[Lii]

I have a specific protein sequence, and now I have to remark on the stability. Not experimentally, but with the use of databases and prediction software and the like. Thing is, I'm not really sure how to use these things to determine protein stability.

I know essentially what stability is; I learned it as the difference between the free energies of the folded and unfolded states.
I also know some of the forces that stabilize proteins such as hydrogen bonds, disulphide bonds, or the burying of hydrophobic groups.

I'm just not entirely sure how to get this required information from these sources.

For example, I believe it would be useful to run a secondary structure analysis, but aren't most types of secondary structures generally stable? Am I meant to focus on regions of disorder?

Is there a way to actually quantify stability?

I'd be grateful if anyone could offer any tips.

[Irlanur]

I'm not really sure how to use these things to determine protein stability.

I don't think anybody is sure about this...

[Babcock_Hall]

To the best of my knowledge, the question of stability of the folded state still has to be addressed empirically.

[Lii]

Haha good to know.

Can sequence give me anything of note?

I predicted secondary structure and it has a mix of helixes and strands. I now also know the binding regions, exposed/buried regions, and disordered regions.

Just not sure how to actually relate anything to stability...

[Yggdrasil]

If you have a structure of your protein and you want to estimate the effect of point mutations on the folding stability of your protein, there are computational methods that can do this.  FoldX is one program I've seen used for this application.

Determining the stability of an arbitrary protein sequence is more difficult. An easy, first-pass method would be to apply the N-end rule.  Here's an online tool that uses the N-end rule and a few other simple algorithms (described in the documentation) to predict the stability of your protein.

In practice, however, I generally don't trust the simple methods described above.  What I would do is BLAST the protein sequence to see if it resembles any other proteins.  If it looks to resemble a conserved domain, I'd be more likely to think that it would be stable.  However, if it is full of regions predicted to be unstructured, I'd be inclined to say it is unstable.  Running a secondary structure prediction is definitely a good start, especially when coupled with software that can predict ordered and disorderd regions.

In the end, I'd say there's no real right or wrong way to answer the question.  Different scientists will approach the question differently, and different methods will yield different answers.

[Lii]

Awesome, thanks for the suggestions!