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

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Abstract

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.

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Acknowledgments

This work was supported by the Czech Science Foundation, grant number GA 13-16842S (P. K., A. R., L. K., L. Ž). The partial support by the project “CEITEC—Central European Institute of Technology” from European Regional Development Fund, grant number CZ.1.05/1.1.00/02.0068, and the Joint Research Activity of the 7th Framework program of the EC (BioNMR, no. 261863) is also acknowledged.

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Authors and Affiliations

  1. Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic

    Pavel Kadeřávek, Vojtěch Zapletal, Vladimír Sklenář & Lukáš Žídek

  2. National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic

    Pavel Kadeřávek, Vojtěch Zapletal, Vladimír Sklenář & Lukáš Žídek

  3. Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 00, Prague 4, Krč, Czech Republic

    Alžbeta Rabatinová & Libor Krásný

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  1. Pavel Kadeřávek
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Correspondence to Lukáš Žídek.

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Kadeřávek, P., Zapletal, V., Rabatinová, A. et al. Spectral density mapping protocols for analysis of molecular motions in disordered proteins. J Biomol NMR 58, 193–207 (2014). https://doi.org/10.1007/s10858-014-9816-4

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