RE: ABF calculations

From: jia (
Date: Tue Nov 20 2007 - 09:14:42 CST


Thank you very much for your response. I came up with the idea of binding
energy calculation after reading Henin and your paper. However, as Jerome
mentioned transmembrane proteins situation reduce quite a number of degrees of
freedom, while for the protein binding in aqueous solution, the sampling may
not be adequate especially when the reaction coordinate is unknown. Any

Thanks much


>===== Original Message From Chris Chipot
<> =====
>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
>> proteins, 140 a.a for one and 57 for another, and I'm wondering if it's a
>> idea to choose the reaction coordinate as the distance separating the
>> 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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Postdoc Research fellow
Center for Molecular Biophysics,
Oak Ridge National Lab
Oak Ridge, TN, 37830

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