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Internal protein dynamics on ps to μs timescales as studied by multi-frequency 15N solid-state NMR relaxation

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Abstract

A comprehensive analysis of the dynamics of the SH3 domain of chicken alpha-spectrin is presented, based upon 15N T 1 and on- and off-resonance T 1ρ relaxation times obtained on deuterated samples with a partial back-exchange of labile protons under a variety of the experimental conditions, taking explicitly into account the dipolar order parameters calculated from 15N–1H dipole–dipole couplings. It is demonstrated that such a multi-frequency approach enables access to motional correlation times spanning about 6 orders of magnitude. We asses the validity of different motional models based upon orientation autocorrelation functions with a different number of motional components. We find that for many residues a “two components” model is not sufficient for a good description of the data and more complicated fitting models must be considered. We show that slow motions with correlation times on the order of 1–10 μs can be determined reliably in spite of rather low apparent amplitudes (below 1 %), and demonstrate that the distribution of the protein backbone mobility along the time scale axis is pronouncedly non-uniform and non-monotonic: two domains of fast (τ < 10−10 s) and intermediate (10−9 s < τ < 10−7 s) motions are separated by a gap of one order of magnitude in time with almost no motions. For slower motions (τ > 10−6 s) we observe a sharp ~1 order of magnitude decrease of the apparent motional amplitudes. Such a distribution obviously reflects different nature of backbone motions on different time scales, where the slow end may be attributed to weakly populated “excited states.” Surprisingly, our data reveal no clearly evident correlations between secondary structure of the protein and motional parameters. We also could not notice any unambiguous correlations between motions in different time scales along the protein backbone emphasizing the importance of the inter-residue interactions and the cooperative nature of protein dynamics.

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Acknowledgments

We thank the Deutsche Forschungsgemeinschaft (DFG, SFB-TRR 102 project A8) for funding this work. Fruitful discussions with Dr. Paul Schanda and Prof. Christian Griesinger are greatly acknowledged.

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Authors and Affiliations

  1. NMRGroup, Faculty of Natural Sciences II, Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, Betty-Heimann-Str. 7, Saale, 06120, Halle, Germany

    Tatiana Zinkevich, Kay Saalwächter & Alexey Krushelnitsky

  2. Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany

    Veniamin Chevelkov

  3. Department Chemie, Technische Universität München, Garching, Germany

    Bernd Reif

  4. Microbiology Department, Kazan Federal University, Kazan, Russia

    Alexey Krushelnitsky

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  1. Tatiana Zinkevich
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  2. Veniamin Chevelkov
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  3. Bernd Reif
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  4. Kay Saalwächter
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  5. Alexey Krushelnitsky
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Correspondence to Alexey Krushelnitsky.

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Zinkevich, T., Chevelkov, V., Reif, B. et al. Internal protein dynamics on ps to μs timescales as studied by multi-frequency 15N solid-state NMR relaxation. J Biomol NMR 57, 219–235 (2013). https://doi.org/10.1007/s10858-013-9782-2

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