Root-mean-square-deviation-based rapid backbone resonance assignments in proteins

We have shown that the methodology based on the estimation of root‐mean‐square deviation (RMSD) between two sets of chemical shifts is very useful to rapidly assign the spectral signatures of 1HN, 13Cα, 13Cβ, 13C′, 1Hα and 15N spins of a given protein in one state from the knowledge of its resonance...

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Bibliographic Details
Published in:Magnetic resonance in chemistry 2010-10, Vol.48 (10), p.793-797
Main Authors: Rout, Ashok K., Barnwal, Ravi P., Agarwal, Geetika, Chary, Kandala V. R.
Format: Article
Language:English
Subjects:
BMRB
Calbindin (D9K)
EhCaBP1
HSQC
M-crystallin
NMR
Nuclear Magnetic Resonance, Biomolecular - methods
PCS
Proteins - chemistry
RMSD
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Summary:We have shown that the methodology based on the estimation of root‐mean‐square deviation (RMSD) between two sets of chemical shifts is very useful to rapidly assign the spectral signatures of 1HN, 13Cα, 13Cβ, 13C′, 1Hα and 15N spins of a given protein in one state from the knowledge of its resonance assignments in a different state, without resorting to routine established procedures (manual and automated). We demonstrate the utility of this methodology to rapidly assign the 3D spectra of a metal‐binding protein in its holo‐state from the knowledge of its assignments in apo‐state, the spectra of a protein in its paramagnetic state from the knowledge of its assignments in diamagnetic state and, finally, the spectra of a mutant protein from the knowledge of the chemical shifts of the corresponding wild‐type protein. The underlying assumption of this methodology is that, it is impossible for any two amino acid residues in a given protein to have all the six chemical shifts degenerate and that the protein under consideration does not undergo large conformational changes in going from one conformational state to another. The methodology has been tested using experimental data on three proteins, M‐crystallin (8.5 kDa, predominantly β‐sheet, for apo‐ to holo‐state), Calbindin (7.5 kDa, predominantly α‐helical, for diamagnetic to paramagnetic state and apo to holo) and EhCaBP1 (14.3 kDa, α‐helical, the wild‐type protein with one of its mutant). In all the cases, the extent of assignment is found to be greater than 85%. Copyright © 2010 John Wiley & Sons, Ltd. We demonstrate the utility of a methodology based on the estimation of root‐mean‐square‐deviation between two sets of chemical shifts to rapidly assign the 3D‐spectra of a metal binding protein in its holo‐state from the knowledge of its assignments in apo‐state, the spectra of a protein in its paramagnetic state from the knowledge of its assignments in diamagnetic state and finally, the spectra of a mutant protein from the knowledge of the chemical shifts of the corresponding wild‐type protein.
ISSN:0749-1581
1097-458X
DOI:10.1002/mrc.2664