Dear all,
I am trying to dock a transient protein complex using only PCS. The issue that I am having is that the PCS are scaled according to the population of the complex i.e. they are much smaller than they would normally be for a tight complex. Is there a way to deal with this in HADDOCK? Any help would be greatly appreciated.
Best,
Taylor
Dear taylortamu,
Let me first point you to both the manual and the paper related to the usage of HADDOCK with only PCS restraints:
C. Schmitz and A.M.J.J. Bonvin Protein-Protein HADDocking using exclusively Pseudocontact Shift. J. Biomol. NMR, 50, 263-266 (2011).
Averaged PCS data over a population of conformations can be tricky. A recent paper shows that unrestrained molecular dynamics (MD) simulations starting from the HADDOCK models can help refining the prediction. Maybe the way to go …
Brewer KD, Bacaj T, Cavalli A, et al. Dynamic Binding Mode of a Synaptotagmin-1-SNARE Complex in Solution. Nature structural & molecular biology. 2015;22(7):555-564.
Best regards
Adrien