difference between two kinds of dimers

From: olivier Walker (olivier_at_hikari.cpe.fr)
Date: Wed Mar 02 2005 - 06:19:56 CST

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'm not so familiar with MD, I was wondering if it can help us
to find any differences in the two dimers that can explain such a
difference. I would appreciate any hints and/or references.

Thanks in advance.


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