SCOP Protein domains + order/disorder

Question

[caribsim]

Hello, the question I wanted to ask is : are protein domains considered ordered proteins?

I understand protein domains to be regions of protein sequence/structure which can fold independently from the rest of the protein and have their own functionality. What I don't understand is how exactly this relates to the concept of order/disorder. I've run a disorder predictor on a SCOP domain and found strong likelihoods of disordered regions however from my understanding this shouldn't have been possible as SCOP domains are proteins whose structure 'should be' solved and annotated. Wouldn't the presence of disorder contradict the relevance of classifying a protein by fold/superfamily/family?

Thank you.

Answer 1

[João Rodrigues]

Well, a certain family 'can' be disordered. It's been suggested that the notion of 'structure = function' is not necessarily true. Also, domains can contain a portion that is disordered and for example, folds only upon binding a specific substrate (look at the chameleon sequence of the c-terminal of P53). Therefore, a disordered domain is still a domain because it can, on its own, perform a function.

As for your last question, maybe. You could argue that function is a better classification but then you have proteins that are entirely different and yet perform the same function, as well as the opposite. So it depends on what you are looking for and it's still very useful to have such classification, despite these (apparent) shortcomings.

[caribsim]

Thank you for the response! It makes sense that domains can of course be considered disordered and thus be used in classification strategies based maybe on function. I just thought that such domains would be left out of the SCOPe database as this database should be protein domains whose structures have 'largely' been determined and thus classified with other domains at the various levels. This implied to me that the protein domains in SCOPe are ordered however I now know that not to be the case.