ArticleJournal of biomolecular NMR2013
Secondary structural analysis of proteins based on (13)C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database.
Article in Journal of biomolecular NMR, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Dipolar Assisted Assignment Protocol (DAAP) for MAS solid-state NMR of rotationally aligned membrane proteins in phospholipid bilayers.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Article
- Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information.Journal of biomolecular NMR · 2013Article
- NMRDSP: an accurate prediction of protein shape strings from NMR chemical shifts and sequence data.PloS one · 2013Article
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3 authors.
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Abstract
Magic-angle-spinning solid-state (13)C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-(13)C,(15)N labeled samples. To overcome this problem, we present a method for assigning (13)C chemical shifts and secondary structures from unresolved two-dimensional (13)C-(13)C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to (13)C(α), (13)C(β), and (13)C' chemical shifts and cross-peak intensities. The experimental (13)C-(13)C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific C(α), C(β), and C' chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50-200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved (13)C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.
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