Hi Chris,
I think I've delved too far into speculation and I probably shouldn't have :)
I'm not talking about applying any sort of restraint during the calculation of
the PMF, that would certainly not be appropriate. An umbrella potential for
restraining the distance is all that's needed, restraining the relative COM
distance and not the absolute COM position.
My concerns were for taking care of an SMD protocol that (in theory) could be
conducted in such a way that caused problems in the system (all very
hypothetical), i.e. hitting a moving target, if you will. This shouldn't happen
if care is taken to conduct the SMD properly. I'll avoid tangents from now on :)
-Justin
[email protected] wrote:
Dear Justin:
I still disagree. I know it's a fine point, but I think it's important.
The PMF would, I presume, be created by applying a relative position
restraint along Z between the center of mass of a large ligand and the
center of mass of a bilayer and slowly changing the relative position to
which the distance is restrained.
I don't see how an absolute restraint on the COM of the bilayer would
affect the stability -- or even the dG results -- in any way. Perhaps
you're talking about using weak position restraints in X,Y,Z on, say,
the lipid phosphates? The shape of the PMF would be all wrong, but I
suppose that there are cases where this might be a good idea.
Chris.
I guess that I am missing something, but how would restraining the
position of the bilayer COM in absolute space have any affect on
anything at all? I certainly agree that one wants to observe if the
membrane has been destabilized, but if so then I think the solution
would be slower pulling and not an additional restraint on the COM of
the bilayer in absolute coordinates. Perhaps this is what you meant
Justin and I just got caught up in your word "unless".
Indeed, by "unless" I am simply considering the case that some large
molecule is
being forced against the membrane, causing it to somehow destabilize. I
guess
that's a bit of a far-fetched hypothetical, but in the absence of any
additional
information about the goals of the SMD, it was more of a broad "just in
case"
scenario.
I certainly agree that the use of absolute restraints shouldn't be
necessary.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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