AMBER Archive (1999)

Subject: Normal mode analysis - breathing motion?

From: J.E. Maxwell (maxwell_at_krebs.ucdavis.edu)
Date: Tue Aug 24 1999 - 20:09:57 CDT

Hi AMBER Community,
   I have a protein in which the active site is partially occluded by a
hairpin loop segment. Access to the site must be accompanied by some breathing like
motion of the two strands and the loop. Low V-max kinetics and
other spectrographic data does provide some credence to this
hypothesis. MD analysis may clarify this if the MD trajectory could be
run for a relatively infinite length of time.

My question is can I use a Normal Mode Analysis to provide me with
some information as to the frequency of this motion?? I guess this
might be a stretch on the original concept of this module but then
again with limited options I would like to know how others may have
approached this problem. Probably this is a querry begging a response
from David Case.

-Joe-

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