Unraveling the Conformational Landscape of Ligand Binding to Glucose/Galactose-Binding Protein by Paramagnetic NMR and MD Simulations

  1. Unione, L. 7
  2. Ortega, Gabriel . 7
  3. Mallagaray, A. 6
  4. Corzana, F. 1
  5. Pérez-Castells, J. 4
  6. Canales, A. 3
  7. Jiménez-Barbero, J. 257
  8. Millet, O. 7
  1. 1 Universidad de La Rioja
    info

    Universidad de La Rioja

    Logroño, España

    ROR https://ror.org/0553yr311

  2. 2 Universidad del País Vasco/Euskal Herriko Unibertsitatea
    info

    Universidad del País Vasco/Euskal Herriko Unibertsitatea

    Lejona, España

    ROR https://ror.org/000xsnr85

  3. 3 Universidad Complutense de Madrid
    info

    Universidad Complutense de Madrid

    Madrid, España

    ROR 02p0gd045

  4. 4 Universidad CEU San Pablo
    info

    Universidad CEU San Pablo

    Madrid, España

    ROR https://ror.org/00tvate34

  5. 5 Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 13, Bilbao, Spain
  6. 6 Luebeck University of Applied Sciences
    info

    Luebeck University of Applied Sciences

    Lubeca, Alemania

    ROR https://ror.org/032xqbj11

  7. 7 Centro de Investigación Cooperativa en Biotecnología
    info

    Centro de Investigación Cooperativa en Biotecnología

    Zamudio, España

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Journal:
ACS chemical biology

ISSN: 1554-8929

Year of publication: 2016

Volume: 11

Issue: 8

Pages: 2149-2157

Type: Article

DOI: 10.1021/ACSCHEMBIO.6B00148 SCOPUS: 2-s2.0-84983315198 WoS: WOS:000381847700010 GOOGLE SCHOLAR

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Abstract

Protein dynamics related to function can nowadays be structurally well characterized (i.e., instances obtained by high resolution structures), but they are still ill-defined energetically, and the energy landscapes are only accessible computationally. This is the case for glucose-galactose binding protein (GGBP), where the crystal structures of the apo and holo states provide structural information for the domain rearrangement upon ligand binding, while the time scale and the energetic determinants for such concerted dynamics have been so far elusive. Here, we use GGBP as a paradigm to define a functional conformational landscape, both structurally and energetically, by using an innovative combination of paramagnetic NMR experiments and MD simulations. Anisotropic NMR parameters induced by self-alignment of paramagnetic metal ions was used to characterize the ensemble of conformations adopted by the protein in solution while the rate of interconversion between conformations was elucidated by long molecular dynamics simulation on two states of GGBP, the closed-liganded (holo-cl) and open-unloaded (apo-op) states. Our results demonstrate that, in its apo state, the protein coexists between open-like (68%) and closed-like (32%) conformations, with an exchange rate around 25 ns. Despite such conformational heterogeneity, the presence of the ligand is the ultimate driving force to unbalance the equilibrium toward the holo-cl form, in a mechanism largely governed by a conformational selection mechanism. © 2016 American Chemical Society.