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

From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Tue, 20 Dec 2011 17:15:55 +0100


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 1401–1412)

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?
http://www.clas.ufl.edu/users/roitberg/research.htm 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

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 Gehrcke
PhD student
Structural Bioinformatics Group
Technische Universität Dresden
Biotechnology Center
Tatzberg 47/49
01307 Dresden, Germany
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Received on Tue Dec 20 2011 - 08:30:03 PST
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