Spectral density mapping protocols for analysis of molecular motions in disordered proteins

Spectral density mapping represents the method of choice for investigations of molecular motions of intrinsically disordered proteins (IDPs). However, the current methodology has been developed for well-folded proteins. In order to find conditions for a reliable analysis of relaxation of IDPs, accur...

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Bibliographic Details
Published in:Journal of biomolecular NMR 2014-03, Vol.58 (3), p.193-207
Main Authors: Kadeřávek, Pavel, Zapletal, Vojtěch, Rabatinová, Alžbeta, Krásný, Libor, Sklenář, Vladimír, Žídek, Lukáš
Format: Article
Language:English
Subjects:
Biochemistry
Biological and Medical Physics
Biophysics
Intrinsically Disordered Proteins - analysis
Intrinsically Disordered Proteins - chemistry
Models, Molecular
Nuclear Magnetic Resonance, Biomolecular - methods
Physics
Physics and Astronomy
Protein Conformation
Protein Folding
Spectroscopy/Spectrometry
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Summary:Spectral density mapping represents the method of choice for investigations of molecular motions of intrinsically disordered proteins (IDPs). However, the current methodology has been developed for well-folded proteins. In order to find conditions for a reliable analysis of relaxation of IDPs, accuracy of the current reduced spectral density mapping protocols applied to IDPs was examined and new spectral density mapping methods employing cross-correlated relaxation rates have been designed. Various sources of possible systematic errors were analyzed theoretically and the presented approaches were tested on a partially disordered protein, delta subunit of bacterial RNA polymerase. Results showed that the proposed protocols provide unbiased description of molecular motions of IDPs and allow to separate slow exchange from fast dynamics.
ISSN:0925-2738
1573-5001
DOI:10.1007/s10858-014-9816-4