Major groove width variations in RNA structures determined by NMR and impact of ~(13)C residual chemical shift anisotropy and ~1H-~(13)C residual dipolar coupling on refinement

摘要

Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by ~1H-~1H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic ~1H-~(13)C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures.