas phase?) etc etc.
What do you mean by “protein-like” here? Like, a stitched together chain of molecules that also folds up, but has much stronger cross-links? Or like a 2d-layering system? Or the gears and manipulators that Drexler proposed and wrote up here? Do any of these sound plausible, or easily built off of regular biological systems?
Are you aware of any potential alternative designs for biology compared to the DNA/RNA approach?
Sorry if these are too many questions, I’m very interested in this subject but have reached the limit of my expertise.
Hi, computational protein engineer and person who-thinks-biology-can-do-amazing-stuff here.
Just wanted to report that while “Proteins are like Folded Spaghetti Held Together By Static Cling” is obviously incorrect as a matter of fact, I immediately thought it was a pretty good analogy for capturing some critical and often under-appreciated aspects of the functionally important character of proteins. When I read the sentences you’ve quoted him saying about proteins held together by covalent bonds, I (think) I understood what he was pointing at with this and roughly agree. I absolutely did not think he was saying proteins did not contain covalent bonds, but rather that you could imagine an alternative protein-like molecular structure which had all of its key structural and functional characteristics determined by covalent bonds. I believe such a “protein” would, among other things, be predicted to function at a much wider range of temperatures than extant proteins, maintain its structure and function in many different solvents (and probably gas phase?) etc etc.
This analogy is also definitely failing to capture other important characteristics of proteins, some of which the OP mentioned and I agree with.
By the way, if I was forced to say one thing which “held together” proteins (in the sense of “is most responsible for determining the functional characteristics of a polypeptide chain) it would be tough but I might pick something I don’t think anyone has mentioned: hydrophobicity/ hydrophilicity.
I’m not sure what’s a truer analogy than static cling for hydrophobia as a force holding things together which the general audience has any experience with. Macroscopic experience of hydrophobia is, like, oil collecting on the surface of water, which isn’t experienced as a binding force the way that static cling is.
Yea, idk. I was thinking of the quotes where you explicitly mentioned Van der Waals forces. Tbc, my preference would be to not be forced to pick a single force
Hey, thanks for replying! I explained my issues with the wording he used in a different comment. I would rather know more about what you think about the subject.
What do you mean by “protein-like” here? Like, a stitched together chain of molecules that also folds up, but has much stronger cross-links? Or like a 2d-layering system? Or the gears and manipulators that Drexler proposed and wrote up here? Do any of these sound plausible, or easily built off of regular biological systems?
Are you aware of any potential alternative designs for biology compared to the DNA/RNA approach?
Sorry if these are too many questions, I’m very interested in this subject but have reached the limit of my expertise.