I'm new to protein backbone assignment by NMR, and my protein is about ~37kDa (about 400 residues). We've acquired a series of triple resonance spectra: HNCA, HNCACB, HNCOCACB, HNCOCA, and HNCACO. I also have an HQCS spectrum. While I know how magnetization is transferred in the above mentioned experiment, how do I start assigning my protein? I use NMRpipe to process the spectra and Sparky for assignment.
Thanks a lot!
asked Jun 28 '12 at 15:06
Have you tried using PINE-SPARKY? I haven't used it myself (I do metabolomics, not protein structures), but I've come across it a few times looking for software. It seems to help you by doing semi-automated assignments.
Hope this helps!
answered Jun 29 '12 at 10:52
Also, here is a tutorial that goes through the basics, as well as whatever software that you might need.
answered Jun 29 '12 at 10:57
For new players in protein structure study by NMR, these books may be useful;
Fundamentals of Protein NMR Spectroscopy (Focus on Structural Biology) by Gordon S. Rule, T. Kevin Hitchens) Protein NMR Techniques (Methods in Molecular Biology) by A. Kristina Downing.
And these articles:
Vuister G W, Fogh R H, Hendrickx P M S, et al. An overview of tools for the validation of protein NMR structures[J]. Journal of biomolecular NMR, 2014, 58(4): 259-285. Wang G, Zhang Z T, Jiang B, et al. Recent advances in protein NMR spectroscopy and their implications in protein therapeutics research[J]. Analytical and bioanalytical chemistry, 2014, 406(9-10): 2279-2288.
Or some useful site:
answered Jun 27 at 21:03