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
