Re: question on ABF

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Apr 18 2008 - 22:14:45 CDT

Hi Michel,

I don't know if you have read this previous thread:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/6992.html

To elaborate on this, I would recommend that you estimate which
degrees of freedom (including protein conformation and overall
rotation) will be involved in the calculation (i.e. will need to relax
and be sampled).

For comparison with the case of GpA discussed in the previous thread,
I would remember that:
1) the system was only the GpA TM segment, much, much smaller than
what you consider;
2) the environment imposed a TM orientation, introducing strong
orientational restraints;
[3) note that we used an alkane medium instead of actual lipids, for
faster relaxation]

One relevant question to ask at this stage is: which degrees of
freedom should absolutely be sampled? (and the flip side, what could
you possibly get away with not sampling, and can be restrained...).
For a system of this size, I would add: would you get any information
by looking at something smaller first?

Cheers,
Jerome

On Fri, Apr 18, 2008 at 7:40 PM, L. Michel Espinoza-Fonseca
<mef_at_ddt.biochem.umn.edu> wrote:
> Dear all,
>
> I was wondering if you any of you (that question is particularly meant
> for Jerome) have used ABF to calculate the unbinding free energy of
> two proteins. I have a homodimer, with each monomer consisting of ~250
> residues; the reaction coordinate will be defined as the distance
> between the COM between each monomer.
>
> Cheers,
> Michel
>
>

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