Proteosomes such as GroEL are large complexes that fold-unfold other proteins. Is there any computational tool/method other than Matlab to study folding-unfolding abilities of a particular proteasome?
Do protein-protein docking followed by simulation study is helpful to understand the folding and unfolding of substrate.Energy landscape theory provides a general physical framework for understanding the energetics of protein folding.
But how does protein-protein docking help understand folding-unfolding mechanism?
The conventional way is to use the molecular dynamics (MD) or monte carlo (MC) simulations with Charmm, Amber or Gromacs packages. However, it is not easy.
If you expect to find a tool where you put in coordinates of GroE and of your protein, press a button, wait and get a movie of how the protein finds to its native state - the answer is no.
However, if you have some hypothesis from experiments (like "GroEL might bind to a misfolded intermediate of domain 1 of my protein"), then an in-silico study might give you a hint what that would mean in detail, and suggest further studies (like "the hydrophobic patch XY is likely to be responsible for binding", which you could test with rational mutations).
Depends on the type of protein.Normal mode analysis and Molecular dynamic simulations using coarse grained based forcefields are used to study the folding-unfolding mechanisms..to understand free energy landscape.
Probably you would have to create an ensemble using Monte Carlo simulations and lattice folding method [please refer to Soler MA, Faísca PFN (2013)]. However, there is no button press solution to your problem as far as I know. You may also refer to Hagai and Levy PNAS 2010 for their work.
I think first there is a big difference in the "different proteasomes" . GroEL function is more of a chaperone activity, linked to protein processing in bacteria. One might argue that bacteria mechanisms of protein degradation would somewhat different than the ones in yeast or even more so than in human cells (as any other biological process). Also there are different proteasome substrates some polyubiquitinated some not, some super folded some disordered a different chaperone assisted (maybe) process is expected in the different cases.
Therefore even before the modeling question (which is very interesting and I dont understand much about) the focus of which proteasome you are actually examining should be resolved.
Goodluck!
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