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DNA-Nanotube-Enabled NMR Structure Determination of Membrane Proteins

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Abstract

One of the most fundamental questions in cell biology concerns how membrane proteins can perform or contribute to cell communication. Over the last few decades, we have seen major advances in understanding the structural mechanisms of membrane proteins. This chapter describes the emergence of DNA nanotechnology as a powerful tool for the structural characterization of membrane-associated protein using solution-state nuclear magnetic resonance (NMR) spectroscopy. Solution-state NMR is currently one of the best known methods for studying membrane protein structure, and a residual dipolar coupling-based refinement approach can be used to solve the structure of membrane proteins up to 40 kDa in size. However, a weak-alignment medium that is detergent-resistant is required. Previously, availability of media suitable for inducing weak alignment of membrane proteins was severely limited. Recently, in the William Shih’s group, we introduced a large-scale synthesis of detergent-resistant DNA nanotubes that can be assembled into dilute liquid crystals for application as weak-alignment media in solution NMR structure determination of membrane proteins. Nanotube-based alignment of membrane proteins represents a fine example of the productive interface between DNA nanotechnology and structural biology.

Keywords

  • DNA origami
  • Nuclear magnetic resonance
  • Structural biology
  • Membrane protein
  • Protein structure determination
  • DNA liquid crystal
  • Residual dipolar coupling

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  • DOI: 10.1007/978-3-642-36077-0_16
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Abbreviations

RCSB:

Research Collaboratory for Structural Bioinformatics

PDB:

Protein Data Bank

IMPs:

Integral membrane proteins

RDC:

Residual dipolar couplings

TROSY:

Transverse-relaxation-optimized spectroscopy

SVD:

Singular value decomposition

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Acknowledgments

The author thanks James Chou (Harvard University) for helpful discussions concerning NMR spectroscopy.

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Correspondence to Gaëtan Bellot .

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Min, J., Shih, W.M., Bellot, G. (2013). DNA-Nanotube-Enabled NMR Structure Determination of Membrane Proteins. In: Fan, C. (eds) DNA Nanotechnology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36077-0_16

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