Biomedical Engineering Reference
In-Depth Information
detected but also cannot be fully excluded with current sampling methods.
Hence, sampling rather than force-field improvement is currently the main
limitation.
4.3 NMR Restraints
This section on NMR data aims to give a succinct overview of the available
types of experimental restraints and a concise description of their physical
origins. Additionally, we discuss how, and to what extent, different
experimental data improve the convergence and accuracy of structure
calculations. References for further reading are supplied where appropriate.
NMR is sensitive to structural and dynamical properties of the probed
molecules on the atomic scale and can thus report with high resolution on
geometrical features like distances or angles, as well as on structural
features such as solvent accessibility
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or binding sites.
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The most common
NMR restraints are illustrated in Figure 4.4, summarised in Table 4.1 and
discussed in more detail below. In Table 4.1 we characterise restraints by
instructiveness and resolution as discussed in the Introduction. Note that this
categorisation is qualitative and merely meant as a guide. The resolution
that can be gained from a set of restraints increases with the number of
restraints and can be enhanced tremendously by combining different sets of
NMR data.
If NMR data is sparse, it is often advantageous to provide data from
complementary methods. Here small-angle scattering (SAS), such as SAXS,
SANS or WAXS, is popular since the experimental conditions and sample
generation is compatible with NMR. These methods provides radius of
gyration and molecular weight at lowest angles, and information on the overall
molecular shape at medium-to-wide angles. The combination of NMR and
SAS has recently been reviewed in detail.
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4.3.1 Nuclear Overhauser Effect
The Nuclear Overhauser Effect (NOE) describes a relaxation process by which
magnetisation is transferred through space between protons and can usually be
detected for distances up to 5
˚
with fully protonated and 8
˚
with deuterated
protein samples. Accordingly, the NOE allows measurement of tertiary
contacts in biomolecules and was crucial for allowing biomolecular structure
determination by NMR.
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Very simply put, in a NOESY experiment between proton A and proton
B, the high-energy state of proton A is populated (magnetised) by suitable
pulse sequences, and subsequent cross-relaxation processes cause this
magnetisation to be transferred to proton B. The transfer efficiency depends
on the properties of the protons involved, the molecular motion and the
distance. In a 2D experiment with the frequency of proton A on the x-axis
and of proton B on the y-axis, an NOE magnetisation transfer causes a
