Re: ABF calculations

From: Chris Chipot (Christophe.Chipot_at_edam.uhp-nancy.fr)
Date: Wed Nov 21 2007 - 18:37:32 CST

Jiancong,

I would like to emphasize once again that the order parameters that
we are commonly using are in fact simple mathematical constructs
aimed at expressing in a unidimensional representation a reality
that is often multidimensional. The pseudo-cylindrical symmetry of
two alpha-helices associating in a membrane appears to reduce somewhat
the configurational entropy. At the same time, in the associated state,
over the time-scales currently accessible, possibilities of visiting
all important states participating to the free energy minimum of the
native dimer through rotation and reorientation of the alpha-helices
are necessarily limited. I certainly cannot imagine why it should be
less so in the case of large, globular proteins.

Chris

jia a écrit :
> 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

_______________________________________________________________________

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
54506 Vandœuvre-lès-Nancy Cedex

                             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
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