4 ms·

> matching less than 60% of the sequence of the most closely related fluorescent protein > When the researchers made around 100 of the resulting designs, sever

by trott 2y ago

> matching less than 60% of the sequence of the most closely related fluorescent protein > When the researchers made around 100 of the resulting designs, several were as bright as natural GFPs, which are still vastly dimmer than lab-engineered variants. So they didn't come up with better functionality, unlike what some commentators imply. They basically introduced a bunch of mutations while preserving the overall function. Relevant: https://en.wikipedia.org/wiki/Conservative_replacement https://en.wikipedia.org/wiki/Conservative_replacement

civilized 2y ago
If the mutations were non-synonymous, resulting in different amino acids, the fact that they keep the natural function is still kinda cool. Very much a pure research result AFAICT, but worth a little something.
- flobosg 2y ago
  This is already a well known fact: protein structure (and consequently function) is much more conserved than sequence, mostly due to biophysical constraints.
  - civilized 2y ago
    Forgive my ignorance - is that true even for non-synonymous mutations? They usually have a hard time disrupting the big structure?
    - flobosg 2y ago
      If non-synonymous mutations do not change the biophysical features of the amino acid residues, then the structure is usually kept. Alternatively, it can be the case that a disruptive mutation is compensated by another one that keeps the structure/function/phenotype. This is the basis for evolutionary coupling based structure prediction methods, such as Alphafold.
- dekhn 2y ago
  It's fairly common for two proteins to have almost identical structures but different (down to 30% or lower sequence identify) and it's also possible to mess up a nice protein that folds easily with a single amino acid change. Depends entirely on the context and details.
throwup238 2y ago
That's still a pretty significant result. Imagine how much more effective directed evolution could be if it weren't driven by random mutation, or if the random mutations were applied on top of already working variants.
0cf8612b2e1e 2y ago
That feels like deliberately cute wording. What was the similarity vs the starting molecule? I could probably hand pick a few point mutations substituting one small hydrophobic AA for another without impacting function.
- flobosg 2y ago
  You’d be surprised by how many failures you get by such an approach. Hydrophobic cores can be easily disrupted by altering some side chain volumes.
COGlory 2y ago
60% is freaking nothing in protein space. Like, that's not something to brag about. I could go through and hand edit GFP to 60% identity and get basically GFP still functional at the end. In grad school, I worked on proteins that were 12%-15% sequence identical but had sub 4 Å RMSDs once the structures were solved. EDIT: Actually, bragging about it could be a nigerian prince thing, where they do it to scare away investors that might actually hold them to some standard.

by trott 2y ago

civilized 2y ago

If the mutations were non-synonymous, resulting in different amino acids, the fact that they keep the natural function is still kinda cool. Very much a pure research result AFAICT, but worth a little something.

flobosg 2y ago
This is already a well known fact: protein structure (and consequently function) is much more conserved than sequence, mostly due to biophysical constraints.
- civilized 2y ago
  Forgive my ignorance - is that true even for non-synonymous mutations? They usually have a hard time disrupting the big structure?
  - flobosg 2y ago
    If non-synonymous mutations do not change the biophysical features of the amino acid residues, then the structure is usually kept. Alternatively, it can be the case that a disruptive mutation is compensated by another one that keeps the structure/function/phenotype. This is the basis for evolutionary coupling based structure prediction methods, such as Alphafold.
dekhn 2y ago
It's fairly common for two proteins to have almost identical structures but different (down to 30% or lower sequence identify) and it's also possible to mess up a nice protein that folds easily with a single amino acid change. Depends entirely on the context and details.

throwup238 2y ago

That's still a pretty significant result. Imagine how much more effective directed evolution could be if it weren't driven by random mutation, or if the random mutations were applied on top of already working variants.

0cf8612b2e1e 2y ago

That feels like deliberately cute wording. What was the similarity vs the starting molecule? I could probably hand pick a few point mutations substituting one small hydrophobic AA for another without impacting function.

flobosg 2y ago
You’d be surprised by how many failures you get by such an approach. Hydrophobic cores can be easily disrupted by altering some side chain volumes.

COGlory 2y ago

60% is freaking nothing in protein space. Like, that's not something to brag about. I could go through and hand edit GFP to 60% identity and get basically GFP still functional at the end. In grad school, I worked on proteins that were 12%-15% sequence identical but had sub 4 Å RMSDs once the structures were solved. EDIT: Actually, bragging about it could be a nigerian prince thing, where they do it to scare away investors that might actually hold them to some standard.