[gmx-users] Discriminating between two kind of dimers

[olivier Walker]

Hi all,

We have synthesized two kind of dimers linked by a different lysine and 
we have studied chemical shift perturbation by NMR. For the first dimer, 
a great perturbation was detected for some residues suggesting that a 
well defined interface was observed. For the second one (same exp 
conditions), no significant perturbation was detected, suggesting that 
no specific interaction exists between the two monomers.  The problem is 
that if we represent the second dimer, we can see the perturbed residues 
of the first homodimer coming in close contact. This is apparently 
contradictory with the experiment.

We can always compare hydrophobicity or accessible surface area between 
the involved residues but it seems that there is not so much difference 
between the two.
Because I've not so familiar with MD, I was wondering if MD can help us 
to find any differences in the two dimers which can explain such a 
difference. I would appreciate any hints and/or references.

Thanks in advance.

Olivier


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Olivier WALKER
Laboratoire de RMN Biomoleculaire Université Claude Bernard - Lyon 1
ESCPE-Lyon,bâtiment 308G
69622 Villeurbanne, France
Phone : +33 4 72 43 18 27
Fax : +33 4 72 43 13 95
mailto: olivier at hikari.cpe.fr
http://sakura.cpe.fr
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