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.

 

[LudusRex]

I can assure you that there are no stupid questions when it comes to scientific inquiry. Now, to answer your question, the behavior of a proline chain in a protein largely depends on its sequence and the interactions it forms with other amino acids and molecules in its environment. In general, proline is known to have a unique role in protein folding as it introduces a bend or kink in the chain due to its rigid structure. This can affect the overall folding of a protein and its interactions with other proteins.

However, in terms of attaching a long proline chain at the C-terminal of a protein and connecting it to another protein, it is possible that the proline chain may not significantly impact the folding of the protein as long as the attachment does not disrupt the native structure of the protein. This can be achieved by careful design and selection of the connecting amino acids and maintaining the appropriate distance between the two proteins.

That being said, it is important to keep in mind that the addition of any extra component to a protein, such as a long proline chain, can potentially affect its behavior and function. It is crucial to thoroughly test and characterize the protein with the attached proline chain to ensure that it still binds to the antigen and can be picked up and disposed of as intended.

Additionally, the molecular weight limit for proteins can vary depending on the specific context and application. While a long proline chain may increase the molecular weight of the protein, it may still be within the acceptable range for your project. I would recommend consulting with your project advisor or conducting further research to determine the appropriate molecular weight limit for your specific application.

In conclusion, it is possible to attach a long proline chain to a protein without significantly impacting its folding, but it is important to carefully design and characterize the protein to ensure its functionality is not compromised. I wish you the best of luck with your project.