RE: ABF calculations

From: jia (jia_at_ornl.gov)
Date: Tue Nov 20 2007 - 09:14:42 CST

Chris,

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
comments?

Thanks much

Jiancong

>===== Original Message From Chris Chipot
<Christophe.Chipot_at_edam.uhp-nancy.fr> =====
>Jia,
>
>
>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.
>
>
>Chris
>
>
>
>
>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
>Nancy Université Phone: +33 (0)3-83-68-40-97
>B.P. 239 Fax: +33 (0)3-83-68-43-87
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>
> E-mail: Christophe.Chipot_at_edam.uhp-nancy.fr
> http://www.edam.uhp-nancy.fr
>
> Science without management is worse than management without science
>
> N. G. van Kampen
>_______________________________________________________________________

Postdoc Research fellow
Center for Molecular Biophysics,
Oak Ridge National Lab
Oak Ridge, TN, 37830

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