Re: ABF calculations

From: Chris Chipot (
Date: Mon Nov 19 2007 - 16:30:42 CST


if you look at Henin et al. J. Am. Chem. Soc. 2005, 127, 8478-8484,
you will see that using a distance separating the COM of two helices
constitutes a reasonable choice of a surrogate reaction coordinate.
The system that you describe is commensurately larger than two 25-aa
helices, but the problem remains the same. The key question is when
the two proteins reversibly form a dimer, will all the configurations
corresponding to distinct spatial arrangements be sampled adequately
to yield a converged ensemble average at constant-xi ? Our experience
is that such was not necessarily the case for two mundane alpha-helices
and I cannot see how it will for entities considerably larger.


jia a écrit :
> Dear NAMD users and Jerome,
> I'm trying to use ABF method to calculate the binding energy of two small size
> proteins, 140 a.a for one and 57 for another, and I'm wondering if it's a good
> idea to choose the reaction coordinate as the distance separating the centers
> of mass of these two domains given the fact that many atoms will be
> participating to the center of mass. Any suggestions will be appreciated.
> Thanks much!
> Jiancong
> Postdoc Research fellow
> Center for Molecular Biophysics,
> Oak Ridge National Lab
> Oak Ridge, TN, 37830

Chris Chipot, Ph.D.
Equipe de dynamique des assemblages membranaires
Unité mixte de recherche CNRS/UHP No 7565
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