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Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains

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Abstract

Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramagnetism-based restraints. These restraints were measured after inclusion of a lanthanide binding tag in the C-terminal domain to supplement the data obtained by substitution of three paramagnetic lanthanide ions to the calcium ion in the second calcium binding loop of the N-terminal domain. The analysis shows that the availability of paramagnetic restraints arising from metal ions placed on both domains, reduces the MO of the conformations to different extents, thereby helping to identify those conformations that can be mostly sampled by the protein.

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Acknowledgments

This work has been supported by MIUR-FIRB contracts RBLA032ZM7, RBRN07BMCT and RBIP06LSS2, by the European Commission, contracts Bio-NMR n. 261863, East-NMR n. 228461, SPINE2-COMPLEXES 031220, and We-NMR 261572, and by the Netherlands Organisation for Scientific Research (NWO), grants 700.58.405 (P.H.J.K.) and 700.58.441 (W.M.L. and M.U.).

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Authors and Affiliations

  1. Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy

    Soumyasri Dasgupta, Xiaoyu Hu, Claudio Luchinat, Malini Nagulapalli & Giacomo Parigi

  2. Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, PO box 9502, 2300 RA, Leiden, Netherlands

    Peter H. J. Keizers, Wei-Min Liu, Mark Overhand & Marcellus Ubbink

  3. Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy

    Claudio Luchinat & Giacomo Parigi

  4. Istituto per le Applicazioni del Calcolo, Sezione di Firenze, CNR, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Italy

    Luca Sgheri

Authors
  1. Soumyasri Dasgupta
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  2. Xiaoyu Hu
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  3. Peter H. J. Keizers
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  4. Wei-Min Liu
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  8. Giacomo Parigi
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  10. Marcellus Ubbink
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Correspondence to Claudio Luchinat.

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Dasgupta, S., Hu, X., Keizers, P.H.J. et al. Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains. J Biomol NMR 51, 253–263 (2011). https://doi.org/10.1007/s10858-011-9532-2

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  • DOI: https://doi.org/10.1007/s10858-011-9532-2

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