Re: [AMBER] studying the pH-dependent stability of a "large" homodimeric protein

From: Adrian Roitberg <>
Date: Tue, 20 Dec 2011 13:18:27 -0500

Hi Jan-Philip

Wow, you are expecting a web site to be up to date ! ;-)

Sorry about that...

We have a couple of papers under review regarding changes in
conformation coupled to pH changes. This is an interesting area, and we
are finding it to be quite challenging and not clear in the field at all.

Basically, when you have two different conformations whose equilibrium
depends on pH, then the pKa for the important residues in each
conformation MUST be different. Hence, while you can measure a 'pKa' as
the midpoint in a titration curve, that result is most likely a sign of
the conformational transition and NOT of the protonation change.

We have succeeded in seeing things like you mention by running MD at
constant pH for a pH where a dimer is stable. Then we 'jump' the pH to a
value where it is unstable, and you see changes. We have seen this in
the ~50 ns MD range, with implicit solvent.

You do not see a full unbinding of the dimer, but you clearly see

The 'correct' way to do this is to do umbrella sampling for instance
versus monomer separation, using the protonation states at both pHs. You
should see two very different profiles in that case, but it is a lot of

As for the replica pH, etc, we will have it all released for Amber12,
and it will have BOTH temperature replicas (with each replica at the
same constant pH) AND tru ph-replica, where each replica has a different pH.

Contact me directly if you have more questions pelase.


On 12/20/11 11:15 AM, Jan-Philip Gehrcke wrote:
> Hey,
> I have read the section about constant pH MD in the manual as well as
> for example
> "Constant pH Replica Exchange Molecular Dynamics in Biomolecules Using a
> Discrete Protonation Model" by Weng, Roitberg (J. Chem. Theory Comput.,
> 2010, 6 (4), pp 14011412)
> That paper closes with
> "our future work will include studies of pH-dependent protein dynamics
> and application of this constant pH REMD to large proteins"
> Is any of this "future work" already published?
> unfortunately is not
> up to date :)
> I'm currently studying a homodimeric protein, each monomer containing
> about 160 amino acids. What particularly interests me is analyzing the
> stability of this dimer in dependence of the solution pH. The dream is
> to "see" when it starts dissociating while decreasing pH.
> I would be very happy to receive some scientific advise with respect to
> tackling this problem using molecular dynamics. Do you think that an
> MD-based study of this problem scientifically makes sense at all? If
> yes, which method would you use?
> From the literature I've read, it seems that I will have to stick to
> implicit solvent approaches. The simplest way would be to use the Mongan
> et al approach (as currently implemented in Amber) during (very long)
> classical MD simulations. How long must "very long" be in this case in
> order to achieve proper conformational sampling? If I have to use REMD
> -- Adrian, how severe have the technical challenges been to implement
> the protonation state exchange scheme you've used in the paper mentioned
> above?
> As this particular problem is a side project of mine, honestly, I would
> very much like to be able to use the best protocol that is already
> implemented. Basically, I am wondering if such a protocol exists for my
> problem. If this is not the case, I am very much interested in
> discussing the difficulties.
> Thanks for your advise,
> Jan-Philip

                            Dr. Adrian E. Roitberg
                Quantum Theory Project, Department of Chemistry
                            University of Florida
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Received on Tue Dec 20 2011 - 10:30:03 PST
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