The influence of stereospecific assignments on the determination of three‐dimensional structures of proteins by nuclear magnetic resonance spectroscopy

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Abstract
The influence of the stereospecific assignments of β-methylene protons and the classification of χ1 torsion angles on the definition of the three-dimensional structures of proteins determined from NMR data is investigated using the sea anemone protein BDS-I (43 residues) as a model system. Two sets of structures are computed. The first set comprises 42 converged structures (denoted STEREO structures) calculated on the basis of the complete list of restraints derived from the NMR data, consisting of 489 interproton and 24 hydrogen bonding distance restraints, supplemented by 23 ϕ backbone and 21 χ1 side chain torsion angle restraints. The second set comprises 31 converged structures (denoted NOSTEREO structures) calculated from a reduced data set in which those restraints arising from stereospecific assignments, and the corresponding χ1 torsion angle restraints, are explicitly omitted. The results show that the inclusion of the stereospecific restraints leads to a significant improvement in the definition of the structure of BDS-I, both with respect to the backbone and the detailed arrangement of the side chains. Average atomic rms differences between the individual structures and the mean structures for the backbone atoms are 0.67±0.12 Å and 0.93±0.16 Å for the STEREO and NOSTEREO structures, respectively; the corresponding values for all atoms are 0.90±0.17 Å and 1.17±0.17 Å, respectively. In addition, while the overall fold remains unchanged, there is a small but significant atomic displacement between the two sets of structures

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