Document Detail


Chemical shift prediction for denatured proteins.
MedLine Citation:
PMID:  23297019     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
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.
Authors:
James H Prestegard; Sarata C Sahu; Wendy K Nkari; Laura C Morris; David Live; Christian Gruta
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2013-01-08
Journal Detail:
Title:  Journal of biomolecular NMR     Volume:  55     ISSN:  1573-5001     ISO Abbreviation:  J. Biomol. NMR     Publication Date:  2013 Feb 
Date Detail:
Created Date:  2013-02-11     Completed Date:  2013-08-27     Revised Date:  2014-02-04    
Medline Journal Info:
Nlm Unique ID:  9110829     Medline TA:  J Biomol NMR     Country:  Netherlands    
Other Details:
Languages:  eng     Pagination:  201-9     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Alanine / chemistry
Hydrogen-Ion Concentration
Models, Molecular
Nitrogen Isotopes
Nuclear Magnetic Resonance, Biomolecular / methods*
Programming Languages
Protein Denaturation*
Proteins / chemistry*
Ubiquitin / chemistry
Urea / chemistry
Grant Support
ID/Acronym/Agency:
1S10RR027155-01/RR/NCRR NIH HHS; P41 GM103390/GM/NIGMS NIH HHS; P41 GM103390-23/GM/NIGMS NIH HHS; P41 RR005351/RR/NCRR NIH HHS; P41 RR005351-23/RR/NCRR NIH HHS; R01 GM061268/GM/NIGMS NIH HHS; R01 GM061268-09/GM/NIGMS NIH HHS; S10RR027097-01A1/RR/NCRR NIH HHS
Chemical
Reg. No./Substance:
0/Nitrogen Isotopes; 0/Proteins; 0/Ubiquitin; 8W8T17847W/Urea; OF5P57N2ZX/Alanine
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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