Local knowledge helps determine protein structures

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Abstract
The nuclear Overhauser effect (NOE) has been the workhorse of structural studies of macromolecules in solution by NMR spectroscopy. The NOE is a measure of the rate of magnetization transfer between nuclei, induced by modulation of the magnetic dipole–dipole coupling between nuclear spins by overall tumbling of the molecule in solution (1). The efficiency of magnetization transfer via this mechanism is low; consequently, NOEs are typically only observed for protons within ≈5 Å, and lengthy experiments are required in order to detect the weak effect. NOE magnitudes provide a “spectroscopic ruler” through the approximate r −6 dependence on the distance between proton pairs. Although it takes surprisingly few such distance estimates to determine the overall fold of a protein (2)—provided the estimates are distributed evenly throughout the protein—even a complete set of NOEs yields far fewer constraints on the structure than are required to determine all 3N − 6 degrees of freedom for an N-atom protein. The fold is even more highly underdetermined when protein flexibility is taken into account. By complementing NMR measurements with prior knowledge of protein structure, usually in the form of a potential energy function that describes the physical plausibility of a model structure, NMR has emerged as a valuable complement to x-ray crystallography for structure determination. The Protein Data Bank (PDB) (3) now contains >7,000 NMR protein structures, and >1,000 new structures are anticipated to be added in 2008. One way to further hasten the rate of protein structure determination by NMR is to develop alternatives that avoid the need to measure and assign NOEs. In this issue of PNAS, Shen et al. (4) describe a viable alternative to NOE-based structure determination for small proteins. Nevertheless, reliance on NOEs for determination of biomolecular structure presents real challenges. A NOE must be assigned to …