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Journal of Biomolecular NMR

, Volume 33, Issue 3, pp 175–186 | Cite as

Describing Partially Unfolded States of Proteins from Sparse NMR Ddata

  • Gloria Fuentes
  • Aart J. Nederveen
  • Robert Kaptein
  • Rolf Boelens
  • Alexandre M. J. J. Bonvin
Article

Abstract

Proteins involved in signal transduction can usually be present in two states: an inactive and an active (signaling) state. In the case of photoreceptors such as PYP, it has been shown that the signaling state has a large degree of structural and dynamic disorder. Conventional structural NMR approaches present difficulties in describing such partially unfolded states. Owing to the disordered dynamical and transient nature of such states classical NOE-based information, when present, is sparse. Chemical shift changes upon partial unfolding can, however, be easily monitored from HSQC spectra. We show here that such states can be modeled by defining native-like inter-residue contacts for those residues that do not shift significantly upon partial unfolding. The feasibility of this approach is demonstrated using lysozyme as a test case and applied to model the partially unfolded signaling state (pB) of a truncated form of the photoactive yellow protein for which a “classical” NOE-based structure is available for validation. This approach should be generally applicable to systems in which part of the structure remains in a well-defined native-like conformation.

Keywords

chemical shifts native contacts partially unfolded states structure calculations 

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Copyright information

© Springer 2005

Authors and Affiliations

  • Gloria Fuentes
    • 1
  • Aart J. Nederveen
    • 1
  • Robert Kaptein
    • 1
  • Rolf Boelens
    • 1
  • Alexandre M. J. J. Bonvin
    • 1
  1. 1.NMR Research Group, Bijvoet Center for Biomolecular ResearchUtrecht UniversityUtrechtThe Netherlands

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