A beginner's guide to protein backbone assignment?

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Hi All,

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!

resonance-assignment tutorial

asked Jun 28 '12 at 15:06

snoopster398
1

Have a look on this good website: http://www.protein-nmr.org.uk/ - Yoan Monneau (Jun 29 '12 at 05:27)

3 Answers:

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Hey!

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.

http://pine.nmrfam.wisc.edu/PINE-SPARKY/

Hope this helps!

–Davis

link

answered Jun 29 '12 at 10:52

DVigneault
3

Davis, just to explain how this forum works - instead of posting multiple answers - edit the one you already gave. - Evgeny Fadeev (Jun 29 '12 at 13:03)

Also, here is a tutorial that goes through the basics, as well as whatever software that you might need.

http://www.protein-nmr.org.uk/

link

answered Jun 29 '12 at 10:57

DVigneault
3

Ahh! Didn't realize that this link had already been suggested in the comments. Sorry! - DVigneault (Jun 29 '12 at 11:03)

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:

http://www.nmr2.buffalo.edu/resources/edu/matr/nmr2_2004.pdf

http://www.protein-nmr.org.uk/

http://www.creative-biostructure.com/

link

answered Jun 27 '16 at 21:03

Justin Frank
1

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Asked: Jun 28 '12 at 15:06

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Last updated: Jun 27 '16 at 21:03

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