4 ms·
is it possible to identify which proteins are intrinsically disordered based on amino acid sequence alone (or even base sequence)? put another way, is it possi
by panabee 5y ago
is it possible to identify which proteins are intrinsically disordered based on amino acid sequence alone (or even base sequence)?
put another way, is it possible to a priori determine if a protein is ID or ordered?
for instance, you said enzymes are highly ordered. is this based on experimental observations (which could later be wrong if imaging techniques improve) or is there some principle that allows us to treat this as a fact?
thanks in advance for your time.
- flobosg 5y ago> is it possible to a priori determine if a protein is ID or ordered? There’s software that attempts to predict intrinsic disorder based on sequence alone, but in general, in the absence of homolog (evolutionarily related) proteins with known structure you would still need to check experimentally for disorder. EDIT: > if the goal is to reliably assess certain viral proteins as ID or ordered, experimental methods are the only methods for achieving this? If you don’t find homologs with solved structures, experimental characterization is the way to go.
- panabee 5y agothanks for the explanation. to clarify, if the goal is to reliably assess certain viral proteins as ID or ordered, are experimental methods the only methods for achieving this?
- deleted 5y ago[deleted]
- dekhn 5y agoA priori? No. Typically this would be determined by synthesizing or expressing the protein of interest and then using something like CD (circular dichroism). There is an absolutely enormous amount of experimental data about enzyme structure, but frankly I think the simplest is to just understand that the modern ideas about the reversible protein folding process came from ribonuclease, a protein that cuts RNA: https://en.wikipedia.org/wiki/Anfinsen%27s_dogma https://en.wikipedia.org/wiki/Anfinsen%27s_dogma There may also be intrinsically disorderd enzymes, I'm not really sure how they would work, but of course, in biology, there's always a weird example that violates normal expectations because evolution once randomly tried somethign a billion years ago and got stuck with it.
- panabee 5y agothanks for the clarification. your papers also seem interesting, will check those out. the goal is to reliably characterize certain viral proteins as ID or ordered. would you happen to have any advice on this?
- alan-hn 5y agoOut of curiosity, what's the relevance of the classification in the context you present?
- panabee 5y agoif viral proteins are ordered, it becomes much easier to predict their functionality.
- alan-hn 5y agoSo would the predictions be based entirely on the primary structure or assumed primary structure based on nucleotide sequence? Sounds to me like you're doing some bioinformatics stuff to understand how some virus works, or am I totally off base on that guess?
- panabee 5y agocorrect. if you downvoted the previous comment, would you mind sharing why? if ordered proteins are not in fact easier to understand than ID ones, it would be helpful to understand why. thanks for the feedback.
- panabee 5y agoinstead of only downvoting, could someone also clarify how this statement is wrong to help educate myself on the facts? thanks for your help.
- paraschopra 5y ago