Rongjin,
With regards to the SAXS part of post: I'm guessing your collaborators are
making this determination from the SAXS data based on a Kratky plot
analysis? Given the inherently low resolution of this technique, it may be
difficult to assign the profile observed to a specific secondary structure
element without more analysis or other data. Is the profile concentration
dependent? How well does the profile correlate with the theoretical
scattering from your crystal structure? It could be simply that your two
helices are not crossing in solution in the conditions tested. Using bead
model approach like GASBOR or the EOM approach with your two atomic models
of the helical portions linked by beads and modeled against the SAXS data
might be very informative (ie: generating an ensemble of shapes and seeing
what type of shapes best agree with the data).
There's a very active community of small-angle scattering geeks on the forum
at www.saxier.org - might be worth posting this question there as well.
Cheers,
Kushol
Kushol Gupta, Ph.D.
Research Associate
Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine
BLOCKED::mailto:kgu...@stwing.upenn.edu kgu...@mail.med.upenn.edu
215-573-7260 / 267-259-0082
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Rongjin Guan
Sent: Thursday, July 15, 2010 11:24 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] SAXS on a coiled coil protein
Sorry for a non-ccp4 question.
We have determined a structure which is mainly a coiled coil motif. The
two helices are from the same protein chain linked by a short turn.
However, the SAXS data indicates that this protein is probably natively
unfolded or may have very flexible domains and linkers as commented by
our collaborators who did the SAXS experiments.
Could this be due to the shifting of the turn connecting the two helices?
Has this kind of flexibility in the turn position in a coiled coil motif
been
observed in other coiled coil structures?
Thank you
Rongjin Guan