Chaperones are special “superior” proteins (specific for each particular protein) enabling (facilitating, stabilizing) post-translating folding of the protein into the final functional conformation. When I was questioning my biology professor if these chaperones can modify the protein against the energy gradient, into an energy disadvantageous and unstable, but functional structure (when energy stable conformation can be inactive), he said yes, that is possible.

I have some questions and I would be happy if someone could answer them:
1.Can chaperones really change the proteins into the one with energy disadvantageous structure while keeping the protein functional?
2.If yes, is Rosetta taking them into account for the simulations?
3.Is Rosetta taking into account disulphide bonding in proteins and are these bonds calculated in the computation?

Thanks, it is very important for me.

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Actually Chaperones are in most cases not specific to the protein they're assisting, ut rather general (see for example GroEL or the some of the heatshock proteins)
It is thought that they act as folding catalysts enabling exchange betwene conformations and preventing aggregation between different molecules.GroEL for example encapsulates a single protein.

1) Usually if you change the protein from its native (favourable) state into any other state the functon is lost.
2) No rosetta does not take chaperones into account. THis is beacuse it is thought they are catalysts only and do not change the underlying thermodynamic landscpae.
3) Yes we are ! We're actuall about to upload some code onto Rosetta@HOME that will deal with disulphides!

MIke

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http://beautifulproteins.blogspot.com/
http://www.miketyka.com/