DNA-Nanotube-Enabled NMR Structure Determination of Membrane Proteins - DNA Nanotechnology: From Structure to Function - page 325

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

16.1 Structural DNA Origami and Structural Biology

Using DNA to organize and orient proteins for structural study is an old dream in
the DNA-nanotechnology field. In fact, the whole field of DNA nanotechnology
evolved from this very concept. While Seeman's original goal of hosting guest
proteins in designed DNA crystals for high-resolution structure determination by
X-ray diffraction remains an important one [ 1 ], DNA nanotechnology can be
expected to contribute to macromolecular structure determination in other ways.
The tools for rationally designing artificial DNA nanostructures are considerably
more advanced today than just a few years ago. Molecular self-assembly using
DNA as a structural building block has proven to be an efficient method for the
construction of nanoscale objects and arrays of ever-increasing complexity [ 2 , 3 ].
Consequently, these advancements have made DNA nanotechnology an attractive
platform for building molecular tools for a plethora of applications [ 4 ]. In fact,
tools have already been developed in structural biology [ 5 ], drug delivery [ 6 , 7 ],
and single-molecule experiments [ 8 , 9 ] over the course of just a few years. This
rapid adoption of DNA nanotechnology across many disciplines is, in part, due
to the precise control and structural homogeneity of nanostructures synthesized
using the DNA-origami method [ 10 ]. The combination of these features allows the
designer to create a structurally uniform sample at the nanometer scale, which is
essential for any structural biology applications. By fulfilling the two criteria of
“high synthesis yield and homogenous sample of properly folded nanostructures,”
DNA nanotechnology presents itself as the ideal medium to facilitate one of
the most remarkable advancements in NMR-based membrane-protein structure
determination (Fig. 16.1 a) [ 11 , 12 ], the details of which shall be present in this
chapter.

16.2 NMR Structure Determination of Membrane Proteins

Membrane proteins comprise roughly 30% of the fully sequenced human genome
[ 13 , 14 ] and fulfill a wide range of important functions. As a result, membrane
proteins are involved in many diseases and represent well over 50% of the targets