4 ms·

"this is a feruloyl esterase with a conserved alpha/beta-hydrolase fold but with an additional flexible 'lid' domain that covers the active site" As educated a

"this is a feruloyl esterase with a conserved alpha/beta-hydrolase fold but with an additional flexible 'lid' domain that covers the active site" As educated as I think I am, it is always humbling to read a hacker news comment that I cannot understand. ELI5?

gilleain 3y ago
Apologies, that was meant for the specialists :) It is mostly just technical jargon so do not feel too humble ... So I'll break it down: - "feruloyl esterase" : an 'esterase' is an enzyme that makes or breaks ester bonds. In this case, 'feruloyl' which I've never heard of but apparently is some small molecule that is normally attached to a sugar. https://en.wikipedia.org/wiki/Feruloyl_esterase https://en.wikipedia.org/wiki/Feruloyl_esterase - "conserved alpha/beta-hydrolase fold" : a structural pattern (fold) that is shared (conserved) between a set of structures. In other words, these enzymes all have roughly the same shape. https://www.cathdb.info/version/v4_3_0/superfamily/3.40.50.1820 https://www.cathdb.info/version/v4_3_0/superfamily/3.40.50.1... - "additional flexible 'lid' domain that covers the active site" : a 'domain' is just a compact part of a protein, without going into too much detail. They are calling it a 'flexible lid' as the idea is that it moves out of the way to bind the substrate to the active site (where the reaction is carried out) and back again when fully bound.
- testfoobar 3y ago
  Thank you.
  - andresgottlieb 3y ago
    I've been using ChatGPT4 for this situtations, with excellent results. Check out this conversation about it (I used a PDF reader plugin, also): https://chat.openai.com/share/a682c5a7-f2c5-4849-a999-5a7218d17877 https://chat.openai.com/share/a682c5a7-f2c5-4849-a999-5a7218...
neftaly 3y ago
Enzymes are kind of like a tool for breaking apart lego blocks, or a jig for assembling them. This sounds like a moving part that covers the "teeth" and makes it more effective (or less likely to get jammed by the wrong molecules?).
- Gibbon1 3y ago
  Two things. Lot of reactions are energetically favorable. But the reactants are stuck in a local minima. So either doesn't happen or is too slow. Enzymes mediate the reaction so it can happen or happen faster. Lot of reactions there are side reactions that produce stuff you don't want. Resulting a terrible yield or maybe none. Enzymes can promote the reaction you want increasing the yield. Interesting thing to watch for is eletrocatalysts. Where you use electricity and a catalist to push a reaction that is energetically unfavorable. Like CO2 + H2O --> methanol. These may become very important as we stop pumping oil and gas out of the ground.
anon84873628 3y ago
I don't think there's much to say besides "slightly different chemical structure makes it better". At some point you hit jargon rock bottom.

gilleain 3y ago

Apologies, that was meant for the specialists :) It is mostly just technical jargon so do not feel too humble ... So I'll break it down: - "feruloyl esterase" : an 'esterase' is an enzyme that makes or breaks ester bonds. In this case, 'feruloyl' which I've never heard of but apparently is some small molecule that is normally attached to a sugar. https://en.wikipedia.org/wiki/Feruloyl_esterase https://en.wikipedia.org/wiki/Feruloyl_esterase - "conserved alpha/beta-hydrolase fold" : a structural pattern (fold) that is shared (conserved) between a set of structures. In other words, these enzymes all have roughly the same shape. https://www.cathdb.info/version/v4_3_0/superfamily/3.40.50.1820 https://www.cathdb.info/version/v4_3_0/superfamily/3.40.50.1... - "additional flexible 'lid' domain that covers the active site" : a 'domain' is just a compact part of a protein, without going into too much detail. They are calling it a 'flexible lid' as the idea is that it moves out of the way to bind the substrate to the active site (where the reaction is carried out) and back again when fully bound.

testfoobar 3y ago
Thank you.
- andresgottlieb 3y ago
  I've been using ChatGPT4 for this situtations, with excellent results. Check out this conversation about it (I used a PDF reader plugin, also): https://chat.openai.com/share/a682c5a7-f2c5-4849-a999-5a7218d17877 https://chat.openai.com/share/a682c5a7-f2c5-4849-a999-5a7218...

neftaly 3y ago

Enzymes are kind of like a tool for breaking apart lego blocks, or a jig for assembling them. This sounds like a moving part that covers the "teeth" and makes it more effective (or less likely to get jammed by the wrong molecules?).

Gibbon1 3y ago
Two things. Lot of reactions are energetically favorable. But the reactants are stuck in a local minima. So either doesn't happen or is too slow. Enzymes mediate the reaction so it can happen or happen faster. Lot of reactions there are side reactions that produce stuff you don't want. Resulting a terrible yield or maybe none. Enzymes can promote the reaction you want increasing the yield. Interesting thing to watch for is eletrocatalysts. Where you use electricity and a catalist to push a reaction that is energetically unfavorable. Like CO2 + H2O --> methanol. These may become very important as we stop pumping oil and gas out of the ground.

anon84873628 3y ago

I don't think there's much to say besides "slightly different chemical structure makes it better". At some point you hit jargon rock bottom.