We are investigating the temperature dependent anomalous activities of an enzyme and identified post translational modifications using tandem MS systems. Using unrestrained, nPT molecular dynamics simulations we have also found the differential dynamics caused by different PTM patterns.

We now want to address why the PTM patterns change, as far as our study goes in vitro, the chaperone is same for both the versions. Therefore, there must be a change in the folding regime at different temperatures which exposes different residues. For that, we started with Simulated Annealing protocols. Temp rise>short nPT>temperature decrease. But, this seems to be flawed as the protein results in a blob (probably the molten globule state).

We want to explore the folding from the unfolded structure to the folded one using adaptive potential biasing. GROMACS doxygen manual on this is not very elusive. Anyone who can guide? We have the folded structures and a heat unfolded structure (400K).

Looking for help.