Molecular Modeling: Does a proline chain fold or tangle up?

[cimmerian]

It's probably a stupid question but is it possible to attach a long proline chain - 8 or more residues - at the C terminal of a protein and have it connect to another protein and not affect folding? It's for a project and it's not actually necessary but I have to make a protein that binds to an antigen. I want to attach that protein to another protein that let's it get picked up and disposed of. Actually, I think that would go beyond the MW limit but still...

 

[Yanick]

This is a very specific question which can't be answered in any general way. It really depends on the secondary and tertiary structure of the protein you are studying.

You can check out Ramachandran plots to see what Pro likes to do. I recall that the tertiary amine and ring structure put restrictions on the conformers of Pro containing peptides such that a loss of secondary structure may result. An old-timer post doc in my lab mentioned mutant proteins where some AA was mutated to a Pro and led to things like unwinding of helices and what not.

Just to reiterate though, this question is very specific to the system you are studying and no general answers can really be given. Looking at the crystal structures can give hints but nothing is fool-proof AFAIK.

 

[Ygggdrasil]

When creating a fusion protein (concatenating two separate proteins or protein domains into a single polypeptide chain), one generally uses a flexible linker composed of small amino acids like glycine, serine, and alanine. Long proline chains tend to form polyproline helices, which would likely result in a somewhat more rigid linker. In some cases, the N- or C-termini of proteins are buried within the structure so adding a protein onto the terminus will destabilize the protein.

Here's a paper that you may find useful:
https://www.ncbi.nlm.nih.gov/pubmed/23026637

Here's another potentially useful resource:
http://partsregistry.org/Protein_domains/Linker

 

[cimmerian]

Thanks! I actually want it to be rigid so I'm going to use GSGPSPTPGSG.