AMBER Archive (2004)

Subject: AMBER: Normal Mode Analysis possibility

From: myang (myang_at_clarku.edu)
Date: Tue May 04 2004 - 10:52:05 CDT

I always think NMA is to investigate harmonic motion of biomolecules. But
nowadays, people utilize this method to study domain motions more and more,
and achive quite impressive results. But usually such motions are not
harmonic, because they always correspond to large scale conformational
change. I did some literature search and found that Go et al. (PNAS 1983,
80, 3696-3700) said, the slowest modes derived from NMA show some
anharmonicity. I suppose this is the theoretical basis for domain motion
analysis.

Now I have a multimeric protein, whose shape looks like '00' (put two eggs
together), and I hope to find out the driving force of its dissociation.
Experiments have found that during the dissociation process, the two parts
of this protein are relatively rigid (do not undergo substantial
conformational change). Can I use NMA in such a case? I couldn't find any
people who use NMA to study protein dissociation, so I am afraid it maybe
not a suitable tool here. But still want to hear some advice.

I know I am not quite clear about some basic concepts of NMA. But I know in
this newsgroup, many experts are 'crouching', so I am seeking some
insightful opinions here. :)

Wish all of you a wonderful summer holiday!

Best,
Yang

BTW: Actually, I already tried NMA with the popular simplified force field,
and found the lowest mode motion generates a gear-wheel motion which has the
potential to drive the protein dissociation.

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