Comment by jebarker
2 years ago
> proteins are molecular machines
Does that imply proteins have some dynamics that need to be predicted too? I remember seeing animations of molecular machines that appeared to be "walking" inside the body - are those proteins or more complex structures?
Reference: https://en.wikipedia.org/wiki/Kinesin , https://en.wikipedia.org/wiki/Dynein , https://en.wikipedia.org/wiki/Myosin
They are called motor proteins because they convert chemical energy into kinetic energy. In the case of kinesin, it forms a dimer (two copies of itself bind together to form the two "legs") and also binds to light chains (accessory proteins that modulate its behavior) so that it can walk along filaments and drag cargo around your cells. They are both proteins and more complex structures because multiple proteins are interacting, as well as binding small molecules and catalyzing them into chemical products, all to produce the motion.
Yes, very much so. Even for proteins that seems like they are just scaffolding for a catalytic centre can have important dynamics.
A classic example is haemoglobin, that 'just' binds to oxygen at the iron in the middle of the haem. Other binding sites remote from the oxygen binding one can bind to other molecules - notably carbon dioxide. The 'Bohr effect' mechanism is outlined here : https://en.wikipedia.org/wiki/Bohr_effect#Allosteric_interac...
Even at the lowest level, there is some evidence that ligand binding can affect the structure of the backbone of the protein. For example, peptide plane flipping https://en.wikipedia.org/wiki/Peptide_plane_flipping although I'm not sure where the research is on this nowadays.
Fascinating. I'm a mathematician turned AI researcher by day. The more I learn about biology the more I feel that our human engineering (hard and soft) is trivially simple compared to what evolution has already created and left for us to study.
Heh, I'm somewhat the opposite, as I went from a degree in biochemistry into bioinformatics (protein folds and structure) and have an amateur interest in maths.
I often recommend the book 'Cats' Paws and Catapults' by Steven Vogel, which discusses the differences between human and biological engineering. There are very different constraints, as well as the more obvious difference between intelligently directed design (by humans) and evolutionary design.
It's not totally true that our engineering is simpler than biological systems. After all, we can now manipulate matter down to the atomic level. There have been attempts to move towards self-assembling systems, or even self-repairing ones. Not quite on the same scale or sophistication as biological systems, of course.
Is a modern computer chip more complex than a virus? Is a large connected system of computers more complex than a mycelial network? Are there more parts connected in more ways in a nuclear power station as there are in a simple bacterial cell?
I think it is definitely worth considering the similarities and differences.
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May career path took me from the very hard sciences to the biological ones. Though bio is experimentally trivial compared to the complexity of astrophysics, bio theory is millennia harder.
One of my favorite quotes about biology goes something like:
"An alien spaceship lands in your yard. You are kindly invited in to study and tour the ship. The technology is clearly billions of years more advanced than our own. Not decades more, not millennia more, not megayears more, but clearly gigayears more.
This is biology"
Sorry, can't find the exact quote and citation right now!
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Yes proteins can be dynamic, and multiple proteins can come together to form bigger structures (like a cell's membrane for example), and they can very much interact with other proteins and molecules in complex ways.
I think AlphaFold gives us more of a static picture that doesn't tell us much about how the protein will interact with the world. Predicting these dynamic aspects, protein-to-protein interactions, and ultimately an entire cell, is probably what they'll like to do next.
I don't know if the walking buddy is a single protein, it may be a handful of different ones joined together.