From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Mon Aug 19 2013 - 22:33:02 CDT
As I believe I've mentioned previously, the current focus of my obsession is a fairly large, somewhat flexible and heavily glycosylated symmetrical dimer. This was crystallised in a state that is rather far from its natural conformation (its C terminus is truncated before a dimerisation interface, and these domains have sprung to roughly 100 Angstroms apart. My approach to addressing this has been to add the missing dimerisation domains and gradually steer these into place in a TMD simulation, allowing the remainder of the protein to follow as it will.
I've actually done this once (over the course of ~80ns) with quite a bit of success - but some tweaking was required during the trajectory to escape obviously erroneous local minima. However, since then the electron density map for the crystal became available, and I've identified and fixed a couple of folding errors. The scope of the changes are sufficient that I believe I should go back and do a new production run, which leads me to the question I'm currently hoping others might provide insight into: are symmetry restraints worthwhile here?
On the one hand, given the scale and flexibility of the structure I'm working with, anything that realistically reduces its degrees of freedom is welcome. On the other, the very nature of symmetry restraints is a regression to the mean - continually pulling the overlaid symmetrical copies back to their average is effectively resisting all change, which if not handled carefully is likely to lead to some interesting artefacts. I suspect on the whole it is still likely to be useful if I keep the force constant low (5-10 kcal/mol/A^2, spread over all protein C-alpha and glycan C1 atoms -1028 per monomer).
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