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-
!~~~~~~~~!~~~~~~~~!~~~~~~~~!~~~~~~~~!~~~~~~~~!~~~~~~~~!~~~~~~~~!~~~~~~!
! J.E. Maxwell |Tel. (530) 752-6571 (O/Lab) !
! Entomology Dept. |Tel. (530) 754-8884 (O/Lab) !
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Received on Tue Aug 24 1999 - 18:09:57 PDT
