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

From: Jason Swails <>
Date: Wed, 21 Dec 2011 00:03:40 -0500

On Tue, Dec 20, 2011 at 8:19 PM, Kshatresh Dutta Dubey

> Hi Jan,
> are sure that no work is published till date. Our recent
> paper, in Biochimica Biophysica Acta with title ' Role of pH on
> dimeric interaction for dengue envelope protein: An insight from MD
> Study' has been published. U can also find many more eg. praksh et
> al, 2010, Biophy Journal etc.

That paper doesn't present constant pH molecular dynamics as I understood
it. It presents molecular dynamics at constant protonation state, with
certain protonation states chosen to emulate high, low, and normal pH
conditions based on the pKa values of the isolated titratable residues in
solution (the model compounds in the constant pH MD sense).

The method discussed above, on the other hand, deals with simulations run
at constant pH rather than constant protonation state.

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Dec 20 2011 - 21:30:03 PST
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