Notably, proteins embedded in the cell membrane—such as the ACE2 receptor that COVID-19 binds to—fold in the lipid bilayer of the cell and are difficult to crystallize.
Could you go into a bit more detail here? Why are these proteins so hard to measure? Can’t you just “remove them from the membrane”? (Sorry if this is completely stupid, my knowledge of experimental biology is very limited)
Also, since you worked in the field, I’m curious about your take on the opinion that protein folding is not really useful, as articulated by John in my link post of the DeepMind blog.
TL;DR: In water, charged parts will tend to rotate outward. In neutrally charged hydrophobic environments, non-charged protein parts will try to face outward. Cell membrane is a partially-hydrophobic environment, so one of the standard protein-folding rules is inverted in its fatty-layer zone. When taken out of it, the protein may literally flip (and also clump, with both itself and other membrane proteins).
Trans-membrane (TM) proteins aren’t woven, they’re sewed (and then folded). They’re threaded in and out of the membrane through a pore, as the ribosome prints them. (While the sewing is loose, not tight, sewing is almost exactly the right way to think about it.*)
Amino acids (AA) can be charged +, charged -, or roughly neutral depending on sequence/peptide. AAs are the component parts of the thread that folds into proteins, and a long string of +charged AAs can help make a whole region on that thread charged (or for 0charge, neutral).
Water molecules are charged and bi-polar. Near a strong charge, they’ll rotate their faces like a magnet to put their + end near a -, or—end near a +. Alternatively phrased: charged molecules are usually hydrophilic and drawn to water molecules (more like water-molecules are drawn to them… but same difference), while large non-charged molecules (ex: the main-body of fats and oils) are hydrophobic by comparison and tend to clump among themselves (something weak Van der Waals forces something).
(You know how oil and water self-assort, and don’t mix? It’s a lot like that.)
The membrane is charged on the surfaces (both inner and outer surface)**, but has a fatty, hydrophobic, neutrally-charged environment in its middle.
This alters the preferred/stable protein structure for the AAs in the (fatty, hydrophobic) threading-zone. In water, charged parts will tend to rotate outward. In neutrally charged hydrophobic environments, non-charged protein parts will try to face outward. While the charged AAs will… wish they had anywhere else to be; usually gravitating harder towards any water they can find, or to each other.
So, one of the standard protein-folding rules is inverted in the fatty-layer zone. Basically.
If you took them out of the embedded fat layer, they would literally flip (to the extent to which that was physically allowed), or that section would clump with the uncharged middle-portions of itself or other TM proteins.***
And since a sizable fraction of TM proteins are cross-membrane pores (transporting a specific molecule from one side of the membrane to the other), getting that cross-membrane portion accurately matters a LOT if you’re trying to understand function.
* For once-through proteins, there’s even a specialized trans-membrane starter-peptide-sequence “needle” that can tell the cell it’s a TM protein in the first place. It’s the first thing to get threaded through, and gets cut off after its job is done. See: Signal Peptide.
** Membrane is a “lipid bi-layer” technically; it’s like a “charged-end—fat & fat—charged-end” sandwich
*** Side-note: TM proteins float around in the membrane like rafts. It’s pretty cool.
I’m not a comp bio expert, but the core of @johnswentworth’s argument seems to be that “protein shape tells us very little about [protein reactions] without extensive additional simulation”, and “the simulation is expensive in much the same way as the folding problem itself.”
Both true as far as I understand, but that doesn’t mean those problems are intractable, any more than protein folding itself was intractable.
So I think you can argue “this doesn’t immediately lead to massive practical applications, there are more hard problems to solve”, but not “this isn’t a big deal and doesn’t really matter” in the long run.
I agree with this answer—it is still likely to be a useful component in a simulation pipeline in the long run, but it’s probably not going to revolutionize things as a standalone tool in the short run.
When you remove membrane proteins from the membrane without great care, they tend to either aggregate into amorphous hydrophobic goo which is impossible to measure well, or take on a shape that is not the shape they ordinarily take in this new different context.
Thanks a lot for the explanation!
Could you go into a bit more detail here? Why are these proteins so hard to measure? Can’t you just “remove them from the membrane”? (Sorry if this is completely stupid, my knowledge of experimental biology is very limited)
Also, since you worked in the field, I’m curious about your take on the opinion that protein folding is not really useful, as articulated by John in my link post of the DeepMind blog.
To give a somewhat-simplified explanation...
TL;DR: In water, charged parts will tend to rotate outward. In neutrally charged hydrophobic environments, non-charged protein parts will try to face outward. Cell membrane is a partially-hydrophobic environment, so one of the standard protein-folding rules is inverted in its fatty-layer zone. When taken out of it, the protein may literally flip (and also clump, with both itself and other membrane proteins).
Trans-membrane (TM) proteins aren’t woven, they’re sewed (and then folded). They’re threaded in and out of the membrane through a pore, as the ribosome prints them. (While the sewing is loose, not tight, sewing is almost exactly the right way to think about it.*)
Amino acids (AA) can be charged +, charged -, or roughly neutral depending on sequence/peptide. AAs are the component parts of the thread that folds into proteins, and a long string of +charged AAs can help make a whole region on that thread charged (or for 0charge, neutral).
Water molecules are charged and bi-polar. Near a strong charge, they’ll rotate their faces like a magnet to put their + end near a -, or—end near a +. Alternatively phrased: charged molecules are usually hydrophilic and drawn to water molecules (more like water-molecules are drawn to them… but same difference), while large non-charged molecules (ex: the main-body of fats and oils) are hydrophobic by comparison and tend to clump among themselves (something weak Van der Waals forces something).
(You know how oil and water self-assort, and don’t mix? It’s a lot like that.)
The membrane is charged on the surfaces (both inner and outer surface)**, but has a fatty, hydrophobic, neutrally-charged environment in its middle.
This alters the preferred/stable protein structure for the AAs in the (fatty, hydrophobic) threading-zone. In water, charged parts will tend to rotate outward. In neutrally charged hydrophobic environments, non-charged protein parts will try to face outward. While the charged AAs will… wish they had anywhere else to be; usually gravitating harder towards any water they can find, or to each other.
So, one of the standard protein-folding rules is inverted in the fatty-layer zone. Basically.
If you took them out of the embedded fat layer, they would literally flip (to the extent to which that was physically allowed), or that section would clump with the uncharged middle-portions of itself or other TM proteins.***
And since a sizable fraction of TM proteins are cross-membrane pores (transporting a specific molecule from one side of the membrane to the other), getting that cross-membrane portion accurately matters a LOT if you’re trying to understand function.
* For once-through proteins, there’s even a specialized trans-membrane starter-peptide-sequence “needle” that can tell the cell it’s a TM protein in the first place. It’s the first thing to get threaded through, and gets cut off after its job is done. See: Signal Peptide.
** Membrane is a “lipid bi-layer” technically; it’s like a “charged-end—fat & fat—charged-end” sandwich
*** Side-note: TM proteins float around in the membrane like rafts. It’s pretty cool.
I’m not a comp bio expert, but the core of @johnswentworth’s argument seems to be that “protein shape tells us very little about [protein reactions] without extensive additional simulation”, and “the simulation is expensive in much the same way as the folding problem itself.”
Both true as far as I understand, but that doesn’t mean those problems are intractable, any more than protein folding itself was intractable.
So I think you can argue “this doesn’t immediately lead to massive practical applications, there are more hard problems to solve”, but not “this isn’t a big deal and doesn’t really matter” in the long run.
I agree with this answer—it is still likely to be a useful component in a simulation pipeline in the long run, but it’s probably not going to revolutionize things as a standalone tool in the short run.
When you remove membrane proteins from the membrane without great care, they tend to either aggregate into amorphous hydrophobic goo which is impossible to measure well, or take on a shape that is not the shape they ordinarily take in this new different context.
I would also love your take on his opinion!