AMBER Archive (2008)

Subject: Re: AMBER: Has anyone seen a protein fall apart due to PBCs?

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Tue Jan 22 2008 - 13:13:42 CST

Oh, we're certain that the protein is falling apart along that interface.
I've dealt with all sorts of imaging problems in the past, so I know when
they pop up. This is an issue of the protein tetramer RMSD becoming 1.0A
greater than the average RMSD of its subunits, then 1.5A, then 3.0A, then
5.0A, and finally rocketing to >20A (but doing so smoothly over a period
of a few ns).

Thanks to all who have replied, I will look into the restrained
equilibration more closely. However, given that the separation happened
110ns into the first simulation, I don't think that this was the issue.
In that first simulation, there were indications of the protein
moving towards its ultimate separation in the first 30ns, but these later
went away and came back around 80ns into the simulation, gradually
building until the separation at 110ns.

A simulation of a small-molecule liganded form of the same tetrameric
protein, known experimentally to be more stable than the unliganded
tetramer, has been solidly together over a simulation of 180ns and
counting. The equilibration was the same in both cases. Experimentally,
this tetrameric protein is known to form a very stable tetramer even
without the ligand, but again binding the ligand is known to further
stabilize the tetramer.

Dave
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