Dear Xplor mailing list,
I am trying to refine the NMR structure of three different stapled peptides (you may have seen my previous emails). For two out of three them, I have (with Charles's help) managed to produce structures that match the expected helical conformations, consistent with our CD data. The third is proving more problematic, in that there are no obvious error messages being produced by Xplor, simply an "incorrect" structure. Our CD data shows that this stapled peptide is adopting a helix, as it was designed to do, but the structures coming out of Xplor have the stapled part disordered. Interestingly, if I refine using the same .tbl files but use an unstapled model, I get a helical conformation (and a lot fewer violations!). I attach results and input files for both stapled and unstapled runs. Does anyone have an suggestions as to why, without the helix-stabilising staple, the helix is returned? But if the staple is included, that part of the peptide it spans returns unstructured (and the violations rocket)? Regards, _________________________________________________________________ Dr. Douglas R. Houston Senior Lecturer in Computational Biochemistry Institute of Quantitative Biology, Biochemistry and Biotechnology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161206/cef33c74/attachment-0001.html> -------------- next part -------------- A non-text attachment was scrubbed... Name: aSyn_wt.zip Type: application/x-zip-compressed Size: 241985 bytes Desc: aSyn_wt.zip URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161206/cef33c74/attachment-0002.bin> -------------- next part -------------- A non-text attachment was scrubbed... Name: aSyn_staple.zip Type: application/x-zip-compressed Size: 313288 bytes Desc: aSyn_staple.zip URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161206/cef33c74/attachment-0003.bin> -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: not available URL: <http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20161206/cef33c74/attachment-0001.ksh>
