| Chemical shift prediction for denatured proteins. | |
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MedLine Citation:
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PMID: 23297019 Owner: NLM Status: Publisher |
Abstract/OtherAbstract:
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While chemical shift prediction has played an important role in aspects of protein NMR that include identification of secondary structure, generation of torsion angle constraints for structure determination, and assignment of resonances in spectra of intrinsically disordered proteins, interest has arisen more recently in using it in alternate assignment strategies for crosspeaks in (1)H-(15)N HSQC spectra of sparsely labeled proteins. One such approach involves correlation of crosspeaks in the spectrum of the native protein with those observed in the spectrum of the denatured protein, followed by assignment of the peaks in the latter spectrum. As in the case of disordered proteins, predicted chemical shifts can aid in these assignments. Some previously developed empirical formulas for chemical shift prediction have depended on basis data sets of 20 pentapeptides. In each case the central residue was varied among the 20 amino common acids, with the flanking residues held constant throughout the given series. However, previous choices of solvent conditions and flanking residues make the parameters in these formulas less than ideal for general application to denatured proteins. Here, we report (1)H and (15)N shifts for a set of alanine based pentapeptides under the low pH urea denaturing conditions that are more appropriate for sparse label assignments. New parameters have been derived and a Perl script was created to facilitate comparison with other parameter sets. A small, but significant, improvement in shift predictions for denatured ubiquitin is demonstrated. |
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Authors:
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James H Prestegard; Sarata C Sahu; Wendy K Nkari; Laura C Morris; David Live; Christian Gruta |
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Publication Detail:
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Type: JOURNAL ARTICLE Date: 2013-1-8 |
Journal Detail:
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Title: Journal of biomolecular NMR Volume: - ISSN: 1573-5001 ISO Abbreviation: J. Biomol. NMR Publication Date: 2013 Jan |
Date Detail:
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Created Date: 2013-1-8 Completed Date: - Revised Date: - |
Medline Journal Info:
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Nlm Unique ID: 9110829 Medline TA: J Biomol NMR Country: - |
Other Details:
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Languages: ENG Pagination: - Citation Subset: - |
Affiliation:
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, Athens, GA, USA, jpresteg@ccrc.uga.edu. |
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine
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